From 379e5658a68032a2dc405472822932560f72c770 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 19 Feb 2026 16:16:58 +0100
Subject: [PATCH 001/127] Use hgvs_position_model dataclass for HGVS position
 results

---
 mutalyzer_crossmapper/hgvs_position_model.py | 40 ++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 mutalyzer_crossmapper/hgvs_position_model.py

diff --git a/mutalyzer_crossmapper/hgvs_position_model.py b/mutalyzer_crossmapper/hgvs_position_model.py
new file mode 100644
index 0000000..59915b7
--- /dev/null
+++ b/mutalyzer_crossmapper/hgvs_position_model.py
@@ -0,0 +1,40 @@
+"""
+HGVS Position Model -
+    a dataclass object to bridge HGVS position component and Crossmapper outputs.
+"""
+from dataclasses import dataclass
+from typing import Optional
+
+@dataclass
+class HGVSPositionModel:
+    """
+    Represent the position component of an HGVS variant description.
+    This model captures details necessary to describe the '[position]' part in an HGVS
+    description of the form
+        [reference sequence]:[sequence type].[position][variant type][change]
+    """
+    position: int
+    offset: Optional[int] = None
+    region: Optional[str] = None
+    position_in_codon: Optional[int] = None
+
+
+    def __post_init__(self):
+        # validate position
+        if self.position <= 0:
+            raise ValueError("Position must be a positive integer.")
+
+        # validate region
+        region_values = {"u", "-", "", "*", "d"}
+        if self.region is not None and self.region not in region_values:
+            raise ValueError(
+                f"Invalid region value: {self.region}. Allowed values are: {region_values}"
+            )
+
+        # validate position_in_codon
+        codon_values = {1, 2, 3}
+        if self.position_in_codon is not None and self.position_in_codon not in codon_values:
+            raise ValueError(
+                f"Invalid position in codon value: {self.position_in_codon}. "
+                f"Allowed values are: {codon_values}"
+            )

From bbd38dabbeeebf960d2012ff8e4a7788f5f71928 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 19 Feb 2026 18:20:30 +0100
Subject: [PATCH 002/127] Add function to convert from tuple to
 HGVSPositionModel

---
 mutalyzer_crossmapper/hgvs_position_model.py | 54 +++++++++++++++++++-
 1 file changed, 53 insertions(+), 1 deletion(-)

diff --git a/mutalyzer_crossmapper/hgvs_position_model.py b/mutalyzer_crossmapper/hgvs_position_model.py
index 59915b7..7992c63 100644
--- a/mutalyzer_crossmapper/hgvs_position_model.py
+++ b/mutalyzer_crossmapper/hgvs_position_model.py
@@ -3,7 +3,7 @@
     a dataclass object to bridge HGVS position component and Crossmapper outputs.
 """
 from dataclasses import dataclass
-from typing import Optional
+from typing import Optional, Tuple
 
 @dataclass
 class HGVSPositionModel:
@@ -38,3 +38,55 @@ def __post_init__(self):
                 f"Invalid position in codon value: {self.position_in_codon}. "
                 f"Allowed values are: {codon_values}"
             )
+
+
+    # Convert from tuple to HGVSPositionModel
+
+    #TODO: check for inverted and degerate options, now only support non-inverted and non-degenerate cases
+    @classmethod
+    def to_hgvs_position_model(cls, raw_tuple:Tuple):
+        """Convert crossmapper tuple to an HGVSPositionModel instance."""
+        if not raw_tuple:
+            raise ValueError("Input tuple position cannot be empty.")
+
+        # Genomic
+        if len(raw_tuple) == 1:
+            return cls(position=raw_tuple[0])
+        # Non-coding
+        if len(raw_tuple) == 3:
+            pass
+
+        # Coding
+        #(c_pos, offset, in_cds, offset_to_exon_boundary)
+        if len(raw_tuple) == 4:
+            c_pos, offset, cds, dis_to_exon_boundary = raw_tuple
+            region = cls._determine_region(cds, dis_to_exon_boundary)
+            return cls(position=c_pos, offset=offset, region=region)
+
+        # Protein (
+        if len(raw_tuple) == 5:
+            p_pos, codon_pos, offset, cds, dis_to_exon_boundary = raw_tuple
+            if cds == 0: # in CDS
+                return cls(
+                    position=p_pos,
+                    region="",
+                    position_in_codon=codon_pos
+                )
+            else:
+                # TODO: shall we support HGVSPositionModel outside of CDS for protein?
+                pass
+
+
+    @staticmethod
+    def _determine_region(cds, dis_to_exon_boundary):
+        if dis_to_exon_boundary < 0:
+            return "u"
+        elif dis_to_exon_boundary > 0:
+            return "d"
+        else: # in translation range, check if in CDS or not
+            if cds < 0: # before CDS
+                return "-"
+            elif cds > 0: # after CDS
+                return "*"
+            else:
+                return ""
\ No newline at end of file

From 5122c556840b7d143bb98f7ff5819a189a5df0ef Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Feb 2026 11:36:05 +0100
Subject: [PATCH 003/127] Refactor(locus):return dict position model and update
 test

---
 mutalyzer_crossmapper/locus.py | 26 +++++++++++++-------------
 tests/test_locus.py            | 32 ++++++++++++++++----------------
 2 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/mutalyzer_crossmapper/locus.py b/mutalyzer_crossmapper/locus.py
index 14a9d20..a692f61 100644
--- a/mutalyzer_crossmapper/locus.py
+++ b/mutalyzer_crossmapper/locus.py
@@ -11,32 +11,32 @@ def __init__(self, location, inverted=False):
         self._end = self.boundary[1] - self.boundary[0]
 
     def to_position(self, coordinate):
-        """Convert a coordinate to a proper position.
+        """Convert a coordinate to a proper position model.
 
         :arg int coordinate: Coordinate.
 
-        :returns tuple: Position.
+        :returns dict: Position model with 'position' and 'offset' keys.
         """
         if self._inverted:
             if coordinate > self.boundary[1]:
-                return 0, self.boundary[1] - coordinate
+                return {"position": 0, "offset": self.boundary[1] - coordinate}
             if coordinate < self.boundary[0]:
-                return self._end, self.boundary[0] - coordinate
-            return self.boundary[1] - coordinate, 0
+                return {"position": self._end, "offset": self.boundary[0] - coordinate}
+            return {"position": self.boundary[1] - coordinate, "offset": 0}
 
-        if coordinate < self.boundary[0]:
-            return 0, coordinate - self.boundary[0]
-        if coordinate > self.boundary[1]:
-            return self._end, coordinate - self.boundary[1]
-        return coordinate - self.boundary[0], 0
+        if coordinate < self.boundary[0]:           # upstream of an exon, re
+            return {"position": 0, "offset": coordinate - self.boundary[0]}
+        if coordinate > self.boundary[1]:           # downstream of an exon
+            return {"position": self._end, "offset": coordinate - self.boundary[1]}
+        return {"position": coordinate - self.boundary[0], "offset": 0}
 
     def to_coordinate(self, position):
         """Convert a position to a coordinate.
 
-        :arg int position: Position.
+        :arg dict position: Position model with 'position' and 'offset' keys.
 
         :returns int: Coordinate.
         """
         if self._inverted:
-            return self.boundary[1] - position[0] - position[1]
-        return self.boundary[0] + position[0] + position[1]
+            return self.boundary[1] - position["position"] - position["offset"]
+        return self.boundary[0] + position["position"] + position["offset"]
diff --git a/tests/test_locus.py b/tests/test_locus.py
index a873416..b650c1a 100644
--- a/tests/test_locus.py
+++ b/tests/test_locus.py
@@ -7,37 +7,37 @@ def test_Locus():
     """Forward orientent Lovus."""
     locus = Locus((30, 35))
 
-    invariant(locus.to_position, 29, locus.to_coordinate, (0, -1))
-    invariant(locus.to_position, 30, locus.to_coordinate, (0, 0))
-    invariant(locus.to_position, 31, locus.to_coordinate, (1, 0))
-    invariant(locus.to_position, 33, locus.to_coordinate, (3, 0))
-    invariant(locus.to_position, 34, locus.to_coordinate, (4, 0))
-    invariant(locus.to_position, 35, locus.to_coordinate, (4, 1))
+    invariant(locus.to_position, 29, locus.to_coordinate, {"position": 0, "offset": -1})
+    invariant(locus.to_position, 30, locus.to_coordinate, {"position": 0, "offset": 0})
+    invariant(locus.to_position, 31, locus.to_coordinate, {"position": 1, "offset": 0})
+    invariant(locus.to_position, 33, locus.to_coordinate, {"position": 3, "offset": 0})
+    invariant(locus.to_position, 34, locus.to_coordinate, {"position": 4, "offset": 0})
+    invariant(locus.to_position, 35, locus.to_coordinate, {"position": 4, "offset": 1})
 
 
 def test_Locus_inverted():
     """Reverse orientent Lovus."""
     locus = Locus((30, 35), True)
 
-    invariant(locus.to_position, 35, locus.to_coordinate, (0, -1))
-    invariant(locus.to_position, 34, locus.to_coordinate, (0, 0))
-    invariant(locus.to_position, 33, locus.to_coordinate, (1, 0))
-    invariant(locus.to_position, 31, locus.to_coordinate, (3, 0))
-    invariant(locus.to_position, 30, locus.to_coordinate, (4, 0))
-    invariant(locus.to_position, 29, locus.to_coordinate, (4, 1))
+    invariant(locus.to_position, 35, locus.to_coordinate, {"position": 0, "offset": -1})
+    invariant(locus.to_position, 34, locus.to_coordinate, {"position": 0, "offset": 0})
+    invariant(locus.to_position, 33, locus.to_coordinate, {"position": 1, "offset": 0})
+    invariant(locus.to_position, 31, locus.to_coordinate, {"position": 3, "offset": 0})
+    invariant(locus.to_position, 30, locus.to_coordinate, {"position": 4, "offset": 0})
+    invariant(locus.to_position, 29, locus.to_coordinate, {"position": 4, "offset": 1})
 
 
 def test_Locus_degenerate():
     """Degenerate positions are silently corrected."""
     locus = Locus((10, 20))
 
-    degenerate_equal(locus.to_coordinate, 9, [(0, -1), (-1, 0)])
-    degenerate_equal(locus.to_coordinate, 20, [(9, 1), (10, 0)])
+    degenerate_equal(locus.to_coordinate, 9, [{"position": 0, "offset": -1}, {"position": -1, "offset": 0}])
+    degenerate_equal(locus.to_coordinate, 20, [{"position": 9, "offset": 1}, {"position": 10, "offset": 0}])
 
 
 def test_Locus_inverted_degenerate():
     """Degenerate positions are silently corrected."""
     locus = Locus((10, 20), True)
 
-    degenerate_equal(locus.to_coordinate, 20, [(0, -1), (-1, 0)])
-    degenerate_equal(locus.to_coordinate, 9, [(9, 1), (10, 0)])
+    degenerate_equal(locus.to_coordinate, 20, [{"position": 0, "offset": -1}, {"position": -1, "offset": 0}])
+    degenerate_equal(locus.to_coordinate, 9, [{"position": 9, "offset": 1}, {"position": 10, "offset": 0}])

From 836d7d3669561bba12e75494daf31c730717f222 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Feb 2026 12:52:19 +0100
Subject: [PATCH 004/127] Refactor(multi_locus):return dict position model and
 update test

---
 mutalyzer_crossmapper/multi_locus.py |  30 ++++----
 tests/test_multi_locus.py            | 110 ++++++++++++++++++---------
 2 files changed, 88 insertions(+), 52 deletions(-)

diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 9836549..d1f65b8 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -19,7 +19,7 @@ def _offsets(locations, orientation):
 
 class MultiLocus(object):
     """MultiLocus object."""
-    def __init__(self, locations, inverted=False):
+    def __init__(self, locations:list, inverted=False):
         """
         :arg list locations: List of locus locations.
         :arg bool inverted: Orientation.
@@ -36,7 +36,7 @@ def _direction(self, index):
             return len(self._offsets) - index - 1
         return index
 
-    def outside(self, coordinate):
+    def outside(self, coordinate:int):
         """Calculate the offset relative to this MultiLocus.
 
         :arg int coordinate: Coordinate.
@@ -49,32 +49,34 @@ def outside(self, coordinate):
             return coordinate - self._loci[-1].boundary[1]
         return 0
 
-    def to_position(self, coordinate):
+    def to_position(self, coordinate:int):
         """Convert a coordinate to a position.
 
         :arg int coordinate: Coordinate.
 
-        :returns tuple: Position.
+        :returns dict: Position model.
         """
         index = nearest_location(self._locations, coordinate, self._inverted)
         outside = self._orientation * self.outside(coordinate)
+        region = "u" if outside < 0 else "d" if outside > 0 else ""
         location = self._loci[index].to_position(coordinate)
 
-        return (
-            location[0] + self._offsets[self._direction(index)],
-            location[1],
-            outside)
+        return {"position": location["position"] + self._offsets[self._direction(index)],
+            "offset": location["offset"],
+            "region": region}
 
-    def to_coordinate(self, position):
-        """Convert a position to a coordinate.
+    def to_coordinate(self, position_model:dict):
+        """Convert a position model to a coordinate.
 
-        :arg int position: Position.
+        :arg dict position: Position.
 
         :returns int: Coordinate.
         """
+        offset_val = position_model["offset"]
         index = min(
             len(self._offsets),
-            max(0, bisect_right(self._offsets, position[0]) - 1))
-
+            max(0, bisect_right(self._offsets, position_model["position"]) - 1)
+        )
         return self._loci[self._direction(index)].to_coordinate(
-            (position[0] - self._offsets[index], position[1]))
+            {"position": position_model["position"] - self._offsets[index], "offset": offset_val}
+        )
\ No newline at end of file
diff --git a/tests/test_multi_locus.py b/tests/test_multi_locus.py
index 6ce0013..1e3812a 100644
--- a/tests/test_multi_locus.py
+++ b/tests/test_multi_locus.py
@@ -1,3 +1,5 @@
+"""Tests for MultiLocus flattening and coordinate conversions."""
+
 from mutalyzer_crossmapper import MultiLocus
 from mutalyzer_crossmapper.multi_locus import _offsets
 
@@ -15,7 +17,11 @@ def test_offsets_inverted():
     """Cummulative location lengths for inverted list of locations."""
     assert _offsets(_locations, -1) == [0, 2, 4, 8, 13, 19]
 
-
+    invariant(
+        multi_locus.to_position,
+        4,
+        multi_locus.to_coordinate,
+        {"position": 0, "offset": -1, "region": "u"},
 def test_offsets_adjacent():
     """Cummulative location lengths for adjacent locations."""
     assert _offsets([(1, 3), (3, 5)], 1) == [0, 2]
@@ -31,30 +37,32 @@ def test_MultiLocus():
     multi_locus = MultiLocus(_locations)
 
     # Boundary between upstream and the first locus.
+    invariant(multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 0, "offset": -1, "region": "u"},
+    )
+
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, (0, -1, -1))
-    invariant(
-        multi_locus.to_position, 5, multi_locus.to_coordinate, (0, 0, 0))
+        multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 0, "offset": 0, "region": ""},
+    )
 
     # Internal locus.
     invariant(
-        multi_locus.to_position, 29, multi_locus.to_coordinate, (9, -1, 0))
+        multi_locus.to_position, 29, multi_locus.to_coordinate, {"position": 9, "offset": -1, "region": ""})
     invariant(
-        multi_locus.to_position, 30, multi_locus.to_coordinate, (9, 0, 0))
+        multi_locus.to_position, 30, multi_locus.to_coordinate, {"position": 9, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 31, multi_locus.to_coordinate, (10, 0, 0))
+        multi_locus.to_position, 31, multi_locus.to_coordinate, {"position": 10, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 33, multi_locus.to_coordinate, (12, 0, 0))
+        multi_locus.to_position, 33, multi_locus.to_coordinate, {"position": 12, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 34, multi_locus.to_coordinate, (13, 0, 0))
+        multi_locus.to_position, 34, multi_locus.to_coordinate, {"position": 13, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 35, multi_locus.to_coordinate, (13, 1, 0))
+        multi_locus.to_position, 35, multi_locus.to_coordinate, {"position": 13, "offset": 1, "region": ""})
 
     # Boundary between the last locus and downstream.
     invariant(
-        multi_locus.to_position, 71, multi_locus.to_coordinate, (21, 0, 0))
+        multi_locus.to_position, 71, multi_locus.to_coordinate, {"position": 21, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 72, multi_locus.to_coordinate, (21, 1, 1))
+        multi_locus.to_position, 72, multi_locus.to_coordinate, {"position": 21, "offset": 1, "region": "d"})
 
 
 def test_MultiLocus_inverted():
@@ -63,29 +71,29 @@ def test_MultiLocus_inverted():
 
     # Boundary between upstream and the first locus.
     invariant(
-        multi_locus.to_position, 72, multi_locus.to_coordinate, (0, -1, -1))
+        multi_locus.to_position, 72, multi_locus.to_coordinate, {"position": 0, "offset": -1, "region": "u"})
     invariant(
-        multi_locus.to_position, 71, multi_locus.to_coordinate, (0, 0, 0))
+        multi_locus.to_position, 71, multi_locus.to_coordinate, {"position": 0, "offset": 0, "region": ""})
 
     # Internal locus.
     invariant(
-        multi_locus.to_position, 35, multi_locus.to_coordinate, (8, -1, 0))
+        multi_locus.to_position, 35, multi_locus.to_coordinate, {"position": 8, "offset": -1, "region": ""})
     invariant(
-        multi_locus.to_position, 34, multi_locus.to_coordinate, (8, 0, 0))
+        multi_locus.to_position, 34, multi_locus.to_coordinate, {"position": 8, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 33, multi_locus.to_coordinate, (9, 0, 0))
+        multi_locus.to_position, 33, multi_locus.to_coordinate, {"position": 9, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 31, multi_locus.to_coordinate, (11, 0, 0))
+        multi_locus.to_position, 31, multi_locus.to_coordinate, {"position": 11, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 30, multi_locus.to_coordinate, (12, 0, 0))
+        multi_locus.to_position, 30, multi_locus.to_coordinate, {"position": 12, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 29, multi_locus.to_coordinate, (12, 1, 0))
+        multi_locus.to_position, 29, multi_locus.to_coordinate, {"position": 12, "offset": 1, "region": ""})
 
     # Boundary between the last locus and downstream.
     invariant(
-        multi_locus.to_position, 5, multi_locus.to_coordinate, (21, 0, 0))
+        multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 21, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, (21, 1, 1))
+        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 21, "offset": 1, "region": "d"})
 
 
 def test_MultiLocus_adjacent_loci():
@@ -93,9 +101,9 @@ def test_MultiLocus_adjacent_loci():
     multi_locus = MultiLocus([(1, 3), (3, 5)])
 
     invariant(
-        multi_locus.to_position, 2, multi_locus.to_coordinate, (1, 0, 0))
+        multi_locus.to_position, 2, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 3, multi_locus.to_coordinate, (2, 0, 0))
+        multi_locus.to_position, 3, multi_locus.to_coordinate, {"position": 2, "offset": 0, "region": ""})
 
 
 def test_MultiLocus_adjacent_loci_inverted():
@@ -103,9 +111,9 @@ def test_MultiLocus_adjacent_loci_inverted():
     multi_locus = MultiLocus([(1, 3), (3, 5)], True)
 
     invariant(
-        multi_locus.to_position, 3, multi_locus.to_coordinate, (1, 0, 0))
+        multi_locus.to_position, 3, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 2, multi_locus.to_coordinate, (2, 0, 0))
+        multi_locus.to_position, 2, multi_locus.to_coordinate, {"position": 2, "offset": 0, "region": ""})
 
 
 def test_MultiLocus_offsets_odd():
@@ -113,9 +121,9 @@ def test_MultiLocus_offsets_odd():
     multi_locus = MultiLocus([(1, 3), (6, 8)])
 
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, (1, 2, 0))
+        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 1, "offset": 2, "region": ""})
     invariant(
-        multi_locus.to_position, 5, multi_locus.to_coordinate, (2, -1, 0))
+        multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 2, "offset": -1, "region": ""})
 
 
 def test_MultiLocus_offsets_odd_inverted():
@@ -123,9 +131,9 @@ def test_MultiLocus_offsets_odd_inverted():
     multi_locus = MultiLocus([(1, 3), (6, 8)], True)
 
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, (1, 2, 0))
+        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 1, "offset": 2, "region": ""})
     invariant(
-        multi_locus.to_position, 3, multi_locus.to_coordinate, (2, -1, 0))
+        multi_locus.to_position, 3, multi_locus.to_coordinate, {"position": 2, "offset": -1, "region": ""})
 
 
 def test_MultiLocus_offsets_even():
@@ -133,9 +141,9 @@ def test_MultiLocus_offsets_even():
     multi_locus = MultiLocus([(1, 3), (7, 9)])
 
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, (1, 2, 0))
+        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 1, "offset": 2, "region": ""})
     invariant(
-        multi_locus.to_position, 5, multi_locus.to_coordinate, (2, -2, 0))
+        multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 2, "offset": -2, "region": ""})
 
 
 def test_MultiLocus_offsets_even_inverted():
@@ -143,9 +151,9 @@ def test_MultiLocus_offsets_even_inverted():
     multi_locus = MultiLocus([(1, 3), (7, 9)], True)
 
     invariant(
-        multi_locus.to_position, 5, multi_locus.to_coordinate, (1, 2, 0))
+        multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 1, "offset": 2, "region": ""})
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, (2, -2, 0))
+        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 2, "offset": -2, "region": ""})
 
 
 def test_MultiLocus_degenerate():
@@ -153,9 +161,22 @@ def test_MultiLocus_degenerate():
     multi_locus = MultiLocus(_locations)
 
     degenerate_equal(
-        multi_locus.to_coordinate, 4, [(0, -1, -1), (-1, 0, -1)])
+        multi_locus.to_coordinate,
+        4,
+        [
+            {"position": 0, "offset": -1, "region": "u"},
+            {"position": -1, "offset": 0, "region": "u"},
+        ],
+    )
+
     degenerate_equal(
-        multi_locus.to_coordinate, 72, [(21, 1, 1), (22, 0, 1)])
+        multi_locus.to_coordinate,
+        72,
+        [
+            {"position": 21, "offset": 1, "region": "d"},
+            {"position": 22, "offset": 0, "region": "d"},
+        ],
+    )
 
 
 def test_MultiLocus_inverted_degenerate():
@@ -163,6 +184,19 @@ def test_MultiLocus_inverted_degenerate():
     multi_locus = MultiLocus(_locations, True)
 
     degenerate_equal(
-        multi_locus.to_coordinate, 72, [(0, -1, -1), (-1, 0, -1)])
+        multi_locus.to_coordinate,
+        72,
+        [
+            {"position": 0, "offset": -1, "region": "u"},
+            {"position": -1, "offset": 0, "region": "u"},
+        ],
+    )
+
     degenerate_equal(
-        multi_locus.to_coordinate, 4, [(21, 1, 1), (22, 0, 1)])
+        multi_locus.to_coordinate,
+        4,
+        [
+            {"position": 21, "offset": 1, "region": "d"},
+            {"position": 22, "offset": 0, "region": "d"},
+        ],
+    )

From 89cdba7fb14545df896b8f20f049cbd4ed931d2e Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Feb 2026 12:56:20 +0100
Subject: [PATCH 005/127] Fix typo

---
 tests/test_multi_locus.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/tests/test_multi_locus.py b/tests/test_multi_locus.py
index 1e3812a..a0eea27 100644
--- a/tests/test_multi_locus.py
+++ b/tests/test_multi_locus.py
@@ -1,5 +1,3 @@
-"""Tests for MultiLocus flattening and coordinate conversions."""
-
 from mutalyzer_crossmapper import MultiLocus
 from mutalyzer_crossmapper.multi_locus import _offsets
 
@@ -17,11 +15,6 @@ def test_offsets_inverted():
     """Cummulative location lengths for inverted list of locations."""
     assert _offsets(_locations, -1) == [0, 2, 4, 8, 13, 19]
 
-    invariant(
-        multi_locus.to_position,
-        4,
-        multi_locus.to_coordinate,
-        {"position": 0, "offset": -1, "region": "u"},
 def test_offsets_adjacent():
     """Cummulative location lengths for adjacent locations."""
     assert _offsets([(1, 3), (3, 5)], 1) == [0, 2]

From 2d4e2eb292ea52b45277ba041609841481ab659a Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Feb 2026 14:11:11 +0100
Subject: [PATCH 006/127] Refactor(crossmapper): convert Genomic to dict-based
 position model

---
 mutalyzer_crossmapper/crossmapper.py | 11 ++++++-----
 tests/test_crossmapper.py            |  4 ++--
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 537efd3..def779b 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -1,3 +1,4 @@
+from turtle import position
 from .multi_locus import MultiLocus
 
 
@@ -8,18 +9,18 @@ def coordinate_to_genomic(self, coordinate):
 
         :arg int coordinate: Coordinate.
 
-        :returns int: Genomic position.
+        :returns dict: Genomic position.
         """
-        return coordinate + 1
+        return {"position": coordinate + 1}
 
-    def genomic_to_coordinate(self, position):
+    def genomic_to_coordinate(self, position_m):
         """Convert a genomic position (g./m./o.) to a coordinate.
 
-        :arg int position: Genomic position.
+        :arg int position: Genomic position model.
 
         :returns int: Coordinate.
         """
-        return position - 1
+        return position_m["position"] - 1
 
 
 class NonCoding(Genomic):
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index dbe6b47..1d019fb 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -11,9 +11,9 @@ def test_Genomic():
     crossmap = Genomic()
 
     invariant(
-        crossmap.coordinate_to_genomic, 0, crossmap.genomic_to_coordinate, 1)
+        crossmap.coordinate_to_genomic, 0, crossmap.genomic_to_coordinate, {"position": 1})
     invariant(
-        crossmap.coordinate_to_genomic, 98, crossmap.genomic_to_coordinate, 99)
+        crossmap.coordinate_to_genomic, 98, crossmap.genomic_to_coordinate, {"position": 99})
 
 
 def test_NonCoding():

From 923cd9fb406b3ee916b17a87ed2a11d6cbc85285 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Feb 2026 17:44:20 +0100
Subject: [PATCH 007/127] Refactor(crossmapper): convert NonCoding to
 dict-based position model

---
 mutalyzer_crossmapper/crossmapper.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index def779b..07285b7 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -1,4 +1,3 @@
-from turtle import position
 from .multi_locus import MultiLocus
 
 
@@ -39,23 +38,24 @@ def coordinate_to_noncoding(self, coordinate):
 
         :arg int coordinate: Coordinate.
 
-        :returns tuple: Noncoding position.
+        :returns dict: Noncoding position model.
         """
-        pos = self._noncoding.to_position(coordinate)
-
-        return pos[0] + 1, pos[1], pos[2]
+        pos_m = self._noncoding.to_position(coordinate)
+        if pos_m["region"] == "":
+            pos_m["position"] = pos_m["position"] + 1
+        return pos_m
 
-    def noncoding_to_coordinate(self, position):
+    def noncoding_to_coordinate(self, position_m):
         """Convert a noncoding position (n./r.) to a coordinate.
 
-        :arg tuple position: Noncoding position.
+        :arg dict postion_m: Noncoding position model.
 
         :returns int: Coordinate.
         """
-        if position[0] > 0:
-            return self._noncoding.to_coordinate(
-                (position[0] - 1, position[1]))
-        return self._noncoding.to_coordinate(position)
+        if position_m["region"] == "":
+        # if position_m["position"] > 0:
+            position_m["position"] = position_m["position"] - 1
+        return self._noncoding.to_coordinate(position_m)
 
 
 class Coding(NonCoding):

From 259481b05d519ebf4df106b2c8112c899ca4e231 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Feb 2026 17:49:41 +0100
Subject: [PATCH 008/127] Refactor (locus, multi_locus): allow 'u', 'd' for UTR
 areas in hgvs model

---
 mutalyzer_crossmapper/locus.py       | 17 +++++++++---
 mutalyzer_crossmapper/multi_locus.py | 39 ++++++++++++++++++----------
 2 files changed, 38 insertions(+), 18 deletions(-)

diff --git a/mutalyzer_crossmapper/locus.py b/mutalyzer_crossmapper/locus.py
index a692f61..7e26235 100644
--- a/mutalyzer_crossmapper/locus.py
+++ b/mutalyzer_crossmapper/locus.py
@@ -30,13 +30,22 @@ def to_position(self, coordinate):
             return {"position": self._end, "offset": coordinate - self.boundary[1]}
         return {"position": coordinate - self.boundary[0], "offset": 0}
 
-    def to_coordinate(self, position):
-        """Convert a position to a coordinate.
+    def to_coordinate(self, position_m):
+        """Convert a position model to a coordinate.
 
         :arg dict position: Position model with 'position' and 'offset' keys.
 
         :returns int: Coordinate.
         """
         if self._inverted:
-            return self.boundary[1] - position["position"] - position["offset"]
-        return self.boundary[0] + position["position"] + position["offset"]
+            if position_m["region"] == "u":
+                return self.boundary[1] + position_m["position"]
+            elif position_m["region"] == "d":
+                return self.boundary[0] - position_m["position"]
+            return self.boundary[1] - position_m["position"] - position_m["offset"]
+        if position_m["region"] == "u":
+            return self.boundary[0] - position_m["position"]
+        elif position_m["region"] == "d":
+            return self.boundary[1] + position_m["position"]
+        else:
+            return self.boundary[0] + position_m["position"] + position_m["offset"]
diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index d1f65b8..a7f1ca4 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -60,23 +60,34 @@ def to_position(self, coordinate:int):
         outside = self._orientation * self.outside(coordinate)
         region = "u" if outside < 0 else "d" if outside > 0 else ""
         location = self._loci[index].to_position(coordinate)
-
-        return {"position": location["position"] + self._offsets[self._direction(index)],
-            "offset": location["offset"],
-            "region": region}
-
-    def to_coordinate(self, position_model:dict):
+        if not outside:
+            return {
+                "position": location["position"] + self._offsets[self._direction(index)],
+                "offset": location["offset"],
+                "region": region}
+        else:
+            return  {
+                "position": abs(self._offsets[self._direction(index)] - self._offsets[self._direction(index)] + 1),
+                "offset": 0,
+                "region":region
+            }
+
+    def to_coordinate(self, position_m:dict):
         """Convert a position model to a coordinate.
 
         :arg dict position: Position.
 
         :returns int: Coordinate.
         """
-        offset_val = position_model["offset"]
-        index = min(
-            len(self._offsets),
-            max(0, bisect_right(self._offsets, position_model["position"]) - 1)
-        )
-        return self._loci[self._direction(index)].to_coordinate(
-            {"position": position_model["position"] - self._offsets[index], "offset": offset_val}
-        )
\ No newline at end of file
+        if position_m["region"] == "":
+            index = min(
+                len(self._offsets),
+                max(0, bisect_right(self._offsets, position_m["position"]) - 1)
+            )
+            position_m["position"] = position_m["position"] - self._offsets[index]
+
+        elif position_m["region"] == "u":
+          index = 0
+        else: # "d"
+            index = len(self._offsets) -1
+        return self._loci[self._direction(index)].to_coordinate(position_m)

From 55fd346994bb8731eb854d03898ae99c3ca72858 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Feb 2026 17:50:30 +0100
Subject: [PATCH 009/127] Refactor test modules for Genomic and NonCoding

---
 tests/test_crossmapper.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 1d019fb..ef68a48 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -23,18 +23,18 @@ def test_NonCoding():
     # Boundary between upstream and transcript.
     invariant(
         crossmap.coordinate_to_noncoding, 4,
-        crossmap.noncoding_to_coordinate, (1, -1, -1))
+        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region":"u"})
     invariant(
         crossmap.coordinate_to_noncoding, 5,
-        crossmap.noncoding_to_coordinate, (1, 0, 0))
+        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region": ""})
 
     # Boundary between downstream and transcript.
     invariant(
         crossmap.coordinate_to_noncoding, 71,
-        crossmap.noncoding_to_coordinate, (22, 0, 0))
+        crossmap.noncoding_to_coordinate, {"position": 22, "offset": 0, "region": ""})
     invariant(
         crossmap.coordinate_to_noncoding, 72,
-        crossmap.noncoding_to_coordinate, (22, 1, 1))
+        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region": "d"})
 
 
 def test_NonCoding_inverted():
@@ -44,18 +44,18 @@ def test_NonCoding_inverted():
     # Boundary between upstream and transcript.
     invariant(
         crossmap.coordinate_to_noncoding, 72,
-        crossmap.noncoding_to_coordinate, (1, -1, -1))
+        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region": "u"})
     invariant(
         crossmap.coordinate_to_noncoding, 71,
-        crossmap.noncoding_to_coordinate, (1, 0, 0))
+        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region": ""})
 
     # Boundary between downstream and transcript.
     invariant(
         crossmap.coordinate_to_noncoding, 5,
-        crossmap.noncoding_to_coordinate, (22, 0, 0))
+        crossmap.noncoding_to_coordinate, {"position": 22, "offset": 0, "region": ""})
     invariant(
         crossmap.coordinate_to_noncoding, 4,
-        crossmap.noncoding_to_coordinate, (22, 1, 1))
+        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region": "d"})
 
 
 def test_NonCoding_degenerate():
@@ -65,12 +65,12 @@ def test_NonCoding_degenerate():
     # Boundary between upstream and transcript.
     degenerate_equal(
         crossmap.noncoding_to_coordinate, 4,
-        [(1, -1, -1), (-1, 0, -1)])
+        [{"position": 1, "offset": 0, "region":"u"}])
 
     # Boundary between downstream and transcript.
     degenerate_equal(
         crossmap.noncoding_to_coordinate, 72,
-        [(22, 1, 1), (23, 0, 1)])
+        [{"position": 1, "offset": 0, "region": "d"}])
 
 
 def test_NonCoding_inverted_degenerate():
@@ -80,12 +80,12 @@ def test_NonCoding_inverted_degenerate():
     # Boundary between upstream and transcript.
     degenerate_equal(
         crossmap.noncoding_to_coordinate, 72,
-        [(1, -1, -1), (-1, 0, -1)])
+        [{"position": 1, "offset": 0, "region": "u"}])
 
     # Boundary between downstream and transcript.
     degenerate_equal(
         crossmap.noncoding_to_coordinate, 4,
-        [(22, 1, 1), (23, 0, 1)])
+        [{"position": 1 , "offset": 0, "region": "d"}])
 
 
 def test_Coding():

From 84127e5aabeca1609c94febd90af7201957b3fb2 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 26 Feb 2026 09:53:56 +0100
Subject: [PATCH 010/127] Remove 'region' in locus position model

---
 mutalyzer_crossmapper/locus.py | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/mutalyzer_crossmapper/locus.py b/mutalyzer_crossmapper/locus.py
index 7e26235..a531ecb 100644
--- a/mutalyzer_crossmapper/locus.py
+++ b/mutalyzer_crossmapper/locus.py
@@ -24,7 +24,7 @@ def to_position(self, coordinate):
                 return {"position": self._end, "offset": self.boundary[0] - coordinate}
             return {"position": self.boundary[1] - coordinate, "offset": 0}
 
-        if coordinate < self.boundary[0]:           # upstream of an exon, re
+        if coordinate < self.boundary[0]:           # upstream of an exon
             return {"position": 0, "offset": coordinate - self.boundary[0]}
         if coordinate > self.boundary[1]:           # downstream of an exon
             return {"position": self._end, "offset": coordinate - self.boundary[1]}
@@ -38,14 +38,5 @@ def to_coordinate(self, position_m):
         :returns int: Coordinate.
         """
         if self._inverted:
-            if position_m["region"] == "u":
-                return self.boundary[1] + position_m["position"]
-            elif position_m["region"] == "d":
-                return self.boundary[0] - position_m["position"]
             return self.boundary[1] - position_m["position"] - position_m["offset"]
-        if position_m["region"] == "u":
-            return self.boundary[0] - position_m["position"]
-        elif position_m["region"] == "d":
-            return self.boundary[1] + position_m["position"]
-        else:
-            return self.boundary[0] + position_m["position"] + position_m["offset"]
+        return self.boundary[0] + position_m["position"] + position_m["offset"]

From eb6ce9b3d393e4089cbd368edfee720d2b150aaa Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 26 Feb 2026 10:01:09 +0100
Subject: [PATCH 011/127] Refactor(multi_locus): replace tuple with dict

---
 mutalyzer_crossmapper/multi_locus.py | 42 ++++++++++++++++++++--------
 tests/test_multi_locus.py            |  8 +++---
 2 files changed, 35 insertions(+), 15 deletions(-)

diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index a7f1ca4..1e3f72a 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -60,16 +60,31 @@ def to_position(self, coordinate:int):
         outside = self._orientation * self.outside(coordinate)
         region = "u" if outside < 0 else "d" if outside > 0 else ""
         location = self._loci[index].to_position(coordinate)
-        if not outside:
+        # UTR
+        if outside:
+            return {
+                "position": abs(location["offset"]),
+                "offset": 0,
+                "region": region
+            }
+        # in exons
+        if location["offset"] == 0: # in an exon
             return {
                 "position": location["position"] + self._offsets[self._direction(index)],
-                "offset": location["offset"],
-                "region": region}
-        else:
-            return  {
-                "position": abs(self._offsets[self._direction(index)] - self._offsets[self._direction(index)] + 1),
                 "offset": 0,
-                "region":region
+                "region": ""
+            }
+        elif location["offset"] < 0: # before an exon
+            return {
+                "position": self._offsets[self._direction(index)],
+                "offset": location["offset"],
+                "region": ""
+            }
+        else: # after an exon
+            return{
+                "position": location["position"] + self._offsets[self._direction(index)],
+                "offset": location["offset"],
+                "region": ""
             }
 
     def to_coordinate(self, position_m:dict):
@@ -85,9 +100,14 @@ def to_coordinate(self, position_m:dict):
                 max(0, bisect_right(self._offsets, position_m["position"]) - 1)
             )
             position_m["position"] = position_m["position"] - self._offsets[index]
+            return self._loci[self._direction(index)].to_coordinate(position_m)
 
         elif position_m["region"] == "u":
-          index = 0
-        else: # "d"
-            index = len(self._offsets) -1
-        return self._loci[self._direction(index)].to_coordinate(position_m)
+            if self._inverted:
+                return position_m["position"] + self._locations[-1][1] - 1
+            return self._locations[0][0] - position_m["position"]
+
+        else: # d
+            if self._inverted:
+                return self._locations[0][0] - position_m["position"]
+            return position_m["position"] + self._locations[-1][1] - 1
diff --git a/tests/test_multi_locus.py b/tests/test_multi_locus.py
index a0eea27..dcd18ef 100644
--- a/tests/test_multi_locus.py
+++ b/tests/test_multi_locus.py
@@ -30,7 +30,7 @@ def test_MultiLocus():
     multi_locus = MultiLocus(_locations)
 
     # Boundary between upstream and the first locus.
-    invariant(multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 0, "offset": -1, "region": "u"},
+    invariant(multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": "u"},
     )
 
     invariant(
@@ -55,7 +55,7 @@ def test_MultiLocus():
     invariant(
         multi_locus.to_position, 71, multi_locus.to_coordinate, {"position": 21, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 72, multi_locus.to_coordinate, {"position": 21, "offset": 1, "region": "d"})
+        multi_locus.to_position, 72, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": "d"})
 
 
 def test_MultiLocus_inverted():
@@ -64,7 +64,7 @@ def test_MultiLocus_inverted():
 
     # Boundary between upstream and the first locus.
     invariant(
-        multi_locus.to_position, 72, multi_locus.to_coordinate, {"position": 0, "offset": -1, "region": "u"})
+        multi_locus.to_position, 72, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": "u"})
     invariant(
         multi_locus.to_position, 71, multi_locus.to_coordinate, {"position": 0, "offset": 0, "region": ""})
 
@@ -86,7 +86,7 @@ def test_MultiLocus_inverted():
     invariant(
         multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 21, "offset": 0, "region": ""})
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 21, "offset": 1, "region": "d"})
+        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": "d"})
 
 
 def test_MultiLocus_adjacent_loci():

From 7d7bc9bd56dcb9ba04125b729a2e92738ed4aba7 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 26 Feb 2026 10:30:27 +0100
Subject: [PATCH 012/127] Refactor crossmapper and tests, allow ''/*/- in
 position model for Coding class

---
 mutalyzer_crossmapper/crossmapper.py |  86 ++++++++++++----
 tests/test_crossmapper.py            | 145 ++++++++++++++++++++-------
 2 files changed, 173 insertions(+), 58 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 07285b7..8efa979 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -53,7 +53,6 @@ def noncoding_to_coordinate(self, position_m):
         :returns int: Coordinate.
         """
         if position_m["region"] == "":
-        # if position_m["position"] > 0:
             position_m["position"] = position_m["position"] - 1
         return self._noncoding.to_coordinate(position_m)
 
@@ -72,11 +71,11 @@ def __init__(self, locations, cds, inverted=False):
         b1 = self._noncoding.to_position(cds[1])
 
         if self._inverted:
-            self._coding = (b1[0] + b1[1] + 1, b0[0] + b0[1] + 1)
-            self._cds_len = (b0[0] + b0[1]) - (b1[0] + b1[1])
+            self._coding = (b1["position"] + b1["offset"] + 1, b0["position"] + b0["offset"] + 1)
+            self._cds_len = (b0["position"] + b0["offset"]) - (b1["position"] + b1["offset"])
         else:
-            self._coding = (b0[0] + b0[1], b1[0] + b1[1])
-            self._cds_len = (b1[0] + b1[1]) - (b0[0] + b0[1])
+            self._coding = (b0["position"] + b0["offset"], b1["position"] + b1["offset"])
+            self._cds_len = (b1["position"] + b1["offset"]) - (b0["position"] + b0["offset"])
 
     def _coordinate_to_coding(self, coordinate):
         """Convert a coordinate to a coding position (c./r.).
@@ -85,13 +84,31 @@ def _coordinate_to_coding(self, coordinate):
 
         :returns tuple: Coding position (c./r.).
         """
-        pos = self._noncoding.to_position(coordinate)
-
-        if pos[0] < self._coding[0]:
-            return pos[0] - self._coding[0], pos[1], -1, pos[2]
-        elif pos[0] >= self._coding[1]:
-            return pos[0] - self._coding[1] + 1, pos[1], 1, pos[2]
-        return pos[0] - self._coding[0] + 1, pos[1], 0, pos[2]
+        noncoding_pos = self._noncoding.to_position(coordinate)
+
+        # on top of the noncoding position model, add CDs info
+        location = noncoding_pos["position"]
+        if noncoding_pos["region"] == "":
+            if location < self._coding[0]: # before CDs
+                return {
+                    "position": self._coding[0] - location,
+                    "offset": noncoding_pos["offset"],
+                    "region": "-"
+                }
+            elif location >= self._coding[1]: # after CDs
+                return {
+                    "position": location - self._coding[1] + 1,
+                    "offset": noncoding_pos["offset"],
+                    "region": "*"
+                }
+            else:
+                return {
+                    "position": location - self._coding[0] + 1,
+                    "offset": noncoding_pos["offset"],
+                    "region": ""
+                }
+        else:
+            return noncoding_pos
 
     def coordinate_to_coding(self, coordinate, degenerate=False):
         """Convert a coordinate to a coding position (c./r.).
@@ -113,21 +130,46 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
 
         return pos
 
-    def coding_to_coordinate(self, position):
+    def coding_to_coordinate(self, pos_m):
         """Convert a coding position (c./r.) to a coordinate.
 
         :arg tuple position: Coding position (c./r.).
 
         :returns int: Coordinate.
         """
-        if position[2] == -1:
-            return self._noncoding.to_coordinate(
-                (position[0] + self._coding[0], position[1]))
-        elif position[2] == 1:
-            return self._noncoding.to_coordinate(
-                (position[0] + self._coding[1] - 1, position[1]))
-        return self._noncoding.to_coordinate(
-            (position[0] + self._coding[0] - 1, position[1]))
+        region = pos_m["region"]
+        if region == "u":
+            noncoding_pos = {
+                "position": pos_m["position"],
+                "offset": 0,
+                "region": "u"
+            }
+        elif region == "d":
+            noncoding_pos = {
+                "position": pos_m["position"],
+                "offset": 0,
+                "region": "d"
+            }
+        elif region == "":
+            noncoding_pos = {
+                "position": pos_m["position"] + self._coding[0] -1,
+                "offset": pos_m["offset"],
+                "region": ""
+            }
+        elif region == "-":
+            noncoding_pos = {
+                "position": self._coding[0] - pos_m["position"],
+                "offset": pos_m["offset"],
+                "region": ""
+            }
+        else: # *
+            noncoding_pos = {
+                "position": self._coding[1] + pos_m["position"] - 1,
+                "offset": pos_m["offset"],
+                "region": ""
+            }
+        return self._noncoding.to_coordinate(noncoding_pos)
+
 
     def coordinate_to_protein(self, coordinate):
         """Convert a coordinate to a protein position (p.).
@@ -138,7 +180,7 @@ def coordinate_to_protein(self, coordinate):
         """
         pos = self.coordinate_to_coding(coordinate)
 
-        if pos[2] == -1:
+        if pos[2] == -1: # before CDs
             return (pos[0] // 3, pos[0] % 3 + 1, *pos[1:])
         return ((pos[0] + 2) // 3, (pos[0] + 2) % 3 + 1, *pos[1:])
 
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index ef68a48..e2080ac 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -95,18 +95,37 @@ def test_Coding():
     # Boundary between 5' and CDS.
     invariant(
         crossmap.coordinate_to_coding, 31,
-        crossmap.coding_to_coordinate, (-1, 0, -1, 0))
+        crossmap.coding_to_coordinate,
+        {"position": 1,
+         "offset":0,
+         "region":"-"
+        }
+    )
     invariant(
         crossmap.coordinate_to_coding, 32,
-        crossmap.coding_to_coordinate, (1, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {"position": 1,
+         "offset":0,
+         "region":""
+        }
+        )
 
     # Boundary between CDS and 3'.
     invariant(
         crossmap.coordinate_to_coding, 42,
-        crossmap.coding_to_coordinate, (6, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {"position": 6,
+         "offset":0,
+         "region":""
+        })
     invariant(
         crossmap.coordinate_to_coding, 43,
-        crossmap.coding_to_coordinate, (1, 0, 1, 0))
+        crossmap.coding_to_coordinate,
+        {"position": 1,
+         "offset":0,
+         "region":"*"
+        }
+        )
 
 
 def test_Coding_inverted():
@@ -116,18 +135,42 @@ def test_Coding_inverted():
     # Boundary between 5' and CDS.
     invariant(
         crossmap.coordinate_to_coding, 43,
-        crossmap.coding_to_coordinate, (-1, 0, -1, 0))
+        crossmap.coding_to_coordinate,
+        {
+            "position": 1,
+            "offset": 0,
+            "region": "-"
+        }
+    )
     invariant(
         crossmap.coordinate_to_coding, 42,
-        crossmap.coding_to_coordinate, (1, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {
+            "position": 1,
+            "offset": 0,
+            "region": ""
+        }
+        )
 
     # Boundary between CDS and 3'.
     invariant(
         crossmap.coordinate_to_coding, 32,
-        crossmap.coding_to_coordinate, (6, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {
+            "position": 6,
+            "offset": 0,
+            "region": ""
+        }
+        )
     invariant(
         crossmap.coordinate_to_coding, 31,
-        crossmap.coding_to_coordinate, (1, 0, 1, 0))
+        crossmap.coding_to_coordinate,
+        {
+            "position": 1,
+            "offset": 0,
+            "region": "*"
+        }
+    )
 
 
 def test_Coding_regions():
@@ -137,18 +180,22 @@ def test_Coding_regions():
     # Upstream odd length intron between two regions.
     invariant(
         crossmap.coordinate_to_coding, 25,
-        crossmap.coding_to_coordinate, (-1, 5, -1, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': 5, 'region': '-'})
     invariant(
         crossmap.coordinate_to_coding, 26,
-        crossmap.coding_to_coordinate, (1, -4, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': -4, 'region': ''})
 
     # Downstream odd length intron between two regions.
     invariant(
         crossmap.coordinate_to_coding, 44,
-        crossmap.coding_to_coordinate, (10, 5, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 10, 'offset': 5, 'region': ''})
     invariant(
         crossmap.coordinate_to_coding, 45,
-        crossmap.coding_to_coordinate, (1, -4, 1, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': -4, 'region': '*'})
 
 
 def test_Coding_regions_inverted():
@@ -158,18 +205,22 @@ def test_Coding_regions_inverted():
     # Upstream odd length intron between two regions.
     invariant(
         crossmap.coordinate_to_coding, 44,
-        crossmap.coding_to_coordinate, (-1, 5, -1, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': 5, 'region': '-'})
     invariant(
         crossmap.coordinate_to_coding, 43,
-        crossmap.coding_to_coordinate, (1, -4, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': -4, 'region': ''})
 
     # Downstream odd length intron between two regions.
     invariant(
         crossmap.coordinate_to_coding, 25,
-        crossmap.coding_to_coordinate, (10, 5, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 10, 'offset': 5, 'region': ''})
     invariant(
         crossmap.coordinate_to_coding, 24,
-        crossmap.coding_to_coordinate, (1, -4, 1, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': -4, 'region': '*'})
 
 
 def test_Coding_no_utr5():
@@ -179,10 +230,12 @@ def test_Coding_no_utr5():
     # Direct transition from upstream to CDS.
     invariant(
         crossmap.coordinate_to_coding, 9,
-        crossmap.coding_to_coordinate, (1, -1, 0, -1))
+        crossmap.coding_to_coordinate, #(1, -1, 0, -1)
+        {'position': 1, 'offset': 0, 'region': 'u'})
     invariant(
         crossmap.coordinate_to_coding, 10,
-        crossmap.coding_to_coordinate, (1, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': 0, 'region': ''})
 
 
 def test_Coding_no_utr5_inverted():
@@ -192,10 +245,12 @@ def test_Coding_no_utr5_inverted():
     # Direct transition from upstream to CDS.
     invariant(
         crossmap.coordinate_to_coding, 20,
-        crossmap.coding_to_coordinate, (1, -1, 0, -1))
+        crossmap.coding_to_coordinate, #(1, -1, 0, -1)
+        {'position': 1, 'offset': 0, 'region': 'u'})
     invariant(
         crossmap.coordinate_to_coding, 19,
-        crossmap.coding_to_coordinate, (1, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 2, 'offset': 0, 'region': '-'})
 
 
 def test_Coding_no_utr3():
@@ -203,12 +258,15 @@ def test_Coding_no_utr3():
     crossmap = Coding([(10, 20)], (15, 20))
 
     # Direct transition from CDS to downstream.
+    #TODO:
     invariant(
         crossmap.coordinate_to_coding, 19,
-        crossmap.coding_to_coordinate, (5, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 9, 'offset': 0, 'region': '*'})
     invariant(
         crossmap.coordinate_to_coding, 20,
-        crossmap.coding_to_coordinate, (5, 1, 0, 1))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': 0, 'region': 'd'})
 
 
 def test_Coding_no_utr3_inverted():
@@ -218,10 +276,12 @@ def test_Coding_no_utr3_inverted():
     # Direct transition from CDS to downstream.
     invariant(
         crossmap.coordinate_to_coding, 10,
-        crossmap.coding_to_coordinate, (5, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 5, 'offset': 0, 'region': ''})
     invariant(
         crossmap.coordinate_to_coding, 9,
-        crossmap.coding_to_coordinate, (5, 1, 0, 1))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': 0, 'region': 'd'})
 
 
 def test_Coding_small_utr5():
@@ -231,13 +291,17 @@ def test_Coding_small_utr5():
     # Transition from upstream to 5' UTR to CDS.
     invariant(
         crossmap.coordinate_to_coding, 9,
-        crossmap.coding_to_coordinate, (-1, -1, -1, -1))
+        crossmap.coding_to_coordinate, #(-1, -1, -1, -1)
+        {'position': 1, 'offset': 0, 'region': 'u'})
     invariant(
         crossmap.coordinate_to_coding, 10,
-        crossmap.coding_to_coordinate, (-1, 0, -1, 0))
+        crossmap.coding_to_coordinate, #(-1, 0, -1, 0))
+        {'position': 1, 'offset': 0, 'region': '-'}
+    )
     invariant(
         crossmap.coordinate_to_coding, 11,
-        crossmap.coding_to_coordinate, (1, 0, 0, 0))
+        crossmap.coding_to_coordinate, #(1, 0, 0, 0))
+        {'position': 1, 'offset': 0, 'region': ''})
 
 
 def test_Coding_small_utr5_inverted():
@@ -247,13 +311,16 @@ def test_Coding_small_utr5_inverted():
     # Transition from upstream to 5' UTR to CDS.
     invariant(
         crossmap.coordinate_to_coding, 20,
-        crossmap.coding_to_coordinate, (-1, -1, -1, -1))
+        crossmap.coding_to_coordinate,# (-1, -1, -1, -1)
+        {'position': 1, 'offset': 0, 'region': 'u'})
     invariant(
         crossmap.coordinate_to_coding, 19,
-        crossmap.coding_to_coordinate, (-1, 0, -1, 0))
+        crossmap.coding_to_coordinate, #(-1, 0, -1, 0))
+        {'position': 1, 'offset': 0, 'region': '-'})
     invariant(
         crossmap.coordinate_to_coding, 18,
-        crossmap.coding_to_coordinate, (1, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': 0, 'region': ''})
 
 
 def test_Coding_small_utr3():
@@ -263,13 +330,16 @@ def test_Coding_small_utr3():
     # Transition from CDS to 3' UTR to downstream.
     invariant(
         crossmap.coordinate_to_coding, 18,
-        crossmap.coding_to_coordinate, (4, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 4, 'offset': 0, 'region': ''})
     invariant(
         crossmap.coordinate_to_coding, 19,
-        crossmap.coding_to_coordinate, (1, 0, 1, 0))
+        crossmap.coding_to_coordinate, #(1, 0, 1, 0)
+        {'position': 1, 'offset': 0, 'region': '*'})
     invariant(
         crossmap.coordinate_to_coding, 20,
-        crossmap.coding_to_coordinate, (1, 1, 1, 1))
+        crossmap.coding_to_coordinate, #(1, 1, 1, 1))
+        {'position': 1, 'offset': 0, 'region': 'd'})
 
 
 def test_Coding_small_utr3_inverted():
@@ -279,13 +349,16 @@ def test_Coding_small_utr3_inverted():
     # Transition from CDS to 3' UTR to downstream.
     invariant(
         crossmap.coordinate_to_coding, 11,
-        crossmap.coding_to_coordinate, (4, 0, 0, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 4, 'offset': 0, 'region': ''})
     invariant(
         crossmap.coordinate_to_coding, 10,
-        crossmap.coding_to_coordinate, (1, 0, 1, 0))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': 0, 'region': '*'})
     invariant(
         crossmap.coordinate_to_coding, 9,
-        crossmap.coding_to_coordinate, (1, 1, 1, 1))
+        crossmap.coding_to_coordinate,
+        {'position': 1, 'offset': 0, 'region': 'd'})
 
 
 def test_Coding_degenerate():

From 043330389c052dc30b399142e2b17b7ec6c1df18 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 26 Feb 2026 18:29:26 +0100
Subject: [PATCH 013/127] Refactor(multi_locus): degenerate positions for
 multi_locus and tests

---
 mutalyzer_crossmapper/multi_locus.py | 13 +++++++------
 tests/test_multi_locus.py            | 13 ++++++++-----
 2 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 1e3f72a..d7a52e9 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -94,7 +94,8 @@ def to_coordinate(self, position_m:dict):
 
         :returns int: Coordinate.
         """
-        if position_m["region"] == "":
+        region = position_m["region"]
+        if region == "":
             index = min(
                 len(self._offsets),
                 max(0, bisect_right(self._offsets, position_m["position"]) - 1)
@@ -102,12 +103,12 @@ def to_coordinate(self, position_m:dict):
             position_m["position"] = position_m["position"] - self._offsets[index]
             return self._loci[self._direction(index)].to_coordinate(position_m)
 
-        elif position_m["region"] == "u":
+        elif region == "u":
             if self._inverted:
-                return position_m["position"] + self._locations[-1][1] - 1
-            return self._locations[0][0] - position_m["position"]
+                return abs(position_m["position"]) + self._locations[-1][1] + position_m["offset"] - 1
+            return self._locations[0][0] - abs(position_m["position"]) + position_m["offset"]
 
         else: # d
             if self._inverted:
-                return self._locations[0][0] - position_m["position"]
-            return position_m["position"] + self._locations[-1][1] - 1
+                return self._locations[0][0] - abs(position_m["position"]) + position_m["offset"]
+            return abs(position_m["position"]) + self._locations[-1][1] + position_m["offset"] - 1
diff --git a/tests/test_multi_locus.py b/tests/test_multi_locus.py
index dcd18ef..922529a 100644
--- a/tests/test_multi_locus.py
+++ b/tests/test_multi_locus.py
@@ -158,6 +158,7 @@ def test_MultiLocus_degenerate():
         4,
         [
             {"position": 0, "offset": -1, "region": "u"},
+            {"position": 1, "offset": 0, "region": "u"},
             {"position": -1, "offset": 0, "region": "u"},
         ],
     )
@@ -166,8 +167,8 @@ def test_MultiLocus_degenerate():
         multi_locus.to_coordinate,
         72,
         [
-            {"position": 21, "offset": 1, "region": "d"},
-            {"position": 22, "offset": 0, "region": "d"},
+            {"position": 0, "offset": 1, "region": "d"},
+            {"position": 1, "offset": 0, "region": "d"},
         ],
     )
 
@@ -180,8 +181,9 @@ def test_MultiLocus_inverted_degenerate():
         multi_locus.to_coordinate,
         72,
         [
-            {"position": 0, "offset": -1, "region": "u"},
+            {"position": 0, "offset": 1, "region": "u"},
             {"position": -1, "offset": 0, "region": "u"},
+            {"position": 1, "offset": 0, "region": "u"},
         ],
     )
 
@@ -189,7 +191,8 @@ def test_MultiLocus_inverted_degenerate():
         multi_locus.to_coordinate,
         4,
         [
-            {"position": 21, "offset": 1, "region": "d"},
-            {"position": 22, "offset": 0, "region": "d"},
+            {"position": 0, "offset": -1, "region": "d"},
+            {"position": 1, "offset": 0, "region": "d"},
+            {"position": 2, "offset": 1, "region": "d"}
         ],
     )

From a583f00fcc038753243c046d9462169996626f7b Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 27 Feb 2026 11:44:31 +0100
Subject: [PATCH 014/127] Refactor(crossmapper): implement hgvs position model
 for protein and write degenerate in the same flow.

---
 mutalyzer_crossmapper/crossmapper.py | 58 ++++++++++++++++++++--------
 tests/test_crossmapper.py            | 36 +++++++++++------
 2 files changed, 67 insertions(+), 27 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 8efa979..af2b3f4 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -119,14 +119,30 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
         :returns tuple: Coding position (c./r.).
         """
         pos = self._coordinate_to_coding(coordinate)
-
-        if degenerate and pos[3]:
-            if pos[2] == 0:
-                if pos[0] == 1 and pos[1] < 0:
-                    return pos[1], 0, -1, pos[3]
-                if pos[0] == self._cds_len and pos[1] > 0:
-                    return pos[0] + pos[1] - self._cds_len, 0, 1, pos[3]
-            return pos[0] + pos[1], 0, pos[2], pos[3]
+        # degenerate option: allow multiple or less correct ways to describe one position,
+        # e.g., neucleo c.10 can be the same location as c.d1 (if CDs ends at c9)
+        # the previous version corrects location+offset to location in UTR  area (c.1-2->c.-2)
+        # or merge the offset to location
+
+        if degenerate and pos["region"] in ["u", "d"]:
+            # if pos["region"] == "": unlikely to happen in biology? maybe used to collapse HGVS location at CDs boundary?
+            if pos["position"] == 1 and pos["offset"] < 0:
+                return {
+                    "position":pos["offset"],
+                    "offset": 0,
+                    "region": "-"
+                }
+            if pos["position"] == self._cds_len and pos["offset"] > 0:
+                return {
+                    "position": pos["position"] + pos["offset"] - self._cds_len,
+                    "offset": 0,
+                    "region": "*"
+                }
+            return {
+                "position": pos["position"] + pos["offset"],
+                "offset": 0,
+                "region":pos["region"]
+            }
 
         return pos
 
@@ -140,13 +156,13 @@ def coding_to_coordinate(self, pos_m):
         region = pos_m["region"]
         if region == "u":
             noncoding_pos = {
-                "position": pos_m["position"],
+                "position": abs(pos_m["position"]) + pos_m["offset"],
                 "offset": 0,
                 "region": "u"
             }
         elif region == "d":
             noncoding_pos = {
-                "position": pos_m["position"],
+                "position": abs(pos_m["position"]) + pos_m["offset"],
                 "offset": 0,
                 "region": "d"
             }
@@ -180,9 +196,15 @@ def coordinate_to_protein(self, coordinate):
         """
         pos = self.coordinate_to_coding(coordinate)
 
-        if pos[2] == -1: # before CDs
-            return (pos[0] // 3, pos[0] % 3 + 1, *pos[1:])
-        return ((pos[0] + 2) // 3, (pos[0] + 2) % 3 + 1, *pos[1:])
+        if pos["region"] in ["-", "*"]:
+            return {
+                "position": pos["position"] // 3 + 1,
+                "position_in_codon": pos["position"] % 3,
+                **{k: v for k, v in pos.items() if k != "position"}}
+        return {
+                "position": (pos["position"]+2) // 3,
+                "position_in_codon": (pos["position"]+2) % 3 + 1,
+                **{k: v for k, v in pos.items() if k != "position"}}
 
     def protein_to_coordinate(self, position):
         """Convert a protein position (p.) to a coordinate.
@@ -191,9 +213,13 @@ def protein_to_coordinate(self, position):
 
         :returns int: Coordinate.
         """
-        if position[3] == -1:
+        if position["region"] in ["-", "*"]:
             return self.coding_to_coordinate(
-                (3 * position[0] + position[1] - 1, *position[2:]))
+                {"position": 3 * position["position"] + position["position_in_codon"] - 3,
+                 "offset": position["offset"],
+                 "region": position["region"]})
 
         return self.coding_to_coordinate(
-            (3 * position[0] + position[1] - 3, *position[2:]))
+                {"position": 3 * position["position"] + position["position_in_codon"] - 3,
+                 "offset": position["offset"],
+                 "region": position["region"]})
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index e2080ac..e39225f 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -70,7 +70,10 @@ def test_NonCoding_degenerate():
     # Boundary between downstream and transcript.
     degenerate_equal(
         crossmap.noncoding_to_coordinate, 72,
-        [{"position": 1, "offset": 0, "region": "d"}])
+        [
+            {"position": 1, "offset": 0, "region": "d"},
+            {"position": 0, "offset": 1, "region": "d"}
+            ])
 
 
 def test_NonCoding_inverted_degenerate():
@@ -87,7 +90,8 @@ def test_NonCoding_inverted_degenerate():
         crossmap.noncoding_to_coordinate, 4,
         [{"position": 1 , "offset": 0, "region": "d"}])
 
-
+_exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
+_cds = (32, 43)
 def test_Coding():
     """Forward oriented coding transcript."""
     crossmap = Coding(_exons, _cds)
@@ -231,11 +235,11 @@ def test_Coding_no_utr5():
     invariant(
         crossmap.coordinate_to_coding, 9,
         crossmap.coding_to_coordinate, #(1, -1, 0, -1)
-        {'position': 1, 'offset': 0, 'region': 'u'})
+        {'position': 1, 'offset': 0, 'region': 'u'}) # serialize result : u1
     invariant(
         crossmap.coordinate_to_coding, 10,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': ''})
+        {'position': 1, 'offset': 0, 'region': ''}) # serialize result: 1
 
 
 def test_Coding_no_utr5_inverted():
@@ -367,7 +371,11 @@ def test_Coding_degenerate():
 
     degenerate_equal(
         crossmap.coding_to_coordinate, 9,
-        [(-1, -1, -1, -1), (-2, 0, -1, -1), (1, -2, 0, -1), (1, -10, 1, -1)])
+        [
+            {'position': 1, 'offset': 8, 'region': 'u'},
+            {'position': 8, 'offset': 1, 'region': 'u'},
+            {'position': -1, 'offset': 10, 'region': 'u'}
+        ])
     degenerate_equal(
         crossmap.coding_to_coordinate, 20,
         [(1, 1, 1, 1), (2, 0, 1, 1), (8, 2, 0, 1), (-1, 10, -1, 1)])
@@ -466,23 +474,29 @@ def test_Coding_protein():
     # Boundary between 5' UTR and CDS.
     invariant(
         crossmap.coordinate_to_protein, 31,
-        crossmap.protein_to_coordinate, (-1, 3, 0, -1, 0))
+        crossmap.protein_to_coordinate,
+        {'position': 1, "position_in_codon": 1, 'offset': 0, 'region': '-'})
     invariant(
         crossmap.coordinate_to_protein, 32,
-        crossmap.protein_to_coordinate, (1, 1, 0, 0, 0))
+        crossmap.protein_to_coordinate,
+        {'position': 1, "position_in_codon": 1, 'offset': 0, 'region': ''})
 
     # Intron boundary.
     invariant(
         crossmap.coordinate_to_protein, 34,
-        crossmap.protein_to_coordinate, (1, 3, 0, 0, 0))
+        crossmap.protein_to_coordinate,
+        {'position': 1, "position_in_codon": 3, 'offset': 0, 'region': ''})
     invariant(
         crossmap.coordinate_to_protein, 35,
-        crossmap.protein_to_coordinate, (1, 3, 1, 0, 0))
+        crossmap.protein_to_coordinate,
+        {'position': 1, "position_in_codon": 3, 'offset': 1, 'region': ''})
 
     # Boundary between CDS and 3' UTR.
     invariant(
         crossmap.coordinate_to_protein, 42,
-        crossmap.protein_to_coordinate, (2, 3, 0, 0, 0))
+        crossmap.protein_to_coordinate,
+        {'position': 2, "position_in_codon": 3, 'offset': 0, 'region': ''})
     invariant(
         crossmap.coordinate_to_protein, 43,
-        crossmap.protein_to_coordinate, (1, 1, 0, 1, 0))
+        crossmap.protein_to_coordinate,
+        {'position': 1, "position_in_codon": 1, 'offset': 0, 'region': '*'})

From a57a3e6177ccb29125f3451f6b34a6b16c24d34c Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 5 Mar 2026 11:54:02 +0100
Subject: [PATCH 015/127] Refactor(crossmapper): discard degenerate option

---
 mutalyzer_crossmapper/crossmapper.py | 27 +--------------------------
 1 file changed, 1 insertion(+), 26 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index af2b3f4..be0d1e1 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -110,7 +110,7 @@ def _coordinate_to_coding(self, coordinate):
         else:
             return noncoding_pos
 
-    def coordinate_to_coding(self, coordinate, degenerate=False):
+    def coordinate_to_coding(self, coordinate):
         """Convert a coordinate to a coding position (c./r.).
 
         :arg int coordinate: Coordinate.
@@ -119,31 +119,6 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
         :returns tuple: Coding position (c./r.).
         """
         pos = self._coordinate_to_coding(coordinate)
-        # degenerate option: allow multiple or less correct ways to describe one position,
-        # e.g., neucleo c.10 can be the same location as c.d1 (if CDs ends at c9)
-        # the previous version corrects location+offset to location in UTR  area (c.1-2->c.-2)
-        # or merge the offset to location
-
-        if degenerate and pos["region"] in ["u", "d"]:
-            # if pos["region"] == "": unlikely to happen in biology? maybe used to collapse HGVS location at CDs boundary?
-            if pos["position"] == 1 and pos["offset"] < 0:
-                return {
-                    "position":pos["offset"],
-                    "offset": 0,
-                    "region": "-"
-                }
-            if pos["position"] == self._cds_len and pos["offset"] > 0:
-                return {
-                    "position": pos["position"] + pos["offset"] - self._cds_len,
-                    "offset": 0,
-                    "region": "*"
-                }
-            return {
-                "position": pos["position"] + pos["offset"],
-                "offset": 0,
-                "region":pos["region"]
-            }
-
         return pos
 
     def coding_to_coordinate(self, pos_m):

From d245cd6ed7749ba25838409ff2090e392ce2cdab Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 5 Mar 2026 14:37:40 +0100
Subject: [PATCH 016/127] Change examples in README.

---
 README.rst | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/README.rst b/README.rst
index 7862443..061f91b 100644
--- a/README.rst
+++ b/README.rst
@@ -53,8 +53,8 @@ positions and coordinates.
     >>> from mutalyzer_crossmapper import Genomic
     >>> crossmap = Genomic()
     >>> crossmap.coordinate_to_genomic(0)
-    1
-    >>> crossmap.genomic_to_coordinate(1)
+    {"position": 1}
+    >>> crossmap.genomic_to_coordinate({"position": 1})
     0
 
 On top of the functionality provided by the ``Genomic`` class, the
@@ -67,8 +67,8 @@ positions and coordinates.
     >>> exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
     >>> crossmap = NonCoding(exons)
     >>> crossmap.coordinate_to_noncoding(35)
-    (14, 1, 0)
-    >>> crossmap.noncoding_to_coordinate((14, 1))
+    {"position": 14, "offset": 1, "region": ""}
+    >>> crossmap.noncoding_to_coordinate({"position": 14, "offset": 1, "region": ""})
     35
 
 Add the flag ``inverted=True`` to the constructor when the transcript resides
@@ -84,8 +84,8 @@ coordinates as well as conversions between protein positions and coordinates.
     >>> cds = (32, 43)
     >>> crossmap = Coding(exons, cds)
     >>> crossmap.coordinate_to_coding(31)
-    (-1, 0, -1, 0)
-    >>> crossmap.coding_to_coordinate((-1, 0, -1))
+    {"position": -1, "offset": 0, "region": "-"}
+    >>> crossmap.coding_to_coordinate({"position": -1, "offset": 0, "region": "-"})
     31
 
 Again, the flag ``inverted=True`` can be used for transcripts that reside on
@@ -96,8 +96,8 @@ Conversions between protein positions and coordinates are done as follows.
 .. code:: python
 
     >>> crossmap.coordinate_to_protein(41)
-    (2, 2, 0, 0, 0)
-    >>> crossmap.protein_to_coordinate((2, 2, 0, 0))
+    {"position": 2, "position_in_codon": 2, "offset": 1, "region": ""}
+    >>> crossmap.protein_to_coordinate({"position": 2, "position_in_codon": 2, "offset": 1, "region": ""})
     41
 
 

From 89559e4f9e5c8ac142cc7683eada5616938bae58 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 6 Mar 2026 10:54:50 +0100
Subject: [PATCH 017/127] Discard dataclass object for hgvs position model

---
 mutalyzer_crossmapper/hgvs_position_model.py | 92 --------------------
 1 file changed, 92 deletions(-)
 delete mode 100644 mutalyzer_crossmapper/hgvs_position_model.py

diff --git a/mutalyzer_crossmapper/hgvs_position_model.py b/mutalyzer_crossmapper/hgvs_position_model.py
deleted file mode 100644
index 7992c63..0000000
--- a/mutalyzer_crossmapper/hgvs_position_model.py
+++ /dev/null
@@ -1,92 +0,0 @@
-"""
-HGVS Position Model -
-    a dataclass object to bridge HGVS position component and Crossmapper outputs.
-"""
-from dataclasses import dataclass
-from typing import Optional, Tuple
-
-@dataclass
-class HGVSPositionModel:
-    """
-    Represent the position component of an HGVS variant description.
-    This model captures details necessary to describe the '[position]' part in an HGVS
-    description of the form
-        [reference sequence]:[sequence type].[position][variant type][change]
-    """
-    position: int
-    offset: Optional[int] = None
-    region: Optional[str] = None
-    position_in_codon: Optional[int] = None
-
-
-    def __post_init__(self):
-        # validate position
-        if self.position <= 0:
-            raise ValueError("Position must be a positive integer.")
-
-        # validate region
-        region_values = {"u", "-", "", "*", "d"}
-        if self.region is not None and self.region not in region_values:
-            raise ValueError(
-                f"Invalid region value: {self.region}. Allowed values are: {region_values}"
-            )
-
-        # validate position_in_codon
-        codon_values = {1, 2, 3}
-        if self.position_in_codon is not None and self.position_in_codon not in codon_values:
-            raise ValueError(
-                f"Invalid position in codon value: {self.position_in_codon}. "
-                f"Allowed values are: {codon_values}"
-            )
-
-
-    # Convert from tuple to HGVSPositionModel
-
-    #TODO: check for inverted and degerate options, now only support non-inverted and non-degenerate cases
-    @classmethod
-    def to_hgvs_position_model(cls, raw_tuple:Tuple):
-        """Convert crossmapper tuple to an HGVSPositionModel instance."""
-        if not raw_tuple:
-            raise ValueError("Input tuple position cannot be empty.")
-
-        # Genomic
-        if len(raw_tuple) == 1:
-            return cls(position=raw_tuple[0])
-        # Non-coding
-        if len(raw_tuple) == 3:
-            pass
-
-        # Coding
-        #(c_pos, offset, in_cds, offset_to_exon_boundary)
-        if len(raw_tuple) == 4:
-            c_pos, offset, cds, dis_to_exon_boundary = raw_tuple
-            region = cls._determine_region(cds, dis_to_exon_boundary)
-            return cls(position=c_pos, offset=offset, region=region)
-
-        # Protein (
-        if len(raw_tuple) == 5:
-            p_pos, codon_pos, offset, cds, dis_to_exon_boundary = raw_tuple
-            if cds == 0: # in CDS
-                return cls(
-                    position=p_pos,
-                    region="",
-                    position_in_codon=codon_pos
-                )
-            else:
-                # TODO: shall we support HGVSPositionModel outside of CDS for protein?
-                pass
-
-
-    @staticmethod
-    def _determine_region(cds, dis_to_exon_boundary):
-        if dis_to_exon_boundary < 0:
-            return "u"
-        elif dis_to_exon_boundary > 0:
-            return "d"
-        else: # in translation range, check if in CDS or not
-            if cds < 0: # before CDS
-                return "-"
-            elif cds > 0: # after CDS
-                return "*"
-            else:
-                return ""
\ No newline at end of file

From 08739ffbad75a76deb56ce4cc1930ad264e7cbf1 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 6 Mar 2026 16:21:40 +0100
Subject: [PATCH 018/127] Refactor(crossmapper): allow degenerate option for
 'u' and 'd' area

---
 mutalyzer_crossmapper/crossmapper.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index be0d1e1..9056ade 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -110,7 +110,7 @@ def _coordinate_to_coding(self, coordinate):
         else:
             return noncoding_pos
 
-    def coordinate_to_coding(self, coordinate):
+    def coordinate_to_coding(self, coordinate, degenerate=False):
         """Convert a coordinate to a coding position (c./r.).
 
         :arg int coordinate: Coordinate.
@@ -119,6 +119,13 @@ def coordinate_to_coding(self, coordinate):
         :returns tuple: Coding position (c./r.).
         """
         pos = self._coordinate_to_coding(coordinate)
+        if degenerate and pos["region"] in ["u", "d"]:
+            if pos["region"] == "u":
+                pos["position"] = pos["position"] + self._coding[0]
+                pos["region"] = "-"
+            else:
+                pos["position"] = pos["position"] + self._coding[1]
+                pos["region"] = "*"
         return pos
 
     def coding_to_coordinate(self, pos_m):

From fecf02617cdbb2a5d7c8c22ef216137d4abde455 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 9 Mar 2026 11:15:12 +0100
Subject: [PATCH 019/127] Cleanup(locus)

---
 mutalyzer_crossmapper/locus.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/mutalyzer_crossmapper/locus.py b/mutalyzer_crossmapper/locus.py
index a531ecb..738e87c 100644
--- a/mutalyzer_crossmapper/locus.py
+++ b/mutalyzer_crossmapper/locus.py
@@ -24,13 +24,13 @@ def to_position(self, coordinate):
                 return {"position": self._end, "offset": self.boundary[0] - coordinate}
             return {"position": self.boundary[1] - coordinate, "offset": 0}
 
-        if coordinate < self.boundary[0]:           # upstream of an exon
+        if coordinate < self.boundary[0]:
             return {"position": 0, "offset": coordinate - self.boundary[0]}
-        if coordinate > self.boundary[1]:           # downstream of an exon
+        if coordinate > self.boundary[1]:
             return {"position": self._end, "offset": coordinate - self.boundary[1]}
         return {"position": coordinate - self.boundary[0], "offset": 0}
 
-    def to_coordinate(self, position_m):
+    def to_coordinate(self, pos_m):
         """Convert a position model to a coordinate.
 
         :arg dict position: Position model with 'position' and 'offset' keys.
@@ -38,5 +38,5 @@ def to_coordinate(self, position_m):
         :returns int: Coordinate.
         """
         if self._inverted:
-            return self.boundary[1] - position_m["position"] - position_m["offset"]
-        return self.boundary[0] + position_m["position"] + position_m["offset"]
+            return self.boundary[1] - pos_m["position"] - pos_m["offset"]
+        return self.boundary[0] + pos_m["position"] + pos_m["offset"]

From 54746ec68c6304e324839987cc392a5554c97392 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 9 Mar 2026 11:37:55 +0100
Subject: [PATCH 020/127] Cleanup(multi_locus)

---
 mutalyzer_crossmapper/multi_locus.py | 37 +++++++++++++++-------------
 1 file changed, 20 insertions(+), 17 deletions(-)

diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index d7a52e9..b7b6ce4 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -54,61 +54,64 @@ def to_position(self, coordinate:int):
 
         :arg int coordinate: Coordinate.
 
-        :returns dict: Position model.
+        :returns dict: Position model 'position', 'offset' and 'region' keys.
         """
         index = nearest_location(self._locations, coordinate, self._inverted)
         outside = self._orientation * self.outside(coordinate)
         region = "u" if outside < 0 else "d" if outside > 0 else ""
         location = self._loci[index].to_position(coordinate)
-        # UTR
+
         if outside:
             return {
                 "position": abs(location["offset"]),
                 "offset": 0,
                 "region": region
             }
-        # in exons
-        if location["offset"] == 0: # in an exon
+
+        if location["offset"] == 0:
             return {
                 "position": location["position"] + self._offsets[self._direction(index)],
                 "offset": 0,
                 "region": ""
             }
-        elif location["offset"] < 0: # before an exon
+
+        elif location["offset"] < 0:
             return {
                 "position": self._offsets[self._direction(index)],
                 "offset": location["offset"],
                 "region": ""
             }
-        else: # after an exon
+
+        else:
             return{
                 "position": location["position"] + self._offsets[self._direction(index)],
                 "offset": location["offset"],
                 "region": ""
             }
 
-    def to_coordinate(self, position_m:dict):
+    def to_coordinate(self, pos_m:dict):
         """Convert a position model to a coordinate.
 
-        :arg dict position: Position.
+        :arg dict position: Position model with 'position','offset' and 'region' keys.
 
         :returns int: Coordinate.
         """
-        region = position_m["region"]
+        region = pos_m["region"]
+
         if region == "":
             index = min(
                 len(self._offsets),
-                max(0, bisect_right(self._offsets, position_m["position"]) - 1)
+                max(0, bisect_right(self._offsets, pos_m["position"]) - 1)
             )
-            position_m["position"] = position_m["position"] - self._offsets[index]
-            return self._loci[self._direction(index)].to_coordinate(position_m)
+            pos_m["position"] = pos_m["position"] - self._offsets[index]
+            return self._loci[self._direction(index)].to_coordinate(pos_m)
 
         elif region == "u":
             if self._inverted:
-                return abs(position_m["position"]) + self._locations[-1][1] + position_m["offset"] - 1
-            return self._locations[0][0] - abs(position_m["position"]) + position_m["offset"]
+                return abs(pos_m["position"]) + self._locations[-1][1] + pos_m["offset"] - 1
+            return self._locations[0][0] - abs(pos_m["position"]) + pos_m["offset"]
 
-        else: # d
+        else:
             if self._inverted:
-                return self._locations[0][0] - abs(position_m["position"]) + position_m["offset"]
-            return abs(position_m["position"]) + self._locations[-1][1] + position_m["offset"] - 1
+                return self._locations[0][0] - abs(pos_m["position"]) + pos_m["offset"]
+            return abs(pos_m["position"]) + self._locations[-1][1] + pos_m["offset"] - 1

From 5ba6a5afdd7bd5395006dd70dc34122f1706aef3 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 9 Mar 2026 11:45:33 +0100
Subject: [PATCH 021/127] Cleanup(multi_locus)

---
 mutalyzer_crossmapper/multi_locus.py | 32 +++++++++++++---------------
 1 file changed, 15 insertions(+), 17 deletions(-)

diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index b7b6ce4..6a71cc4 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -75,19 +75,18 @@ def to_position(self, coordinate:int):
                 "region": ""
             }
 
-        elif location["offset"] < 0:
+        if location["offset"] < 0:
             return {
                 "position": self._offsets[self._direction(index)],
                 "offset": location["offset"],
                 "region": ""
             }
 
-        else:
-            return{
-                "position": location["position"] + self._offsets[self._direction(index)],
-                "offset": location["offset"],
-                "region": ""
-            }
+        return{
+            "position": location["position"] + self._offsets[self._direction(index)],
+            "offset": location["offset"],
+            "region": ""
+        }
 
     def to_coordinate(self, pos_m:dict):
         """Convert a position model to a coordinate.
@@ -98,20 +97,19 @@ def to_coordinate(self, pos_m:dict):
         """
         region = pos_m["region"]
 
-        if region == "":
-            index = min(
-                len(self._offsets),
-                max(0, bisect_right(self._offsets, pos_m["position"]) - 1)
-            )
-            pos_m["position"] = pos_m["position"] - self._offsets[index]
-            return self._loci[self._direction(index)].to_coordinate(pos_m)
-
-        elif region == "u":
+        if region == "u":
             if self._inverted:
                 return abs(pos_m["position"]) + self._locations[-1][1] + pos_m["offset"] - 1
             return self._locations[0][0] - abs(pos_m["position"]) + pos_m["offset"]
 
-        else:
+        if region == "d":
             if self._inverted:
                 return self._locations[0][0] - abs(pos_m["position"]) + pos_m["offset"]
             return abs(pos_m["position"]) + self._locations[-1][1] + pos_m["offset"] - 1
+
+        index = min(
+            len(self._offsets),
+            max(0, bisect_right(self._offsets, pos_m["position"]) - 1)
+        )
+        pos_m["position"] = pos_m["position"] - self._offsets[index]
+        return self._loci[self._direction(index)].to_coordinate(pos_m)

From 7f32afcc2cff00fdcbc7ba92d242548f1027b7f2 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 9 Mar 2026 11:50:43 +0100
Subject: [PATCH 022/127] Format(multi locus test)

---
 tests/test_multi_locus.py | 194 +++++++++++++++++++++++++++++++-------
 1 file changed, 161 insertions(+), 33 deletions(-)

diff --git a/tests/test_multi_locus.py b/tests/test_multi_locus.py
index 922529a..c08ff7f 100644
--- a/tests/test_multi_locus.py
+++ b/tests/test_multi_locus.py
@@ -15,6 +15,7 @@ def test_offsets_inverted():
     """Cummulative location lengths for inverted list of locations."""
     assert _offsets(_locations, -1) == [0, 2, 4, 8, 13, 19]
 
+
 def test_offsets_adjacent():
     """Cummulative location lengths for adjacent locations."""
     assert _offsets([(1, 3), (3, 5)], 1) == [0, 2]
@@ -30,32 +31,71 @@ def test_MultiLocus():
     multi_locus = MultiLocus(_locations)
 
     # Boundary between upstream and the first locus.
-    invariant(multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": "u"},
+    invariant(
+        multi_locus.to_position,
+        4,
+        multi_locus.to_coordinate,
+        {"position": 1, "offset": 0, "region": "u"},
     )
 
     invariant(
-        multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 0, "offset": 0, "region": ""},
+        multi_locus.to_position,
+        5,
+        multi_locus.to_coordinate,
+        {"position": 0, "offset": 0, "region": ""},
     )
 
     # Internal locus.
     invariant(
-        multi_locus.to_position, 29, multi_locus.to_coordinate, {"position": 9, "offset": -1, "region": ""})
+        multi_locus.to_position,
+        29,
+        multi_locus.to_coordinate,
+        {"position": 9, "offset": -1, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 30, multi_locus.to_coordinate, {"position": 9, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        30,
+        multi_locus.to_coordinate,
+        {"position": 9, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 31, multi_locus.to_coordinate, {"position": 10, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        31,
+        multi_locus.to_coordinate,
+        {"position": 10, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 33, multi_locus.to_coordinate, {"position": 12, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        33,
+        multi_locus.to_coordinate,
+        {"position": 12, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 34, multi_locus.to_coordinate, {"position": 13, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        34,
+        multi_locus.to_coordinate,
+        {"position": 13, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 35, multi_locus.to_coordinate, {"position": 13, "offset": 1, "region": ""})
+        multi_locus.to_position,
+        35,
+        multi_locus.to_coordinate,
+        {"position": 13, "offset": 1, "region": ""},
+    )
 
     # Boundary between the last locus and downstream.
     invariant(
-        multi_locus.to_position, 71, multi_locus.to_coordinate, {"position": 21, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        71,
+        multi_locus.to_coordinate,
+        {"position": 21, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 72, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": "d"})
+        multi_locus.to_position,
+        72,
+        multi_locus.to_coordinate,
+        {"position": 1, "offset": 0, "region": "d"},
+    )
 
 
 def test_MultiLocus_inverted():
@@ -64,29 +104,69 @@ def test_MultiLocus_inverted():
 
     # Boundary between upstream and the first locus.
     invariant(
-        multi_locus.to_position, 72, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": "u"})
+        multi_locus.to_position,
+        72,
+        multi_locus.to_coordinate,
+        {"position": 1, "offset": 0, "region": "u"},
+    )
     invariant(
-        multi_locus.to_position, 71, multi_locus.to_coordinate, {"position": 0, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        71,
+        multi_locus.to_coordinate,
+        {"position": 0, "offset": 0, "region": ""},
+    )
 
     # Internal locus.
     invariant(
-        multi_locus.to_position, 35, multi_locus.to_coordinate, {"position": 8, "offset": -1, "region": ""})
+        multi_locus.to_position,
+        35,
+        multi_locus.to_coordinate,
+        {"position": 8, "offset": -1, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 34, multi_locus.to_coordinate, {"position": 8, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        34,
+        multi_locus.to_coordinate,
+        {"position": 8, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 33, multi_locus.to_coordinate, {"position": 9, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        33,
+        multi_locus.to_coordinate,
+        {"position": 9, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 31, multi_locus.to_coordinate, {"position": 11, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        31,
+        multi_locus.to_coordinate,
+        {"position": 11, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 30, multi_locus.to_coordinate, {"position": 12, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        30,
+        multi_locus.to_coordinate,
+        {"position": 12, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 29, multi_locus.to_coordinate, {"position": 12, "offset": 1, "region": ""})
+        multi_locus.to_position,
+        29,
+        multi_locus.to_coordinate,
+        {"position": 12, "offset": 1, "region": ""},
+    )
 
     # Boundary between the last locus and downstream.
     invariant(
-        multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 21, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        5,
+        multi_locus.to_coordinate,
+        {"position": 21, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": "d"})
+        multi_locus.to_position,
+        4,
+        multi_locus.to_coordinate,
+        {"position": 1, "offset": 0, "region": "d"},
+    )
 
 
 def test_MultiLocus_adjacent_loci():
@@ -94,9 +174,17 @@ def test_MultiLocus_adjacent_loci():
     multi_locus = MultiLocus([(1, 3), (3, 5)])
 
     invariant(
-        multi_locus.to_position, 2, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        2,
+        multi_locus.to_coordinate,
+        {"position": 1, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 3, multi_locus.to_coordinate, {"position": 2, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        3,
+        multi_locus.to_coordinate,
+        {"position": 2, "offset": 0, "region": ""},
+    )
 
 
 def test_MultiLocus_adjacent_loci_inverted():
@@ -104,9 +192,17 @@ def test_MultiLocus_adjacent_loci_inverted():
     multi_locus = MultiLocus([(1, 3), (3, 5)], True)
 
     invariant(
-        multi_locus.to_position, 3, multi_locus.to_coordinate, {"position": 1, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        3,
+        multi_locus.to_coordinate,
+        {"position": 1, "offset": 0, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 2, multi_locus.to_coordinate, {"position": 2, "offset": 0, "region": ""})
+        multi_locus.to_position,
+        2,
+        multi_locus.to_coordinate,
+        {"position": 2, "offset": 0, "region": ""},
+    )
 
 
 def test_MultiLocus_offsets_odd():
@@ -114,9 +210,17 @@ def test_MultiLocus_offsets_odd():
     multi_locus = MultiLocus([(1, 3), (6, 8)])
 
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 1, "offset": 2, "region": ""})
+        multi_locus.to_position,
+        4,
+        multi_locus.to_coordinate,
+        {"position": 1, "offset": 2, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 2, "offset": -1, "region": ""})
+        multi_locus.to_position,
+        5,
+        multi_locus.to_coordinate,
+        {"position": 2, "offset": -1, "region": ""},
+    )
 
 
 def test_MultiLocus_offsets_odd_inverted():
@@ -124,9 +228,17 @@ def test_MultiLocus_offsets_odd_inverted():
     multi_locus = MultiLocus([(1, 3), (6, 8)], True)
 
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 1, "offset": 2, "region": ""})
+        multi_locus.to_position,
+        4,
+        multi_locus.to_coordinate,
+        {"position": 1, "offset": 2, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 3, multi_locus.to_coordinate, {"position": 2, "offset": -1, "region": ""})
+        multi_locus.to_position,
+        3,
+        multi_locus.to_coordinate,
+        {"position": 2, "offset": -1, "region": ""},
+    )
 
 
 def test_MultiLocus_offsets_even():
@@ -134,9 +246,17 @@ def test_MultiLocus_offsets_even():
     multi_locus = MultiLocus([(1, 3), (7, 9)])
 
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 1, "offset": 2, "region": ""})
+        multi_locus.to_position,
+        4,
+        multi_locus.to_coordinate,
+        {"position": 1, "offset": 2, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 2, "offset": -2, "region": ""})
+        multi_locus.to_position,
+        5,
+        multi_locus.to_coordinate,
+        {"position": 2, "offset": -2, "region": ""},
+    )
 
 
 def test_MultiLocus_offsets_even_inverted():
@@ -144,9 +264,17 @@ def test_MultiLocus_offsets_even_inverted():
     multi_locus = MultiLocus([(1, 3), (7, 9)], True)
 
     invariant(
-        multi_locus.to_position, 5, multi_locus.to_coordinate, {"position": 1, "offset": 2, "region": ""})
+        multi_locus.to_position,
+        5,
+        multi_locus.to_coordinate,
+        {"position": 1, "offset": 2, "region": ""},
+    )
     invariant(
-        multi_locus.to_position, 4, multi_locus.to_coordinate, {"position": 2, "offset": -2, "region": ""})
+        multi_locus.to_position,
+        4,
+        multi_locus.to_coordinate,
+        {"position": 2, "offset": -2, "region": ""},
+    )
 
 
 def test_MultiLocus_degenerate():
@@ -193,6 +321,6 @@ def test_MultiLocus_inverted_degenerate():
         [
             {"position": 0, "offset": -1, "region": "d"},
             {"position": 1, "offset": 0, "region": "d"},
-            {"position": 2, "offset": 1, "region": "d"}
+            {"position": 2, "offset": 1, "region": "d"},
         ],
     )

From e23fe2abd02ebd8a2267f783cab225c2d7c10ebb Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 9 Mar 2026 13:41:45 +0100
Subject: [PATCH 023/127] Cleanup(crossmapper): on Genomic and NonCoding

---
 mutalyzer_crossmapper/crossmapper.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 9056ade..c90c15a 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -8,18 +8,18 @@ def coordinate_to_genomic(self, coordinate):
 
         :arg int coordinate: Coordinate.
 
-        :returns dict: Genomic position.
+        :returns dict: Genomic position model.
         """
         return {"position": coordinate + 1}
 
-    def genomic_to_coordinate(self, position_m):
+    def genomic_to_coordinate(self, pos_m):
         """Convert a genomic position (g./m./o.) to a coordinate.
 
-        :arg int position: Genomic position model.
+        :arg dict position: Genomic position model.
 
         :returns int: Coordinate.
         """
-        return position_m["position"] - 1
+        return pos_m["position"] - 1
 
 
 class NonCoding(Genomic):
@@ -45,16 +45,16 @@ def coordinate_to_noncoding(self, coordinate):
             pos_m["position"] = pos_m["position"] + 1
         return pos_m
 
-    def noncoding_to_coordinate(self, position_m):
+    def noncoding_to_coordinate(self, pos_m):
         """Convert a noncoding position (n./r.) to a coordinate.
 
         :arg dict postion_m: Noncoding position model.
 
         :returns int: Coordinate.
         """
-        if position_m["region"] == "":
-            position_m["position"] = position_m["position"] - 1
-        return self._noncoding.to_coordinate(position_m)
+        if pos_m["region"] == "":
+            pos_m["position"] = pos_m["position"] - 1
+        return self._noncoding.to_coordinate(pos_m)
 
 
 class Coding(NonCoding):

From 8f05341e9cde5b26c675bc4780be079ad5874038 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 9 Mar 2026 13:44:08 +0100
Subject: [PATCH 024/127] Cleanup

---
 mutalyzer_crossmapper/crossmapper.py | 4 ++--
 mutalyzer_crossmapper/multi_locus.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index c90c15a..9762598 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -15,7 +15,7 @@ def coordinate_to_genomic(self, coordinate):
     def genomic_to_coordinate(self, pos_m):
         """Convert a genomic position (g./m./o.) to a coordinate.
 
-        :arg dict position: Genomic position model.
+        :arg dict pos_m: Genomic position model.
 
         :returns int: Coordinate.
         """
@@ -48,7 +48,7 @@ def coordinate_to_noncoding(self, coordinate):
     def noncoding_to_coordinate(self, pos_m):
         """Convert a noncoding position (n./r.) to a coordinate.
 
-        :arg dict postion_m: Noncoding position model.
+        :arg dict pos_m: Noncoding position model.
 
         :returns int: Coordinate.
         """
diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 6a71cc4..2853ee6 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -91,7 +91,7 @@ def to_position(self, coordinate:int):
     def to_coordinate(self, pos_m:dict):
         """Convert a position model to a coordinate.
 
-        :arg dict position: Position model with 'position','offset' and 'region' keys.
+        :arg dict pos_m: Position model with 'position','offset' and 'region' keys.
 
         :returns int: Coordinate.
         """

From 09f721ff0c74cedab27410ddf0cba198cdf8a581 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 09:56:23 +0100
Subject: [PATCH 025/127] Refactor degenerate tests

---
 tests/test_crossmapper.py | 114 +++++++++++++++++++++++++++++---------
 1 file changed, 88 insertions(+), 26 deletions(-)

diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index e39225f..6ba2d83 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -65,7 +65,10 @@ def test_NonCoding_degenerate():
     # Boundary between upstream and transcript.
     degenerate_equal(
         crossmap.noncoding_to_coordinate, 4,
-        [{"position": 1, "offset": 0, "region":"u"}])
+        [
+            {"position": 1, "offset": 0, "region":"u"},
+            {"position": 0, "offset": -1, "region":"u"}
+            ])
 
     # Boundary between downstream and transcript.
     degenerate_equal(
@@ -234,7 +237,7 @@ def test_Coding_no_utr5():
     # Direct transition from upstream to CDS.
     invariant(
         crossmap.coordinate_to_coding, 9,
-        crossmap.coding_to_coordinate, #(1, -1, 0, -1)
+        crossmap.coding_to_coordinate,
         {'position': 1, 'offset': 0, 'region': 'u'}) # serialize result : u1
     invariant(
         crossmap.coordinate_to_coding, 10,
@@ -249,7 +252,7 @@ def test_Coding_no_utr5_inverted():
     # Direct transition from upstream to CDS.
     invariant(
         crossmap.coordinate_to_coding, 20,
-        crossmap.coding_to_coordinate, #(1, -1, 0, -1)
+        crossmap.coding_to_coordinate,
         {'position': 1, 'offset': 0, 'region': 'u'})
     invariant(
         crossmap.coordinate_to_coding, 19,
@@ -295,16 +298,16 @@ def test_Coding_small_utr5():
     # Transition from upstream to 5' UTR to CDS.
     invariant(
         crossmap.coordinate_to_coding, 9,
-        crossmap.coding_to_coordinate, #(-1, -1, -1, -1)
+        crossmap.coding_to_coordinate,
         {'position': 1, 'offset': 0, 'region': 'u'})
     invariant(
         crossmap.coordinate_to_coding, 10,
-        crossmap.coding_to_coordinate, #(-1, 0, -1, 0))
+        crossmap.coding_to_coordinate,
         {'position': 1, 'offset': 0, 'region': '-'}
     )
     invariant(
         crossmap.coordinate_to_coding, 11,
-        crossmap.coding_to_coordinate, #(1, 0, 0, 0))
+        crossmap.coding_to_coordinate,
         {'position': 1, 'offset': 0, 'region': ''})
 
 
@@ -372,13 +375,29 @@ def test_Coding_degenerate():
     degenerate_equal(
         crossmap.coding_to_coordinate, 9,
         [
-            {'position': 1, 'offset': 8, 'region': 'u'},
-            {'position': 8, 'offset': 1, 'region': 'u'},
-            {'position': -1, 'offset': 10, 'region': 'u'}
+            {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 2, 'offset': 1, 'region': 'u'},
+            {'position': 0, 'offset': -1, 'region': 'u'},
+            {'position': 1, 'offset': -1, 'region': '-'},
+            {'position': 2, 'offset': 0, 'region': '-'},
+            {'position': 1, 'offset': -2, 'region': ''},
         ])
     degenerate_equal(
         crossmap.coding_to_coordinate, 20,
-        [(1, 1, 1, 1), (2, 0, 1, 1), (8, 2, 0, 1), (-1, 10, -1, 1)])
+        [
+            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 8, 'offset': -7, 'region': 'd'},
+            {'position': 0, 'offset': -1, 'region': 'd'},
+            {'position': 2, 'offset': 0, 'region': '*'},
+            {'position': 1, 'offset': 1, 'region': '*'},
+            {'position': 8, 'offset': 2, 'region': ''},
+        ]
+    )
+
+
+#TODO: Add tests for silently degenerate,
+#   position value <= 0
+#   offset value > intron length
 
 
 def test_Coding_inverted_degenerate():
@@ -387,26 +406,46 @@ def test_Coding_inverted_degenerate():
 
     degenerate_equal(
         crossmap.coding_to_coordinate, 20,
-        [(-1, -1, -1, -1), (-2, 0, -1, -1), (1, -2, 0, -1), (1, -10, 1, -1)])
+        [
+            {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 2, 'offset': 1, 'region': 'u'},
+            {'position': 0, 'offset': -1, 'region': 'u'},
+            {'position': 1, 'offset': -2, 'region': ''},
+            {'position': 1, 'offset': -1, 'region': '-'},
+            {'position': 2, 'offset': 0, 'region': '-'}
+        ]
+    )
     degenerate_equal(
         crossmap.coding_to_coordinate, 9,
-        [(1, 1, 1, 1), (2, 0, 1, 1), (8, 2, 0, 1), (-1, 10, -1, 1)])
+        [
+            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 2, 'offset': -1, 'region': 'd'},
+            {'position': 1, 'offset': 1, 'region': '*'},
+            {'position': 1, 'offset': 1, 'region': '*'},
+            {'position': 10, 'offset': 0, 'region': ''},
+        ]
+    )
 
 
 def test_Coding_degenerate_return():
     """Degenerate upstream and downstream positions may be returned."""
     crossmap = Coding([(10, 20)], (11, 19))
 
-    assert crossmap.coordinate_to_coding(9, True) == (-2, 0, -1, -1)
-    assert crossmap.coordinate_to_coding(20, True) == (2, 0, 1, 1)
+    for i in range(0, 30):
+        print(i, crossmap.coordinate_to_coding(i), crossmap.coordinate_to_coding(i, True))
+
+    assert crossmap.coordinate_to_coding(9, True) == {'position': 2, 'offset': 0, 'region': '-'}
+    assert crossmap.coordinate_to_coding(20, True) == {'position': 2, 'offset': 0, 'region': '*'}
 
 
 def test_Coding_inverted_degenerate_return():
     """Degenerate upstream and downstream positions may be returned."""
     crossmap = Coding([(10, 20)], (11, 19), True)
+    for i in range(0, 30):
+        print(i, crossmap.coordinate_to_coding(i), crossmap.coordinate_to_coding(i, True))
 
-    assert crossmap.coordinate_to_coding(20, True) == (-2, 0, -1, -1)
-    assert crossmap.coordinate_to_coding(9, True) == (2, 0, 1, 1)
+    assert crossmap.coordinate_to_coding(20, True) == {'position': 2, 'offset': 0, 'region': '-'}
+    assert crossmap.coordinate_to_coding(9, True) == {'position': 2, 'offset': 0, 'region': '*'}
 
 
 def test_Coding_degenerate_no_return():
@@ -431,32 +470,55 @@ def test_Coding_no_utr_degenerate():
 
     degenerate_equal(
         crossmap.coding_to_coordinate, 9,
-        [(1, -1, 0, -1), (-1, 0, -1, -1), (1, -2, 1, -1)])
+        [
+            {'position': 1, 'offset': 0, 'region': '-'},
+            {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 1, 'offset': -1, 'region': ''},
+        ]
+    )
     degenerate_equal(
         crossmap.coding_to_coordinate, 11,
-        [(1, 1, 0, 1), (1, 0, 1, 1), (-1, 2, -1, 1)])
-
+        [
+            {'position': 1, 'offset': 0, 'region': '*'},
+            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 1, 'offset': 1, 'region': ''}
+        ]
+    )
 
 def test_Coding_inverted_no_utr_degenerate():
     """UTRs may be missing."""
     crossmap = Coding([(10, 11)], (10, 11), True)
 
+        # [(1, -1, 0, -1), (-1, 0, -1, -1), (1, -2, 1, -1)])
     degenerate_equal(
         crossmap.coding_to_coordinate, 11,
-        [(1, -1, 0, -1), (-1, 0, -1, -1), (1, -2, 1, -1)])
+        [
+            {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 2, 'offset': 1, 'region': 'u'},
+            {'position': 1, 'offset': 0, 'region': '-'},
+            {'position': 1, 'offset': 0, 'region': '*'},
+        ]
+)
     degenerate_equal(
         crossmap.coding_to_coordinate, 9,
-        [(1, 1, 0, 1), (1, 0, 1, 1), (-1, 2, -1, 1)])
-
+        [
+            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 1, 'offset': 0, 'region': '*'},
+            {'position': 1, 'offset': -1, 'region': ''},
+        ]
+    )
 
 def test_Coding_no_utr_degenerate_return():
     """UTRs may be missing."""
     crossmap = Coding([(10, 11)], (10, 11))
 
-    assert crossmap.coordinate_to_coding(8, True) == (-2, 0, -1, -2)
-    assert crossmap.coordinate_to_coding(9, True) == (-1, 0, -1, -1)
-    assert crossmap.coordinate_to_coding(11, True) == (1, 0, 1, 1)
-    assert crossmap.coordinate_to_coding(12, True) == (2, 0, 1, 2)
+    print(crossmap.coordinate_to_coding(11), crossmap.coordinate_to_coding(11, True))
+    print(crossmap.coordinate_to_coding(12), crossmap.coordinate_to_coding(12, True))
+
+    assert crossmap.coordinate_to_coding(8, True) == {'position': 2, 'offset': 0, 'region': '-'}#(-2, 0, -1, -2)
+    assert crossmap.coordinate_to_coding(9, True) == {'position': 1, 'offset': 0, 'region': '-'}#(-1, 0, -1, -1)
+    assert crossmap.coordinate_to_coding(11, True) == {'position': 1, 'offset': 0, 'region': '*'}#(1, 0, 1, 1)
+    assert crossmap.coordinate_to_coding(12, True) == {'position': 2, 'offset': 0, 'region': '*'}#(2, 0, 1, 2)
 
 
 def test_Coding_inverted_no_utr_degenerate_return():

From abead481a3df79ef50a378788f2a3b136f05aae7 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 12:26:37 +0100
Subject: [PATCH 026/127] Add position model description for g.,n.,c.,and p.

---
 README.rst | 76 +++++++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 70 insertions(+), 6 deletions(-)

diff --git a/README.rst b/README.rst
index 061f91b..03088d3 100644
--- a/README.rst
+++ b/README.rst
@@ -41,13 +41,22 @@ resides on the complement strand.
 
 Please see ReadTheDocs_ for the latest documentation.
 
-
 Quick start
 -----------
+The `Genomic` class provides an interface to conversions between genomic positions and coordinates.
 
-The ``Genomic`` class provides an interface to conversions between genomic
-positions and coordinates.
+***Genomic Position Model***
+Genomic positions follow the HGVS ``g`` coordinate system. They are represented
+as dictionaries:
+
+.. code:: json
+
+    {"position": int}
 
+Where:
+- ``position`` is a positive integer
+
+***Genomic Position Conversion***
 .. code:: python
 
     >>> from mutalyzer_crossmapper import Genomic
@@ -61,6 +70,23 @@ On top of the functionality provided by the ``Genomic`` class, the
 ``NonCoding`` class provides an interface to conversions between noncoding
 positions and coordinates.
 
+***NonCoding Position Model***
+Noncoding positions follow the HGVS `n` coordinate system. They are represented
+as dictionaries:
+.. code:: json
+   {
+    "position": int,
+    "offset": int,
+    "region": str
+   }
+Where:
+- `position` is a positive interger
+- `offset` is an interger indicating the offset relative to the position (e.g.,
+negative for upstream or positive for downstream)
+- `region` uses string describing the region type (empty string `""` for standard
+noncoding positions, `"u"` for upstream and `"d"` for downstream.)
+
+***NonCoding Position Conversion***
 .. code:: python
 
     >>> from mutalyzer_crossmapper import NonCoding
@@ -71,13 +97,32 @@ positions and coordinates.
     >>> crossmap.noncoding_to_coordinate({"position": 14, "offset": 1, "region": ""})
     35
 
-Add the flag ``inverted=True`` to the constructor when the transcript resides
+****Notes****
+- Add the flag ``inverted=True`` to the constructor when the transcript resides
 on the reverse complement strand.
 
 On top of the functionality provided by the ``NonCoding`` class, the ``Coding``
 class provides an interface to conversions between coding positions and
 coordinates as well as conversions between protein positions and coordinates.
 
+***Coding Position Model***
+Coding positions follow the HGVS `c`` coordinate system. They are represented as
+dictionaries:
+.. code:: json
+   {
+    "position": int,
+    "offset": int,
+    "region": str
+   }
+Where:
+- `position` is a positive interger
+- `offset` is an interger indicating the offset relative to the position (e.g.,
+negative for upstream or positive for downstream)
+- `region` uses string describing the region type (empty string `""` for standard
+coding positions, `"-"` for 5' UTR, `"*"` for 3' UTR, `"u"` for upstream and `"d"`
+for downstream.)
+
+***Coding Position Conversion***
 .. code:: python
 
     >>> from mutalyzer_crossmapper import Coding
@@ -88,11 +133,30 @@ coordinates as well as conversions between protein positions and coordinates.
     >>> crossmap.coding_to_coordinate({"position": -1, "offset": 0, "region": "-"})
     31
 
-Again, the flag ``inverted=True`` can be used for transcripts that reside on
+****Notes****
+- Again, the flag ``inverted=True`` can be used for transcripts that reside on
 the reverse complement strand.
 
-Conversions between protein positions and coordinates are done as follows.
 
+***Protein Position Model***
+Protein positions follow the HGVS `p`` coordinate system. They are represented
+as dictionaries:
+.. code:: json
+{
+    "position": int,
+    "position_in_codon": int,
+    "offset": int,
+    "region": str
+}
+Where:
+- **position**: the amino acid position (1-based)
+- **position_in_codon**: the codon nucleotide index (1, 2, or 3)
+- **offset**: an integer indicating offset relative to the codon
+- **region**: a string describing the region type (empty string `""`` for standard positions)
+
+***Protein Position Conversion***
+
+Conversions between protein positions and coordinates are done as follows.
 .. code:: python
 
     >>> crossmap.coordinate_to_protein(41)

From b528f926333ce8297aff3e21de15f5e3415d32f3 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 12:29:57 +0100
Subject: [PATCH 027/127] Format document

---
 README.rst | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/README.rst b/README.rst
index 03088d3..2aff9d5 100644
--- a/README.rst
+++ b/README.rst
@@ -45,7 +45,7 @@ Quick start
 -----------
 The `Genomic` class provides an interface to conversions between genomic positions and coordinates.
 
-***Genomic Position Model***
+**Genomic Position Model**
 Genomic positions follow the HGVS ``g`` coordinate system. They are represented
 as dictionaries:
 
@@ -56,7 +56,7 @@ as dictionaries:
 Where:
 - ``position`` is a positive integer
 
-***Genomic Position Conversion***
+**Genomic Position Conversion**
 .. code:: python
 
     >>> from mutalyzer_crossmapper import Genomic
@@ -70,7 +70,7 @@ On top of the functionality provided by the ``Genomic`` class, the
 ``NonCoding`` class provides an interface to conversions between noncoding
 positions and coordinates.
 
-***NonCoding Position Model***
+**NonCoding Position Model**
 Noncoding positions follow the HGVS `n` coordinate system. They are represented
 as dictionaries:
 .. code:: json
@@ -86,7 +86,7 @@ negative for upstream or positive for downstream)
 - `region` uses string describing the region type (empty string `""` for standard
 noncoding positions, `"u"` for upstream and `"d"` for downstream.)
 
-***NonCoding Position Conversion***
+**NonCoding Position Conversion**
 .. code:: python
 
     >>> from mutalyzer_crossmapper import NonCoding
@@ -97,7 +97,7 @@ noncoding positions, `"u"` for upstream and `"d"` for downstream.)
     >>> crossmap.noncoding_to_coordinate({"position": 14, "offset": 1, "region": ""})
     35
 
-****Notes****
+***Notes***
 - Add the flag ``inverted=True`` to the constructor when the transcript resides
 on the reverse complement strand.
 
@@ -105,7 +105,7 @@ On top of the functionality provided by the ``NonCoding`` class, the ``Coding``
 class provides an interface to conversions between coding positions and
 coordinates as well as conversions between protein positions and coordinates.
 
-***Coding Position Model***
+**Coding Position Model**
 Coding positions follow the HGVS `c`` coordinate system. They are represented as
 dictionaries:
 .. code:: json
@@ -122,7 +122,7 @@ negative for upstream or positive for downstream)
 coding positions, `"-"` for 5' UTR, `"*"` for 3' UTR, `"u"` for upstream and `"d"`
 for downstream.)
 
-***Coding Position Conversion***
+**Coding Position Conversion**
 .. code:: python
 
     >>> from mutalyzer_crossmapper import Coding
@@ -133,12 +133,12 @@ for downstream.)
     >>> crossmap.coding_to_coordinate({"position": -1, "offset": 0, "region": "-"})
     31
 
-****Notes****
+***Notes***
 - Again, the flag ``inverted=True`` can be used for transcripts that reside on
 the reverse complement strand.
 
 
-***Protein Position Model***
+**Protein Position Model**
 Protein positions follow the HGVS `p`` coordinate system. They are represented
 as dictionaries:
 .. code:: json
@@ -154,7 +154,7 @@ Where:
 - **offset**: an integer indicating offset relative to the codon
 - **region**: a string describing the region type (empty string `""`` for standard positions)
 
-***Protein Position Conversion***
+**Protein Position Conversion**
 
 Conversions between protein positions and coordinates are done as follows.
 .. code:: python

From 6c1b52ed17a947f8565c4e9d48b9ad71663a4783 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 12:34:40 +0100
Subject: [PATCH 028/127] Format document

---
 README.rst | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/README.rst b/README.rst
index 2aff9d5..3d58a55 100644
--- a/README.rst
+++ b/README.rst
@@ -54,7 +54,7 @@ as dictionaries:
     {"position": int}
 
 Where:
-- ``position`` is a positive integer
+- **position**: a positive integer
 
 **Genomic Position Conversion**
 .. code:: python
@@ -80,10 +80,10 @@ as dictionaries:
     "region": str
    }
 Where:
-- `position` is a positive interger
-- `offset` is an interger indicating the offset relative to the position (e.g.,
+- **position**: a positive interger
+- **offset**: an interger indicating the offset relative to the position (e.g.,
 negative for upstream or positive for downstream)
-- `region` uses string describing the region type (empty string `""` for standard
+- **region**: a string describing the region type (empty string `""` for standard
 noncoding positions, `"u"` for upstream and `"d"` for downstream.)
 
 **NonCoding Position Conversion**
@@ -115,10 +115,10 @@ dictionaries:
     "region": str
    }
 Where:
-- `position` is a positive interger
-- `offset` is an interger indicating the offset relative to the position (e.g.,
+- **position**: a positive interger
+- **offset**: an interger indicating the offset relative to the position (e.g.,
 negative for upstream or positive for downstream)
-- `region` uses string describing the region type (empty string `""` for standard
+- **region**: a string describing the region type (empty string `""` for standard
 coding positions, `"-"` for 5' UTR, `"*"` for 3' UTR, `"u"` for upstream and `"d"`
 for downstream.)
 

From b87160189983184859c90c8833811340d306baeb Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 12:40:34 +0100
Subject: [PATCH 029/127] Format document

---
 README.rst | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/README.rst b/README.rst
index 3d58a55..cb9198a 100644
--- a/README.rst
+++ b/README.rst
@@ -54,6 +54,7 @@ as dictionaries:
     {"position": int}
 
 Where:
+
 - **position**: a positive integer
 
 **Genomic Position Conversion**
@@ -71,8 +72,7 @@ On top of the functionality provided by the ``Genomic`` class, the
 positions and coordinates.
 
 **NonCoding Position Model**
-Noncoding positions follow the HGVS `n` coordinate system. They are represented
-as dictionaries:
+Noncoding positions follow the HGVS `n` coordinate system. They are represented as dictionaries:
 .. code:: json
    {
     "position": int,
@@ -80,6 +80,7 @@ as dictionaries:
     "region": str
    }
 Where:
+
 - **position**: a positive interger
 - **offset**: an interger indicating the offset relative to the position (e.g.,
 negative for upstream or positive for downstream)
@@ -97,7 +98,7 @@ noncoding positions, `"u"` for upstream and `"d"` for downstream.)
     >>> crossmap.noncoding_to_coordinate({"position": 14, "offset": 1, "region": ""})
     35
 
-***Notes***
+**Notes**
 - Add the flag ``inverted=True`` to the constructor when the transcript resides
 on the reverse complement strand.
 
@@ -115,6 +116,7 @@ dictionaries:
     "region": str
    }
 Where:
+
 - **position**: a positive interger
 - **offset**: an interger indicating the offset relative to the position (e.g.,
 negative for upstream or positive for downstream)
@@ -133,10 +135,8 @@ for downstream.)
     >>> crossmap.coding_to_coordinate({"position": -1, "offset": 0, "region": "-"})
     31
 
-***Notes***
-- Again, the flag ``inverted=True`` can be used for transcripts that reside on
-the reverse complement strand.
-
+**Notes**
+- Again, the flag ``inverted=True`` can be used for transcripts that reside on the reverse complement strand.
 
 **Protein Position Model**
 Protein positions follow the HGVS `p`` coordinate system. They are represented
@@ -149,6 +149,7 @@ as dictionaries:
     "region": str
 }
 Where:
+
 - **position**: the amino acid position (1-based)
 - **position_in_codon**: the codon nucleotide index (1, 2, or 3)
 - **offset**: an integer indicating offset relative to the codon

From 9e91d1dd91b0168e8e51c7576db7f3036a9ffccb Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 13:50:43 +0100
Subject: [PATCH 030/127] Format document in .rst style

---
 README.rst | 167 ++++++++++++++++++++++++++++++-----------------------
 1 file changed, 96 insertions(+), 71 deletions(-)

diff --git a/README.rst b/README.rst
index cb9198a..cf51664 100644
--- a/README.rst
+++ b/README.rst
@@ -41,24 +41,30 @@ resides on the complement strand.
 
 Please see ReadTheDocs_ for the latest documentation.
 
-Quick start
------------
-The `Genomic` class provides an interface to conversions between genomic positions and coordinates.
+Quick Start
+===========
 
-**Genomic Position Model**
-Genomic positions follow the HGVS ``g`` coordinate system. They are represented
-as dictionaries:
+The ``Genomic`` class provides an interface for conversions between genomic positions and coordinates.
 
-.. code:: json
+Genomic Position Model
+---------------------
 
-    {"position": int}
+Genomic positions follow the HGVS ``g`` coordinate system. They are represented as dictionaries:
+
+.. code-block:: json
+
+    {
+        "position": int
+    }
 
 Where:
 
 - **position**: a positive integer
 
-**Genomic Position Conversion**
-.. code:: python
+Genomic Position Conversion
+--------------------------
+
+.. code-block:: python
 
     >>> from mutalyzer_crossmapper import Genomic
     >>> crossmap = Genomic()
@@ -67,28 +73,34 @@ Where:
     >>> crossmap.genomic_to_coordinate({"position": 1})
     0
 
-On top of the functionality provided by the ``Genomic`` class, the
-``NonCoding`` class provides an interface to conversions between noncoding
-positions and coordinates.
-
-**NonCoding Position Model**
-Noncoding positions follow the HGVS `n` coordinate system. They are represented as dictionaries:
-.. code:: json
-   {
-    "position": int,
-    "offset": int,
-    "region": str
-   }
+NonCoding Class
+---------------
+
+The ``NonCoding`` class provides conversions between noncoding positions and coordinates.
+
+NonCoding Position Model
+~~~~~~~~~~~~~~~~~~~~~~~
+
+Noncoding positions follow the HGVS ``n`` coordinate system. They are represented as dictionaries:
+
+.. code-block:: json
+
+    {
+        "position": int,
+        "offset": int,
+        "region": str
+    }
+
 Where:
 
-- **position**: a positive interger
-- **offset**: an interger indicating the offset relative to the position (e.g.,
-negative for upstream or positive for downstream)
-- **region**: a string describing the region type (empty string `""` for standard
-noncoding positions, `"u"` for upstream and `"d"` for downstream.)
+- **position**: a positive integer
+- **offset**: an integer indicating the offset relative to the position (negative for upstream, positive for downstream)
+- **region**: a string describing the region type (``""`` for standard, ``"u"`` for upstream, ``"d"`` for downstream)
+
+NonCoding Position Conversion
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-**NonCoding Position Conversion**
-.. code:: python
+.. code-block:: python
 
     >>> from mutalyzer_crossmapper import NonCoding
     >>> exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
@@ -98,34 +110,39 @@ noncoding positions, `"u"` for upstream and `"d"` for downstream.)
     >>> crossmap.noncoding_to_coordinate({"position": 14, "offset": 1, "region": ""})
     35
 
-**Notes**
-- Add the flag ``inverted=True`` to the constructor when the transcript resides
-on the reverse complement strand.
-
-On top of the functionality provided by the ``NonCoding`` class, the ``Coding``
-class provides an interface to conversions between coding positions and
-coordinates as well as conversions between protein positions and coordinates.
-
-**Coding Position Model**
-Coding positions follow the HGVS `c`` coordinate system. They are represented as
-dictionaries:
-.. code:: json
-   {
-    "position": int,
-    "offset": int,
-    "region": str
-   }
+Notes
+~~~~~
+
+- Add the flag ``inverted=True`` to the constructor when the transcript resides on the reverse complement strand.
+
+Coding Class
+------------
+
+The ``Coding`` class provides conversions between coding positions and coordinates, as well as protein positions.
+
+Coding Position Model
+~~~~~~~~~~~~~~~~~~~~
+
+Coding positions follow the HGVS ``c`` coordinate system. They are represented as dictionaries:
+
+.. code-block:: json
+
+    {
+        "position": int,
+        "offset": int,
+        "region": str
+    }
+
 Where:
 
-- **position**: a positive interger
-- **offset**: an interger indicating the offset relative to the position (e.g.,
-negative for upstream or positive for downstream)
-- **region**: a string describing the region type (empty string `""` for standard
-coding positions, `"-"` for 5' UTR, `"*"` for 3' UTR, `"u"` for upstream and `"d"`
-for downstream.)
+- **position**: a positive integer
+- **offset**: an integer indicating the offset relative to the position
+- **region**: a string describing the region type (``""`` for standard coding positions, ``"-"`` for 5' UTR, ``"*"`` for 3' UTR, ``"u"`` for upstream, ``"d"`` for downstream)
+
+Coding Position Conversion
+~~~~~~~~~~~~~~~~~~~~~~~~~
 
-**Coding Position Conversion**
-.. code:: python
+.. code-block:: python
 
     >>> from mutalyzer_crossmapper import Coding
     >>> cds = (32, 43)
@@ -135,30 +152,38 @@ for downstream.)
     >>> crossmap.coding_to_coordinate({"position": -1, "offset": 0, "region": "-"})
     31
 
-**Notes**
-- Again, the flag ``inverted=True`` can be used for transcripts that reside on the reverse complement strand.
-
-**Protein Position Model**
-Protein positions follow the HGVS `p`` coordinate system. They are represented
-as dictionaries:
-.. code:: json
-{
-    "position": int,
-    "position_in_codon": int,
-    "offset": int,
-    "region": str
-}
+Notes
+~~~~~
+
+- The flag ``inverted=True`` can be used for transcripts on the reverse complement strand.
+
+Protein Position Model
+---------------------
+
+Protein positions follow the HGVS ``p`` coordinate system. They are represented as dictionaries:
+
+.. code-block:: json
+
+    {
+        "position": int,
+        "position_in_codon": int,
+        "offset": int,
+        "region": str
+    }
+
 Where:
 
 - **position**: the amino acid position (1-based)
 - **position_in_codon**: the codon nucleotide index (1, 2, or 3)
 - **offset**: an integer indicating offset relative to the codon
-- **region**: a string describing the region type (empty string `""`` for standard positions)
+- **region**: a string describing the region type (``""`` for standard positions)
+
+Protein Position Conversion
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-**Protein Position Conversion**
+Conversions between protein positions and coordinates:
 
-Conversions between protein positions and coordinates are done as follows.
-.. code:: python
+.. code-block:: python
 
     >>> crossmap.coordinate_to_protein(41)
     {"position": 2, "position_in_codon": 2, "offset": 1, "region": ""}

From 35359b8916925356449fb8a084b0060db0e37eaa Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 14:05:21 +0100
Subject: [PATCH 031/127] Format document in .rst style

---
 README.rst | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/README.rst b/README.rst
index cf51664..630e9c1 100644
--- a/README.rst
+++ b/README.rst
@@ -44,10 +44,13 @@ Please see ReadTheDocs_ for the latest documentation.
 Quick Start
 ===========
 
+Genomic Class
+-------------
+
 The ``Genomic`` class provides an interface for conversions between genomic positions and coordinates.
 
 Genomic Position Model
----------------------
+~~~~~~~~~~~~~~~~~~~~~~~
 
 Genomic positions follow the HGVS ``g`` coordinate system. They are represented as dictionaries:
 
@@ -58,11 +61,10 @@ Genomic positions follow the HGVS ``g`` coordinate system. They are represented
     }
 
 Where:
-
 - **position**: a positive integer
 
 Genomic Position Conversion
---------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: python
 
@@ -92,7 +94,6 @@ Noncoding positions follow the HGVS ``n`` coordinate system. They are represente
     }
 
 Where:
-
 - **position**: a positive integer
 - **offset**: an integer indicating the offset relative to the position (negative for upstream, positive for downstream)
 - **region**: a string describing the region type (``""`` for standard, ``"u"`` for upstream, ``"d"`` for downstream)
@@ -134,7 +135,6 @@ Coding positions follow the HGVS ``c`` coordinate system. They are represented a
     }
 
 Where:
-
 - **position**: a positive integer
 - **offset**: an integer indicating the offset relative to the position
 - **region**: a string describing the region type (``""`` for standard coding positions, ``"-"`` for 5' UTR, ``"*"`` for 3' UTR, ``"u"`` for upstream, ``"d"`` for downstream)
@@ -157,8 +157,11 @@ Notes
 
 - The flag ``inverted=True`` can be used for transcripts on the reverse complement strand.
 
+Protein
+-------
+
 Protein Position Model
----------------------
+~~~~~~~~~~~~~~~~~~~~~~
 
 Protein positions follow the HGVS ``p`` coordinate system. They are represented as dictionaries:
 
@@ -179,7 +182,7 @@ Where:
 - **region**: a string describing the region type (``""`` for standard positions)
 
 Protein Position Conversion
-~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Conversions between protein positions and coordinates:
 

From d48f99d4a1a152d535ffb3b4ff2330815c06e4db Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 14:14:21 +0100
Subject: [PATCH 032/127] Format and add an example

---
 README.rst | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/README.rst b/README.rst
index 630e9c1..73cd6a2 100644
--- a/README.rst
+++ b/README.rst
@@ -44,6 +44,14 @@ Please see ReadTheDocs_ for the latest documentation.
 Quick Start
 ===========
 
+An example below uses the following transcript data:
+
+.. code-block:: python
+
+    >>>_exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
+    >>>_cds = (32, 43)
+
+
 Genomic Class
 -------------
 
@@ -61,6 +69,7 @@ Genomic positions follow the HGVS ``g`` coordinate system. They are represented
     }
 
 Where:
+
 - **position**: a positive integer
 
 Genomic Position Conversion
@@ -94,6 +103,7 @@ Noncoding positions follow the HGVS ``n`` coordinate system. They are represente
     }
 
 Where:
+
 - **position**: a positive integer
 - **offset**: an integer indicating the offset relative to the position (negative for upstream, positive for downstream)
 - **region**: a string describing the region type (``""`` for standard, ``"u"`` for upstream, ``"d"`` for downstream)
@@ -104,8 +114,7 @@ NonCoding Position Conversion
 .. code-block:: python
 
     >>> from mutalyzer_crossmapper import NonCoding
-    >>> exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
-    >>> crossmap = NonCoding(exons)
+    >>> crossmap = NonCoding(_exons)
     >>> crossmap.coordinate_to_noncoding(35)
     {"position": 14, "offset": 1, "region": ""}
     >>> crossmap.noncoding_to_coordinate({"position": 14, "offset": 1, "region": ""})
@@ -135,9 +144,10 @@ Coding positions follow the HGVS ``c`` coordinate system. They are represented a
     }
 
 Where:
+
 - **position**: a positive integer
 - **offset**: an integer indicating the offset relative to the position
-- **region**: a string describing the region type (``""`` for standard coding positions, ``"-"`` for 5' UTR, ``"*"`` for 3' UTR, ``"u"`` for upstream, ``"d"`` for downstream)
+- **region**: a string describing the region type (``""`` for standard coding positions, ``"-"`` for 5' UTR, ``"*"`` for 3' UTR, ``"u"`` for upstream and ``"d"`` for downstream)
 
 Coding Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -145,8 +155,7 @@ Coding Position Conversion
 .. code-block:: python
 
     >>> from mutalyzer_crossmapper import Coding
-    >>> cds = (32, 43)
-    >>> crossmap = Coding(exons, cds)
+    >>> crossmap = Coding(_exons, _cds)
     >>> crossmap.coordinate_to_coding(31)
     {"position": -1, "offset": 0, "region": "-"}
     >>> crossmap.coding_to_coordinate({"position": -1, "offset": 0, "region": "-"})

From d16278bf1938fb965c331faae541aabf0a94c406 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 14:23:39 +0100
Subject: [PATCH 033/127] Add table for Genomic positions and coordinate
 mapping

---
 README.rst | 45 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/README.rst b/README.rst
index 73cd6a2..6a3f600 100644
--- a/README.rst
+++ b/README.rst
@@ -84,6 +84,51 @@ Genomic Position Conversion
     >>> crossmap.genomic_to_coordinate({"position": 1})
     0
 
+Here is the mapping of coordinates to genomic positions:
++------------+----------+
+| Coordinate | Position |
++============+==========+
+| 0          | 1        |
++------------+----------+
+| 1          | 2        |
++------------+----------+
+| 2          | 3        |
++------------+----------+
+| 3          | 4        |
++------------+----------+
+| 4          | 5        |
++------------+----------+
+| 5          | 6        |
++------------+----------+
+| 6          | 7        |
++------------+----------+
+| 7          | 8        |
++------------+----------+
+| 8          | 9        |
++------------+----------+
+| 9          | 10       |
++------------+----------+
+| 10         | 11       |
++------------+----------+
+| 11         | 12       |
++------------+----------+
+| 12         | 13       |
++------------+----------+
+| 13         | 14       |
++------------+----------+
+| 14         | 15       |
++------------+----------+
+| 15         | 16       |
++------------+----------+
+| 16         | 17       |
++------------+----------+
+| 17         | 18       |
++------------+----------+
+| 18         | 19       |
++------------+----------+
+| 19         | 20       |
++------------+----------+
+
 NonCoding Class
 ---------------
 

From b29309a5a6edeee544c36980e678fd910db59fa7 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 14:25:09 +0100
Subject: [PATCH 034/127] Format table

---
 README.rst | 21 +--------------------
 1 file changed, 1 insertion(+), 20 deletions(-)

diff --git a/README.rst b/README.rst
index 6a3f600..c84eade 100644
--- a/README.rst
+++ b/README.rst
@@ -83,49 +83,30 @@ Genomic Position Conversion
     {"position": 1}
     >>> crossmap.genomic_to_coordinate({"position": 1})
     0
-
 Here is the mapping of coordinates to genomic positions:
+
 +------------+----------+
 | Coordinate | Position |
 +============+==========+
 | 0          | 1        |
-+------------+----------+
 | 1          | 2        |
-+------------+----------+
 | 2          | 3        |
-+------------+----------+
 | 3          | 4        |
-+------------+----------+
 | 4          | 5        |
-+------------+----------+
 | 5          | 6        |
-+------------+----------+
 | 6          | 7        |
-+------------+----------+
 | 7          | 8        |
-+------------+----------+
 | 8          | 9        |
-+------------+----------+
 | 9          | 10       |
-+------------+----------+
 | 10         | 11       |
-+------------+----------+
 | 11         | 12       |
-+------------+----------+
 | 12         | 13       |
-+------------+----------+
 | 13         | 14       |
-+------------+----------+
 | 14         | 15       |
-+------------+----------+
 | 15         | 16       |
-+------------+----------+
 | 16         | 17       |
-+------------+----------+
 | 17         | 18       |
-+------------+----------+
 | 18         | 19       |
-+------------+----------+
 | 19         | 20       |
 +------------+----------+
 

From d1c4c2ff2190433f34916fb017264df9af461148 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 14:37:26 +0100
Subject: [PATCH 035/127] Format table

---
 README.rst | 64 +++++++++++++++++++++++++++++++++---------------------
 1 file changed, 39 insertions(+), 25 deletions(-)

diff --git a/README.rst b/README.rst
index c84eade..f68c424 100644
--- a/README.rst
+++ b/README.rst
@@ -84,31 +84,45 @@ Genomic Position Conversion
     >>> crossmap.genomic_to_coordinate({"position": 1})
     0
 Here is the mapping of coordinates to genomic positions:
-
-+------------+----------+
-| Coordinate | Position |
-+============+==========+
-| 0          | 1        |
-| 1          | 2        |
-| 2          | 3        |
-| 3          | 4        |
-| 4          | 5        |
-| 5          | 6        |
-| 6          | 7        |
-| 7          | 8        |
-| 8          | 9        |
-| 9          | 10       |
-| 10         | 11       |
-| 11         | 12       |
-| 12         | 13       |
-| 13         | 14       |
-| 14         | 15       |
-| 15         | 16       |
-| 16         | 17       |
-| 17         | 18       |
-| 18         | 19       |
-| 19         | 20       |
-+------------+----------+
+Here are example mappings for the transcript:
+
+.. note::
+
+   These examples use the following data:
+
+   .. code-block:: python
+
+       _exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
+       _cds = (32, 43)
+
+---
+
+Genomic Positions
+=================
+
+.. csv-table:: Coordinate to Genomic Position
+   :header: "Coordinate", "Position"
+
+   0, 1
+   1, 2
+   2, 3
+   3, 4
+   4, 5
+   5, 6
+   6, 7
+   7, 8
+   8, 9
+   9, 10
+   10, 11
+   11, 12
+   12, 13
+   13, 14
+   14, 15
+   15, 16
+   16, 17
+   17, 18
+   18, 19
+   19, 20
 
 NonCoding Class
 ---------------

From 7966a14d10d0c87cfd1de803da70f26e0ee26dc3 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 14:40:39 +0100
Subject: [PATCH 036/127] Format table

---
 README.rst | 20 ++++++--------------
 1 file changed, 6 insertions(+), 14 deletions(-)

diff --git a/README.rst b/README.rst
index f68c424..6b67229 100644
--- a/README.rst
+++ b/README.rst
@@ -84,21 +84,9 @@ Genomic Position Conversion
     >>> crossmap.genomic_to_coordinate({"position": 1})
     0
 Here is the mapping of coordinates to genomic positions:
-Here are example mappings for the transcript:
+.. raw:: html
 
-.. note::
-
-   These examples use the following data:
-
-   .. code-block:: python
-
-       _exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
-       _cds = (32, 43)
-
----
-
-Genomic Positions
-=================
+   <div style="overflow-x:auto;">
 
 .. csv-table:: Coordinate to Genomic Position
    :header: "Coordinate", "Position"
@@ -124,6 +112,10 @@ Genomic Positions
    18, 19
    19, 20
 
+.. raw:: html
+
+   </div>
+
 NonCoding Class
 ---------------
 

From 035c479aa2500310445655c2ef55c8cd13650c77 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 14:59:23 +0100
Subject: [PATCH 037/127] Add tables

---
 README.rst | 197 ++++++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 174 insertions(+), 23 deletions(-)

diff --git a/README.rst b/README.rst
index 6b67229..4f6f084 100644
--- a/README.rst
+++ b/README.rst
@@ -84,11 +84,8 @@ Genomic Position Conversion
     >>> crossmap.genomic_to_coordinate({"position": 1})
     0
 Here is the mapping of coordinates to genomic positions:
-.. raw:: html
 
-   <div style="overflow-x:auto;">
-
-.. csv-table:: Coordinate to Genomic Position
+.. csv-table:: Coordinate to Genomic Position (0-4)
    :header: "Coordinate", "Position"
 
    0, 1
@@ -96,25 +93,7 @@ Here is the mapping of coordinates to genomic positions:
    2, 3
    3, 4
    4, 5
-   5, 6
-   6, 7
-   7, 8
-   8, 9
-   9, 10
-   10, 11
-   11, 12
-   12, 13
-   13, 14
-   14, 15
-   15, 16
-   16, 17
-   17, 18
-   18, 19
-   19, 20
-
-.. raw:: html
-
-   </div>
+   ...
 
 NonCoding Class
 ---------------
@@ -157,6 +136,92 @@ Notes
 
 - Add the flag ``inverted=True`` to the constructor when the transcript resides on the reverse complement strand.
 
+Here is the mapping of coordinates to noncoding positions:
+.. csv-table:: Coordinate Mapping
+   :header: "Coordinate", "Position", "Offset", "Region"
+
+   0, 5, 0, u
+   1, 4, 0, u
+   2, 3, 0, u
+   3, 2, 0, u
+   4, 1, 0, u
+   5, 1, 0,
+   6, 2, 0,
+   7, 3, 0,
+   8, 3, 1,
+   9, 3, 2,
+   10, 3, 3,
+   11, 4, -3,
+   12, 4, -2,
+   13, 4, -1,
+   14, 4, 0,
+   15, 5, 0,
+   16, 6, 0,
+   17, 7, 0,
+   18, 8, 0,
+   19, 9, 0,
+   20, 9, 1,
+   21, 9, 2,
+   22, 9, 3,
+   23, 9, 4,
+   24, 9, 5,
+   25, 10, -5,
+   26, 10, -4,
+   27, 10, -3,
+   28, 10, -2,
+   29, 10, -1,
+   30, 10, 0,
+   31, 11, 0,
+   32, 12, 0,
+   33, 13, 0,
+   34, 14, 0,
+   35, 14, 1,
+   36, 14, 2,
+   37, 14, 3,
+   38, 15, -2,
+   39, 15, -1,
+   40, 15, 0,
+   41, 16, 0,
+   42, 17, 0,
+   43, 18, 0,
+   44, 18, 1,
+   45, 18, 2,
+   46, 18, 3,
+   47, 19, -3,
+   48, 19, -2,
+   49, 19, -1,
+   50, 19, 0,
+   51, 20, 0,
+   52, 20, 1,
+   53, 20, 2,
+   54, 20, 3,
+   55, 20, 4,
+   56, 20, 5,
+   57, 20, 6,
+   58, 20, 7,
+   59, 20, 8,
+   60, 20, 9,
+   61, 21, -9,
+   62, 21, -8,
+   63, 21, -7,
+   64, 21, -6,
+   65, 21, -5,
+   66, 21, -4,
+   67, 21, -3,
+   68, 21, -2,
+   69, 21, -1,
+   70, 21, 0,
+   71, 22, 0,
+   72, 1, 0, d
+   73, 2, 0, d
+   74, 3, 0, d
+   75, 4, 0, d
+   76, 5, 0, d
+   77, 6, 0, d
+   78, 7, 0, d
+   79, 8, 0, d
+
+
 Coding Class
 ------------
 
@@ -198,6 +263,92 @@ Notes
 
 - The flag ``inverted=True`` can be used for transcripts on the reverse complement strand.
 
+Here is the mapping of coordinates to coding positions:
+
+.. csv-table:: Coordinate Mapping
+   :header: "Coordinate", "Position", "Offset", "Region"
+
+   0, 5, 0, u
+   1, 4, 0, u
+   2, 3, 0, u
+   3, 2, 0, u
+   4, 1, 0, u
+   5, 11, 0, -
+   6, 10, 0, -
+   7, 9, 0, -
+   8, 9, 1, -
+   9, 9, 2, -
+   10, 9, 3, -
+   11, 8, -3, -
+   12, 8, -2, -
+   13, 8, -1, -
+   14, 8, 0, -
+   15, 7, 0, -
+   16, 6, 0, -
+   17, 5, 0, -
+   18, 4, 0, -
+   19, 3, 0, -
+   20, 3, 1, -
+   21, 3, 2, -
+   22, 3, 3, -
+   23, 3, 4, -
+   24, 3, 5, -
+   25, 2, -5, -
+   26, 2, -4, -
+   27, 2, -3, -
+   28, 2, -2, -
+   29, 2, -1, -
+   30, 2, 0, -
+   31, 1, 0, -
+   32, 1, 0,
+   33, 2, 0,
+   34, 3, 0,
+   35, 3, 1,
+   36, 3, 2,
+   37, 3, 3,
+   38, 4, -2,
+   39, 4, -1,
+   40, 4, 0,
+   41, 5, 0,
+   42, 6, 0,
+   43, 1, 0, *
+   44, 1, 1, *
+   45, 1, 2, *
+   46, 1, 3, *
+   47, 2, -3, *
+   48, 2, -2, *
+   49, 2, -1, *
+   50, 2, 0, *
+   51, 3, 0, *
+   52, 3, 1, *
+   53, 3, 2, *
+   54, 3, 3, *
+   55, 3, 4, *
+   56, 3, 5, *
+   57, 3, 6, *
+   58, 3, 7, *
+   59, 3, 8, *
+   60, 3, 9, *
+   61, 4, -9, *
+   62, 4, -8, *
+   63, 4, -7, *
+   64, 4, -6, *
+   65, 4, -5, *
+   66, 4, -4, *
+   67, 4, -3, *
+   68, 4, -2, *
+   69, 4, -1, *
+   70, 4, 0, *
+   71, 5, 0, *
+   72, 1, 0, d
+   73, 2, 0, d
+   74, 3, 0, d
+   75, 4, 0, d
+   76, 5, 0, d
+   77, 6, 0, d
+   78, 7, 0, d
+   79, 8, 0, d
+
 Protein
 -------
 

From f116376749732c8546f7727b889cc87aaff50548 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 15:04:51 +0100
Subject: [PATCH 038/127] Fix table syntax

---
 README.rst | 135 +++++++++++++++++++++++++++--------------------------
 1 file changed, 68 insertions(+), 67 deletions(-)

diff --git a/README.rst b/README.rst
index 4f6f084..1783078 100644
--- a/README.rst
+++ b/README.rst
@@ -137,6 +137,7 @@ Notes
 - Add the flag ``inverted=True`` to the constructor when the transcript resides on the reverse complement strand.
 
 Here is the mapping of coordinates to noncoding positions:
+
 .. csv-table:: Coordinate Mapping
    :header: "Coordinate", "Position", "Offset", "Region"
 
@@ -145,73 +146,73 @@ Here is the mapping of coordinates to noncoding positions:
    2, 3, 0, u
    3, 2, 0, u
    4, 1, 0, u
-   5, 1, 0,
-   6, 2, 0,
-   7, 3, 0,
-   8, 3, 1,
-   9, 3, 2,
-   10, 3, 3,
-   11, 4, -3,
-   12, 4, -2,
-   13, 4, -1,
-   14, 4, 0,
-   15, 5, 0,
-   16, 6, 0,
-   17, 7, 0,
-   18, 8, 0,
-   19, 9, 0,
-   20, 9, 1,
-   21, 9, 2,
-   22, 9, 3,
-   23, 9, 4,
-   24, 9, 5,
-   25, 10, -5,
-   26, 10, -4,
-   27, 10, -3,
-   28, 10, -2,
-   29, 10, -1,
-   30, 10, 0,
-   31, 11, 0,
-   32, 12, 0,
-   33, 13, 0,
-   34, 14, 0,
-   35, 14, 1,
-   36, 14, 2,
-   37, 14, 3,
-   38, 15, -2,
-   39, 15, -1,
-   40, 15, 0,
-   41, 16, 0,
-   42, 17, 0,
-   43, 18, 0,
-   44, 18, 1,
-   45, 18, 2,
-   46, 18, 3,
-   47, 19, -3,
-   48, 19, -2,
-   49, 19, -1,
-   50, 19, 0,
-   51, 20, 0,
-   52, 20, 1,
-   53, 20, 2,
-   54, 20, 3,
-   55, 20, 4,
-   56, 20, 5,
-   57, 20, 6,
-   58, 20, 7,
-   59, 20, 8,
-   60, 20, 9,
-   61, 21, -9,
-   62, 21, -8,
-   63, 21, -7,
-   64, 21, -6,
-   65, 21, -5,
-   66, 21, -4,
-   67, 21, -3,
-   68, 21, -2,
-   69, 21, -1,
-   70, 21, 0,
-   71, 22, 0,
+   5, 1, 0, ""
+   6, 2, 0, ""
+   7, 3, 0, ""
+   8, 3, 1, ""
+   9, 3, 2, ""
+   10, 3, 3, ""
+   11, 4, -3, ""
+   12, 4, -2, ""
+   13, 4, -1, ""
+   14, 4, 0, ""
+   15, 5, 0, ""
+   16, 6, 0, ""
+   17, 7, 0, ""
+   18, 8, 0, ""
+   19, 9, 0, ""
+   20, 9, 1, ""
+   21, 9, 2, ""
+   22, 9, 3, ""
+   23, 9, 4, ""
+   24, 9, 5, ""
+   25, 10, -5, ""
+   26, 10, -4, ""
+   27, 10, -3, ""
+   28, 10, -2, ""
+   29, 10, -1, ""
+   30, 10, 0, ""
+   31, 11, 0, ""
+   32, 12, 0, ""
+   33, 13, 0, ""
+   34, 14, 0, ""
+   35, 14, 1, ""
+   36, 14, 2, ""
+   37, 14, 3, ""
+   38, 15, -2, ""
+   39, 15, -1, ""
+   40, 15, 0, ""
+   41, 16, 0, ""
+   42, 17, 0, ""
+   43, 18, 0, ""
+   44, 18, 1, ""
+   45, 18, 2, ""
+   46, 18, 3, ""
+   47, 19, -3, ""
+   48, 19, -2, ""
+   49, 19, -1, ""
+   50, 19, 0, ""
+   51, 20, 0, ""
+   52, 20, 1, ""
+   53, 20, 2, ""
+   54, 20, 3, ""
+   55, 20, 4, ""
+   56, 20, 5, ""
+   57, 20, 6, ""
+   58, 20, 7, ""
+   59, 20, 8, ""
+   60, 20, 9, ""
+   61, 21, -9, ""
+   62, 21, -8, ""
+   63, 21, -7, ""
+   64, 21, -6, ""
+   65, 21, -5, ""
+   66, 21, -4, ""
+   67, 21, -3, ""
+   68, 21, -2, ""
+   69, 21, -1, ""
+   70, 21, 0, ""
+   71, 22, 0, ""
    72, 1, 0, d
    73, 2, 0, d
    74, 3, 0, d

From 89787e6b0662bd544d77554fba30107df06e5d19 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 15:20:37 +0100
Subject: [PATCH 039/127] Fix table syntax

---
 README.rst | 134 ++++++++++++++++++++++++++---------------------------
 1 file changed, 67 insertions(+), 67 deletions(-)

diff --git a/README.rst b/README.rst
index 1783078..3db86a5 100644
--- a/README.rst
+++ b/README.rst
@@ -274,73 +274,73 @@ Here is the mapping of coordinates to coding positions:
    2, 3, 0, u
    3, 2, 0, u
    4, 1, 0, u
-   5, 11, 0, -
-   6, 10, 0, -
-   7, 9, 0, -
-   8, 9, 1, -
-   9, 9, 2, -
-   10, 9, 3, -
-   11, 8, -3, -
-   12, 8, -2, -
-   13, 8, -1, -
-   14, 8, 0, -
-   15, 7, 0, -
-   16, 6, 0, -
-   17, 5, 0, -
-   18, 4, 0, -
-   19, 3, 0, -
-   20, 3, 1, -
-   21, 3, 2, -
-   22, 3, 3, -
-   23, 3, 4, -
-   24, 3, 5, -
-   25, 2, -5, -
-   26, 2, -4, -
-   27, 2, -3, -
-   28, 2, -2, -
-   29, 2, -1, -
-   30, 2, 0, -
-   31, 1, 0, -
-   32, 1, 0,
-   33, 2, 0,
-   34, 3, 0,
-   35, 3, 1,
-   36, 3, 2,
-   37, 3, 3,
-   38, 4, -2,
-   39, 4, -1,
-   40, 4, 0,
-   41, 5, 0,
-   42, 6, 0,
-   43, 1, 0, *
-   44, 1, 1, *
-   45, 1, 2, *
-   46, 1, 3, *
-   47, 2, -3, *
-   48, 2, -2, *
-   49, 2, -1, *
-   50, 2, 0, *
-   51, 3, 0, *
-   52, 3, 1, *
-   53, 3, 2, *
-   54, 3, 3, *
-   55, 3, 4, *
-   56, 3, 5, *
-   57, 3, 6, *
-   58, 3, 7, *
-   59, 3, 8, *
-   60, 3, 9, *
-   61, 4, -9, *
-   62, 4, -8, *
-   63, 4, -7, *
-   64, 4, -6, *
-   65, 4, -5, *
-   66, 4, -4, *
-   67, 4, -3, *
-   68, 4, -2, *
-   69, 4, -1, *
-   70, 4, 0, *
-   71, 5, 0, *
+   5, 11, 0, "-"
+   6, 10, 0, "-"
+   7, 9, 0, "-"
+   8, 9, 1, "-"
+   9, 9, 2, "-"
+   10, 9, 3, "-"
+   11, 8, -3, "-"
+   12, 8, -2, "-"
+   13, 8, -1, "-"
+   14, 8, 0, "-"
+   15, 7, 0, "-"
+   16, 6, 0, "-"
+   17, 5, 0, "-"
+   18, 4, 0, "-"
+   19, 3, 0, "-"
+   20, 3, 1, "-"
+   21, 3, 2, "-"
+   22, 3, 3, "-"
+   23, 3, 4, "-"
+   24, 3, 5, "-"
+   25, 2, -5, "-"
+   26, 2, -4, "-"
+   27, 2, -3, "-"
+   28, 2, -2, "-"
+   29, 2, -1, "-"
+   30, 2, 0, "-"
+   31, 1, 0, "-"
+   32, 1, 0, ""
+   33, 2, 0, ""
+   34, 3, 0, ""
+   35, 3, 1, ""
+   36, 3, 2, ""
+   37, 3, 3, ""
+   38, 4, -2, ""
+   39, 4, -1, ""
+   40, 4, 0, ""
+   41, 5, 0, ""
+   42, 6, 0, ""
+   43, 1, 0, "*"
+   44, 1, 1, "*"
+   45, 1, 2, "*"
+   46, 1, 3, "*"
+   47, 2, -3, "*"
+   48, 2, -2, "*"
+   49, 2, -1, "*"
+   50, 2, 0, "*"
+   51, 3, 0, "*"
+   52, 3, 1, "*"
+   53, 3, 2, "*"
+   54, 3, 3, "*"
+   55, 3, 4, "*"
+   56, 3, 5, "*"
+   57, 3, 6, "*"
+   58, 3, 7, "*"
+   59, 3, 8, "*"
+   60, 3, 9, "*"
+   61, 4, -9, "*"
+   62, 4, -8, "*"
+   63, 4, -7, "*"
+   64, 4, -6, "*"
+   65, 4, -5, "*"
+   66, 4, -4, "*"
+   67, 4, -3, "*"
+   68, 4, -2, "*"
+   69, 4, -1, "*"
+   70, 4, 0, "*"
+   71, 5, 0, "*"
    72, 1, 0, d
    73, 2, 0, d
    74, 3, 0, d

From 5e601dc5ae6edf5598cb314b7cb2a1ff1be4829c Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 15:25:32 +0100
Subject: [PATCH 040/127] Fix table syntax

---
 README.rst | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/README.rst b/README.rst
index 3db86a5..ef3fcb1 100644
--- a/README.rst
+++ b/README.rst
@@ -138,6 +138,10 @@ Notes
 
 Here is the mapping of coordinates to noncoding positions:
 
+.. raw:: html
+
+    <div style="overflow-x:auto;">
+
 .. csv-table:: Coordinate Mapping
    :header: "Coordinate", "Position", "Offset", "Region"
 
@@ -222,6 +226,8 @@ Here is the mapping of coordinates to noncoding positions:
    78, 7, 0, d
    79, 8, 0, d
 
+.. raw:: html
+    </div>
 
 Coding Class
 ------------

From 751bc3b49cba7d04efb38889ca323215fa7b5663 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 15:29:00 +0100
Subject: [PATCH 041/127] Fix table syntax

---
 README.rst | 119 ++++++++++++++---------------------------------------
 1 file changed, 32 insertions(+), 87 deletions(-)

diff --git a/README.rst b/README.rst
index ef3fcb1..46f5404 100644
--- a/README.rst
+++ b/README.rst
@@ -140,94 +140,39 @@ Here is the mapping of coordinates to noncoding positions:
 
 .. raw:: html
 
-    <div style="overflow-x:auto;">
+   <div style="overflow-x:auto;">
+
+   .. csv-table:: Coordinate Mapping
+      :header: "Coordinate", "Position", "Offset", "Region"
+
+      0, 5, 0, u
+      1, 4, 0, u
+      2, 3, 0, u
+      3, 2, 0, u
+      4, 1, 0, u
+      5, 1, 0, ""
+      6, 2, 0, ""
+      7, 3, 0, ""
+      8, 3, 1, ""
+      9, 3, 2, ""
+      10, 3, 3, ""
+      11, 4, -3, ""
+      12, 4, -2, ""
+      13, 4, -1, ""
+      14, 4, 0, ""
+      15, 5, 0, ""
+      16, 6, 0, ""
+      17, 7, 0, ""
+      18, 8, 0, ""
+      19, 9, 0, ""
+      20, 9, 1, ""
+      ...
+      79, 8, 0, d
+
+   .. raw:: html
+
+        </div>
 
-.. csv-table:: Coordinate Mapping
-   :header: "Coordinate", "Position", "Offset", "Region"
-
-   0, 5, 0, u
-   1, 4, 0, u
-   2, 3, 0, u
-   3, 2, 0, u
-   4, 1, 0, u
-   5, 1, 0, ""
-   6, 2, 0, ""
-   7, 3, 0, ""
-   8, 3, 1, ""
-   9, 3, 2, ""
-   10, 3, 3, ""
-   11, 4, -3, ""
-   12, 4, -2, ""
-   13, 4, -1, ""
-   14, 4, 0, ""
-   15, 5, 0, ""
-   16, 6, 0, ""
-   17, 7, 0, ""
-   18, 8, 0, ""
-   19, 9, 0, ""
-   20, 9, 1, ""
-   21, 9, 2, ""
-   22, 9, 3, ""
-   23, 9, 4, ""
-   24, 9, 5, ""
-   25, 10, -5, ""
-   26, 10, -4, ""
-   27, 10, -3, ""
-   28, 10, -2, ""
-   29, 10, -1, ""
-   30, 10, 0, ""
-   31, 11, 0, ""
-   32, 12, 0, ""
-   33, 13, 0, ""
-   34, 14, 0, ""
-   35, 14, 1, ""
-   36, 14, 2, ""
-   37, 14, 3, ""
-   38, 15, -2, ""
-   39, 15, -1, ""
-   40, 15, 0, ""
-   41, 16, 0, ""
-   42, 17, 0, ""
-   43, 18, 0, ""
-   44, 18, 1, ""
-   45, 18, 2, ""
-   46, 18, 3, ""
-   47, 19, -3, ""
-   48, 19, -2, ""
-   49, 19, -1, ""
-   50, 19, 0, ""
-   51, 20, 0, ""
-   52, 20, 1, ""
-   53, 20, 2, ""
-   54, 20, 3, ""
-   55, 20, 4, ""
-   56, 20, 5, ""
-   57, 20, 6, ""
-   58, 20, 7, ""
-   59, 20, 8, ""
-   60, 20, 9, ""
-   61, 21, -9, ""
-   62, 21, -8, ""
-   63, 21, -7, ""
-   64, 21, -6, ""
-   65, 21, -5, ""
-   66, 21, -4, ""
-   67, 21, -3, ""
-   68, 21, -2, ""
-   69, 21, -1, ""
-   70, 21, 0, ""
-   71, 22, 0, ""
-   72, 1, 0, d
-   73, 2, 0, d
-   74, 3, 0, d
-   75, 4, 0, d
-   76, 5, 0, d
-   77, 6, 0, d
-   78, 7, 0, d
-   79, 8, 0, d
-
-.. raw:: html
-    </div>
 
 Coding Class
 ------------

From 9d156c80483a166dcaec27fff965bf51a9873f5d Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 15:31:27 +0100
Subject: [PATCH 042/127] Fix table indent

---
 README.rst | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.rst b/README.rst
index 46f5404..87e3fc9 100644
--- a/README.rst
+++ b/README.rst
@@ -138,6 +138,8 @@ Notes
 
 Here is the mapping of coordinates to noncoding positions:
 
+Here is the mapping of coordinates to noncoding positions:
+
 .. raw:: html
 
    <div style="overflow-x:auto;">
@@ -171,8 +173,7 @@ Here is the mapping of coordinates to noncoding positions:
 
    .. raw:: html
 
-        </div>
-
+   </div>
 
 Coding Class
 ------------

From ebbb90a8c72eb44fc7c835859721a59978ee9fbb Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Tue, 10 Mar 2026 15:37:29 +0100
Subject: [PATCH 043/127] Update README.rst

---
 README.rst | 66 ++++++++++++++++++++++++++++++------------------------
 1 file changed, 37 insertions(+), 29 deletions(-)

diff --git a/README.rst b/README.rst
index 87e3fc9..f366eaa 100644
--- a/README.rst
+++ b/README.rst
@@ -144,34 +144,34 @@ Here is the mapping of coordinates to noncoding positions:
 
    <div style="overflow-x:auto;">
 
-   .. csv-table:: Coordinate Mapping
-      :header: "Coordinate", "Position", "Offset", "Region"
-
-      0, 5, 0, u
-      1, 4, 0, u
-      2, 3, 0, u
-      3, 2, 0, u
-      4, 1, 0, u
-      5, 1, 0, ""
-      6, 2, 0, ""
-      7, 3, 0, ""
-      8, 3, 1, ""
-      9, 3, 2, ""
-      10, 3, 3, ""
-      11, 4, -3, ""
-      12, 4, -2, ""
-      13, 4, -1, ""
-      14, 4, 0, ""
-      15, 5, 0, ""
-      16, 6, 0, ""
-      17, 7, 0, ""
-      18, 8, 0, ""
-      19, 9, 0, ""
-      20, 9, 1, ""
-      ...
-      79, 8, 0, d
-
-   .. raw:: html
+.. csv-table:: Coordinate Mapping to Noncoding
+   :header: "Coordinate", "Position", "Offset", "Region"
+
+   0, 5, 0, u
+   1, 4, 0, u
+   2, 3, 0, u
+   3, 2, 0, u
+   4, 1, 0, u
+   5, 1, 0, ""
+   6, 2, 0, ""
+   7, 3, 0, ""
+   8, 3, 1, ""
+   9, 3, 2, ""
+   10, 3, 3, ""
+   11, 4, -3, ""
+   12, 4, -2, ""
+   13, 4, -1, ""
+   14, 4, 0, ""
+   15, 5, 0, ""
+   16, 6, 0, ""
+   17, 7, 0, ""
+   18, 8, 0, ""
+   19, 9, 0, ""
+   20, 9, 1, ""
+   ...
+   79, 8, 0, d
+
+.. raw:: html
 
    </div>
 
@@ -218,7 +218,11 @@ Notes
 
 Here is the mapping of coordinates to coding positions:
 
-.. csv-table:: Coordinate Mapping
+.. raw:: html
+
+   <div style="overflow-x:auto;">
+
+.. csv-table:: Coordinate Mapping to Coding
    :header: "Coordinate", "Position", "Offset", "Region"
 
    0, 5, 0, u
@@ -302,6 +306,10 @@ Here is the mapping of coordinates to coding positions:
    78, 7, 0, d
    79, 8, 0, d
 
+.. raw:: html
+
+   </div>
+
 Protein
 -------
 

From 9ffa9bfc2bb558017b0e25e7cec06123fc688f2a Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Tue, 10 Mar 2026 15:41:32 +0100
Subject: [PATCH 044/127] Make scrollable tables in README

---
 README.rst | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/README.rst b/README.rst
index f366eaa..8d0bc03 100644
--- a/README.rst
+++ b/README.rst
@@ -138,13 +138,11 @@ Notes
 
 Here is the mapping of coordinates to noncoding positions:
 
-Here is the mapping of coordinates to noncoding positions:
-
 .. raw:: html
 
-   <div style="overflow-x:auto;">
+   <div style="max-height:300px; overflow-y:auto;">
 
-.. csv-table:: Coordinate Mapping to Noncoding
+.. csv-table::
    :header: "Coordinate", "Position", "Offset", "Region"
 
    0, 5, 0, u
@@ -220,7 +218,7 @@ Here is the mapping of coordinates to coding positions:
 
 .. raw:: html
 
-   <div style="overflow-x:auto;">
+   <div style="max-height:300px; overflow-y:auto;">
 
 .. csv-table:: Coordinate Mapping to Coding
    :header: "Coordinate", "Position", "Offset", "Region"

From 90f3d7192d197fb15145e470887d44e356e508f3 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Tue, 10 Mar 2026 15:54:25 +0100
Subject: [PATCH 045/127] Update README.rst

---
 README.rst | 178 ++++++++++++++++++++++++++---------------------------
 1 file changed, 88 insertions(+), 90 deletions(-)

diff --git a/README.rst b/README.rst
index 8d0bc03..3cafd15 100644
--- a/README.rst
+++ b/README.rst
@@ -216,97 +216,95 @@ Notes
 
 Here is the mapping of coordinates to coding positions:
 
-.. raw:: html
-
-   <div style="max-height:300px; overflow-y:auto;">
-
-.. csv-table:: Coordinate Mapping to Coding
-   :header: "Coordinate", "Position", "Offset", "Region"
+<details>
+<summary>Coordinate Mapping Table</summary>
+
+::
+
+   Coordinate  Position  Offset  Region
+   0           5         0       u
+   1           4         0       u
+   2           3         0       u
+   3           2         0       u
+   4           1         0       u
+   5           11        0       -
+   6           10        0       -
+   7           9         0       -
+   8           9         1       -
+   9           9         2       -
+   10          9         3       -
+   11          8         -3      -
+   12          8         -2      -
+   13          8         -1      -
+   14          8         0       -
+   15          7         0       -
+   16          6         0       -
+   17          5         0       -
+   18          4         0       -
+   19          3         0       -
+   20          3         1       -
+   21          3         2       -
+   22          3         3       -
+   23          3         4       -
+   24          3         5       -
+   25          2         -5      -
+   26          2         -4      -
+   27          2         -3      -
+   28          2         -2      -
+   29          2         -1      -
+   30          2         0       -
+   31          1         0       -
+   32          1         0
+   33          2         0
+   34          3         0
+   35          3         1
+   36          3         2
+   37          3         3
+   38          4         -2
+   39          4         -1
+   40          4         0
+   41          5         0
+   42          6         0
+   43          1         0       *
+   44          1         1       *
+   45          1         2       *
+   46          1         3       *
+   47          2         -3      *
+   48          2         -2      *
+   49          2         -1      *
+   50          2         0       *
+   51          3         0       *
+   52          3         1       *
+   53          3         2       *
+   54          3         3       *
+   55          3         4       *
+   56          3         5       *
+   57          3         6       *
+   58          3         7       *
+   59          3         8       *
+   60          3         9       *
+   61          4         -9      *
+   62          4         -8      *
+   63          4         -7      *
+   64          4         -6      *
+   65          4         -5      *
+   66          4         -4      *
+   67          4         -3      *
+   68          4         -2      *
+   69          4         -1      *
+   70          4         0       *
+   71          5         0       *
+   72          1         0       d
+   73          2         0       d
+   74          3         0       d
+   75          4         0       d
+   76          5         0       d
+   77          6         0       d
+   78          7         0       d
+   79          8         0       d
+
+</details>
 
-   0, 5, 0, u
-   1, 4, 0, u
-   2, 3, 0, u
-   3, 2, 0, u
-   4, 1, 0, u
-   5, 11, 0, "-"
-   6, 10, 0, "-"
-   7, 9, 0, "-"
-   8, 9, 1, "-"
-   9, 9, 2, "-"
-   10, 9, 3, "-"
-   11, 8, -3, "-"
-   12, 8, -2, "-"
-   13, 8, -1, "-"
-   14, 8, 0, "-"
-   15, 7, 0, "-"
-   16, 6, 0, "-"
-   17, 5, 0, "-"
-   18, 4, 0, "-"
-   19, 3, 0, "-"
-   20, 3, 1, "-"
-   21, 3, 2, "-"
-   22, 3, 3, "-"
-   23, 3, 4, "-"
-   24, 3, 5, "-"
-   25, 2, -5, "-"
-   26, 2, -4, "-"
-   27, 2, -3, "-"
-   28, 2, -2, "-"
-   29, 2, -1, "-"
-   30, 2, 0, "-"
-   31, 1, 0, "-"
-   32, 1, 0, ""
-   33, 2, 0, ""
-   34, 3, 0, ""
-   35, 3, 1, ""
-   36, 3, 2, ""
-   37, 3, 3, ""
-   38, 4, -2, ""
-   39, 4, -1, ""
-   40, 4, 0, ""
-   41, 5, 0, ""
-   42, 6, 0, ""
-   43, 1, 0, "*"
-   44, 1, 1, "*"
-   45, 1, 2, "*"
-   46, 1, 3, "*"
-   47, 2, -3, "*"
-   48, 2, -2, "*"
-   49, 2, -1, "*"
-   50, 2, 0, "*"
-   51, 3, 0, "*"
-   52, 3, 1, "*"
-   53, 3, 2, "*"
-   54, 3, 3, "*"
-   55, 3, 4, "*"
-   56, 3, 5, "*"
-   57, 3, 6, "*"
-   58, 3, 7, "*"
-   59, 3, 8, "*"
-   60, 3, 9, "*"
-   61, 4, -9, "*"
-   62, 4, -8, "*"
-   63, 4, -7, "*"
-   64, 4, -6, "*"
-   65, 4, -5, "*"
-   66, 4, -4, "*"
-   67, 4, -3, "*"
-   68, 4, -2, "*"
-   69, 4, -1, "*"
-   70, 4, 0, "*"
-   71, 5, 0, "*"
-   72, 1, 0, d
-   73, 2, 0, d
-   74, 3, 0, d
-   75, 4, 0, d
-   76, 5, 0, d
-   77, 6, 0, d
-   78, 7, 0, d
-   79, 8, 0, d
-
-.. raw:: html
-
-   </div>
 
 Protein
 -------

From 93f59ca3864ab4850794f5af4696bda52429689e Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Tue, 10 Mar 2026 16:04:14 +0100
Subject: [PATCH 046/127] Update README.rst

---
 README.rst | 284 +++++++++++++++++++++++++++++++----------------------
 1 file changed, 166 insertions(+), 118 deletions(-)

diff --git a/README.rst b/README.rst
index 3cafd15..74a7272 100644
--- a/README.rst
+++ b/README.rst
@@ -138,40 +138,91 @@ Notes
 
 Here is the mapping of coordinates to noncoding positions:
 
-.. raw:: html
-
-   <div style="max-height:300px; overflow-y:auto;">
-
 .. csv-table::
+   :class: table-scroll
    :header: "Coordinate", "Position", "Offset", "Region"
 
-   0, 5, 0, u
-   1, 4, 0, u
-   2, 3, 0, u
-   3, 2, 0, u
-   4, 1, 0, u
-   5, 1, 0, ""
-   6, 2, 0, ""
-   7, 3, 0, ""
-   8, 3, 1, ""
-   9, 3, 2, ""
-   10, 3, 3, ""
-   11, 4, -3, ""
-   12, 4, -2, ""
-   13, 4, -1, ""
-   14, 4, 0, ""
-   15, 5, 0, ""
-   16, 6, 0, ""
-   17, 7, 0, ""
-   18, 8, 0, ""
-   19, 9, 0, ""
-   20, 9, 1, ""
-   ...
-   79, 8, 0, d
-
-.. raw:: html
+   "0", "5","0", "u"
+   "1", "4","0", "u"
+   "2", "3","0", "u"
+   "3", "2","0", "u"
+   "4", "1","0", "u"
+   "5", "1","0", ""
+   "6", "2","0", ""
+   "7", "3","0", ""
+   "8", "3","1", ""
+   "9", "3","2", ""
+   "10", "3","3", ""
+   "11", "4","-3", ""
+   "12", "4","-2", ""
+   "13", "4","-1", ""
+   "14", "4","0", ""
+   "15", "5","0", ""
+   "16", "6","0", ""
+   "17", "7","0", ""
+   "18", "8","0", ""
+   "19", "9","0", ""
+   "20", "9","1", ""
+   "21", "9","2", ""
+   "22", "9","3", ""
+   "23", "9","4", ""
+   "24", "9","5", ""
+   "25", "10","-5", ""
+   "26", "10","-4", ""
+   "27", "10","-3", ""
+   "28", "10","-2", ""
+   "29", "10","-1", ""
+   "30", "10","0", ""
+   "31", "11","0", ""
+   "32", "12","0", ""
+   "33", "13","0", ""
+   "34", "14","0", ""
+   "35", "14","1", ""
+   "36", "14","2", ""
+   "37", "14","3", ""
+   "38", "15","-2", ""
+   "39", "15","-1", ""
+   "40", "15","0", ""
+   "41", "16","0", ""
+   "42", "17","0", ""
+   "43", "18","0", ""
+   "44", "18","1", ""
+   "45", "18","2", ""
+   "46", "18","3", ""
+   "47", "19","-3", ""
+   "48", "19","-2", ""
+   "49", "19","-1", ""
+   "50", "19","0", ""
+   "51", "20","0", ""
+   "52", "20","1", ""
+   "53", "20","2", ""
+   "54", "20","3", ""
+   "55", "20","4", ""
+   "56", "20","5", ""
+   "57", "20","6", ""
+   "58", "20","7", ""
+   "59", "20","8", ""
+   "60", "20","9", ""
+   "61", "21","-9", ""
+   "62", "21","-8", ""
+   "63", "21","-7", ""
+   "64", "21","-6", ""
+   "65", "21","-5", ""
+   "66", "21","-4", ""
+   "67", "21","-3", ""
+   "68", "21","-2", ""
+   "69", "21","-1", ""
+   "70", "21","0", ""
+   "71", "22","0", ""
+   "72", "1","0", "d"
+   "73", "2","0", "d"
+   "74", "3","0", "d"
+   "75", "4","0", "d"
+   "76", "5","0", "d"
+   "77", "6","0", "d"
+   "78", "7","0", "d"
+   "79", "8","0", "d"
 
-   </div>
 
 Coding Class
 ------------
@@ -216,94 +267,91 @@ Notes
 
 Here is the mapping of coordinates to coding positions:
 
-<details>
-<summary>Coordinate Mapping Table</summary>
-
-::
-
-   Coordinate  Position  Offset  Region
-   0           5         0       u
-   1           4         0       u
-   2           3         0       u
-   3           2         0       u
-   4           1         0       u
-   5           11        0       -
-   6           10        0       -
-   7           9         0       -
-   8           9         1       -
-   9           9         2       -
-   10          9         3       -
-   11          8         -3      -
-   12          8         -2      -
-   13          8         -1      -
-   14          8         0       -
-   15          7         0       -
-   16          6         0       -
-   17          5         0       -
-   18          4         0       -
-   19          3         0       -
-   20          3         1       -
-   21          3         2       -
-   22          3         3       -
-   23          3         4       -
-   24          3         5       -
-   25          2         -5      -
-   26          2         -4      -
-   27          2         -3      -
-   28          2         -2      -
-   29          2         -1      -
-   30          2         0       -
-   31          1         0       -
-   32          1         0
-   33          2         0
-   34          3         0
-   35          3         1
-   36          3         2
-   37          3         3
-   38          4         -2
-   39          4         -1
-   40          4         0
-   41          5         0
-   42          6         0
-   43          1         0       *
-   44          1         1       *
-   45          1         2       *
-   46          1         3       *
-   47          2         -3      *
-   48          2         -2      *
-   49          2         -1      *
-   50          2         0       *
-   51          3         0       *
-   52          3         1       *
-   53          3         2       *
-   54          3         3       *
-   55          3         4       *
-   56          3         5       *
-   57          3         6       *
-   58          3         7       *
-   59          3         8       *
-   60          3         9       *
-   61          4         -9      *
-   62          4         -8      *
-   63          4         -7      *
-   64          4         -6      *
-   65          4         -5      *
-   66          4         -4      *
-   67          4         -3      *
-   68          4         -2      *
-   69          4         -1      *
-   70          4         0       *
-   71          5         0       *
-   72          1         0       d
-   73          2         0       d
-   74          3         0       d
-   75          4         0       d
-   76          5         0       d
-   77          6         0       d
-   78          7         0       d
-   79          8         0       d
-
-</details>
+.. csv-table:: My Scrollable Table
+   :class: table-scroll
+   :header: "Coordinate", "Position", "Offset", "Region"
+   
+   "0", "5","0", "u"
+   "1", "4","0", "u"
+   "2", "3","0", "u"
+   "3", "2","0", "u"
+   "4", "1","0", "u"
+   "5", "11","0", "-"
+   "6", "10","0", "-"
+   "7", "9","0", "-"
+   "8", "9","1", "-"
+   "9", "9","2", "-"
+   "10", "9","3", "-"
+   "11", "8","-3", "-"
+   "12", "8","-2", "-"
+   "13", "8","-1", "-"
+   "14", "8","0", "-"
+   "15", "7","0", "-"
+   "16", "6","0", "-"
+   "17", "5","0", "-"
+   "18", "4","0", "-"
+   "19", "3","0", "-"
+   "20", "3","1", "-"
+   "21", "3","2", "-"
+   "22", "3","3", "-"
+   "23", "3","4", "-"
+   "24", "3","5", "-"
+   "25", "2","-5", "-"
+   "26", "2","-4", "-"
+   "27", "2","-3", "-"
+   "28", "2","-2", "-"
+   "29", "2","-1", "-"
+   "30", "2","0", "-"
+   "31", "1","0", "-"
+   "32", "1","0", ""
+   "33", "2","0", ""
+   "34", "3","0", ""
+   "35", "3","1", ""
+   "36", "3","2", ""
+   "37", "3","3", ""
+   "38", "4","-2", ""
+   "39", "4","-1", ""
+   "40", "4","0", ""
+   "41", "5","0", ""
+   "42", "6","0", ""
+   "43", "1","0", "*"
+   "44", "1","1", "*"
+   "45", "1","2", "*"
+   "46", "1","3", "*"
+   "47", "2","-3", "*"
+   "48", "2","-2", "*"
+   "49", "2","-1", "*"
+   "50", "2","0", "*"
+   "51", "3","0", "*"
+   "52", "3","1", "*"
+   "53", "3","2", "*"
+   "54", "3","3", "*"
+   "55", "3","4", "*"
+   "56", "3","5", "*"
+   "57", "3","6", "*"
+   "58", "3","7", "*"
+   "59", "3","8", "*"
+   "60", "3","9", "*"
+   "61", "4","-9", "*"
+   "62", "4","-8", "*"
+   "63", "4","-7", "*"
+   "64", "4","-6", "*"
+   "65", "4","-5", "*"
+   "66", "4","-4", "*"
+   "67", "4","-3", "*"
+   "68", "4","-2", "*"
+   "69", "4","-1", "*"
+   "70", "4","0", "*"
+   "71", "5","0", "*"
+   "72", "1","0", "d"
+   "73", "2","0", "d"
+   "74", "3","0", "d"
+   "75", "4","0", "d"
+   "76", "5","0", "d"
+   "77", "6","0", "d"
+   "78", "7","0", "d"
+   "79", "8","0", "d"
+
 
 
 Protein

From 0ef6003debfe9aa6770cfbe46e41f04c07962fad Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 16:13:41 +0100
Subject: [PATCH 047/127] Format table

---
 README.rst | 120 ++++++++++++++++++++++++++---------------------------
 1 file changed, 60 insertions(+), 60 deletions(-)

diff --git a/README.rst b/README.rst
index 74a7272..ee4ab6f 100644
--- a/README.rst
+++ b/README.rst
@@ -246,7 +246,7 @@ Where:
 
 - **position**: a positive integer
 - **offset**: an integer indicating the offset relative to the position
-- **region**: a string describing the region type (``""`` for standard coding positions, ``"-"`` for 5' UTR, ``"*"`` for 3' UTR, ``"u"`` for upstream and ``"d"`` for downstream)
+- **region**: a string describing the region type (`""` for standard coding positions, `'-'` for 5' UTR, `'*'` for 3' UTR, `'u'` for upstream and ``"d"`` for downstream)
 
 Coding Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -256,8 +256,8 @@ Coding Position Conversion
     >>> from mutalyzer_crossmapper import Coding
     >>> crossmap = Coding(_exons, _cds)
     >>> crossmap.coordinate_to_coding(31)
-    {"position": -1, "offset": 0, "region": "-"}
-    >>> crossmap.coding_to_coordinate({"position": -1, "offset": 0, "region": "-"})
+    {"position": -1, "offset": 0, "region": '-'}
+    >>> crossmap.coding_to_coordinate({"position": -1, "offset": 0, "region": '-'})
     31
 
 Notes
@@ -270,39 +270,39 @@ Here is the mapping of coordinates to coding positions:
 .. csv-table:: My Scrollable Table
    :class: table-scroll
    :header: "Coordinate", "Position", "Offset", "Region"
-   
+
    "0", "5","0", "u"
    "1", "4","0", "u"
    "2", "3","0", "u"
    "3", "2","0", "u"
    "4", "1","0", "u"
-   "5", "11","0", "-"
-   "6", "10","0", "-"
-   "7", "9","0", "-"
-   "8", "9","1", "-"
-   "9", "9","2", "-"
-   "10", "9","3", "-"
-   "11", "8","-3", "-"
-   "12", "8","-2", "-"
-   "13", "8","-1", "-"
-   "14", "8","0", "-"
-   "15", "7","0", "-"
-   "16", "6","0", "-"
-   "17", "5","0", "-"
-   "18", "4","0", "-"
-   "19", "3","0", "-"
-   "20", "3","1", "-"
-   "21", "3","2", "-"
-   "22", "3","3", "-"
-   "23", "3","4", "-"
-   "24", "3","5", "-"
-   "25", "2","-5", "-"
-   "26", "2","-4", "-"
-   "27", "2","-3", "-"
-   "28", "2","-2", "-"
-   "29", "2","-1", "-"
-   "30", "2","0", "-"
-   "31", "1","0", "-"
+   "5", "11","0", '-'
+   "6", "10","0", '-'
+   "7", "9","0", '-'
+   "8", "9","1", '-'
+   "9", "9","2", '-'
+   "10", "9","3", '-'
+   "11", "8","-3", '-'
+   "12", "8","-2", '-'
+   "13", "8","-1", '-'
+   "14", "8","0", '-'
+   "15", "7","0", '-'
+   "16", "6","0", '-'
+   "17", "5","0", '-'
+   "18", "4","0", '-'
+   "19", "3","0", '-'
+   "20", "3","1", '-'
+   "21", "3","2", '-'
+   "22", "3","3", '-'
+   "23", "3","4", '-'
+   "24", "3","5", '-'
+   "25", "2","-5", '-'
+   "26", "2","-4", '-'
+   "27", "2","-3", '-'
+   "28", "2","-2", '-'
+   "29", "2","-1", '-'
+   "30", "2","0", '-'
+   "31", "1","0", '-'
    "32", "1","0", ""
    "33", "2","0", ""
    "34", "3","0", ""
@@ -314,35 +314,35 @@ Here is the mapping of coordinates to coding positions:
    "40", "4","0", ""
    "41", "5","0", ""
    "42", "6","0", ""
-   "43", "1","0", "*"
-   "44", "1","1", "*"
-   "45", "1","2", "*"
-   "46", "1","3", "*"
-   "47", "2","-3", "*"
-   "48", "2","-2", "*"
-   "49", "2","-1", "*"
-   "50", "2","0", "*"
-   "51", "3","0", "*"
-   "52", "3","1", "*"
-   "53", "3","2", "*"
-   "54", "3","3", "*"
-   "55", "3","4", "*"
-   "56", "3","5", "*"
-   "57", "3","6", "*"
-   "58", "3","7", "*"
-   "59", "3","8", "*"
-   "60", "3","9", "*"
-   "61", "4","-9", "*"
-   "62", "4","-8", "*"
-   "63", "4","-7", "*"
-   "64", "4","-6", "*"
-   "65", "4","-5", "*"
-   "66", "4","-4", "*"
-   "67", "4","-3", "*"
-   "68", "4","-2", "*"
-   "69", "4","-1", "*"
-   "70", "4","0", "*"
-   "71", "5","0", "*"
+   "43", "1","0", '*'
+   "44", "1","1", '*'
+   "45", "1","2", '*'
+   "46", "1","3", '*'
+   "47", "2","-3", '*'
+   "48", "2","-2", '*'
+   "49", "2","-1", '*'
+   "50", "2","0", '*'
+   "51", "3","0", '*'
+   "52", "3","1", '*'
+   "53", "3","2", '*'
+   "54", "3","3", '*'
+   "55", "3","4", '*'
+   "56", "3","5", '*'
+   "57", "3","6", '*'
+   "58", "3","7", '*'
+   "59", "3","8", '*'
+   "60", "3","9", '*'
+   "61", "4","-9", '*'
+   "62", "4","-8", '*'
+   "63", "4","-7", '*'
+   "64", "4","-6", '*'
+   "65", "4","-5", '*'
+   "66", "4","-4", '*'
+   "67", "4","-3", '*'
+   "68", "4","-2", '*'
+   "69", "4","-1", '*'
+   "70", "4","0", '*'
+   "71", "5","0", '*'
    "72", "1","0", "d"
    "73", "2","0", "d"
    "74", "3","0", "d"

From 2704e52de49a55960aa60f6f67fd2f144ffbd292 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Tue, 10 Mar 2026 16:30:59 +0100
Subject: [PATCH 048/127] Use code block for table

---
 README.rst | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.rst b/README.rst
index ee4ab6f..7406023 100644
--- a/README.rst
+++ b/README.rst
@@ -138,10 +138,9 @@ Notes
 
 Here is the mapping of coordinates to noncoding positions:
 
-.. csv-table::
-   :class: table-scroll
-   :header: "Coordinate", "Position", "Offset", "Region"
+.. code-block:: text
 
+   Coordinate, Position, Offset, Region
    "0", "5","0", "u"
    "1", "4","0", "u"
    "2", "3","0", "u"
@@ -224,6 +223,7 @@ Here is the mapping of coordinates to noncoding positions:
    "79", "8","0", "d"
 
 
+
 Coding Class
 ------------
 
@@ -267,7 +267,7 @@ Notes
 
 Here is the mapping of coordinates to coding positions:
 
-.. csv-table:: My Scrollable Table
+.. csv-table::
    :class: table-scroll
    :header: "Coordinate", "Position", "Offset", "Region"
 

From 78183fdd586950fae3f971640ff0c7dd70be04fa Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Tue, 10 Mar 2026 16:39:14 +0100
Subject: [PATCH 049/127] Update README.rst

---
 README.rst | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.rst b/README.rst
index 7406023..afeb981 100644
--- a/README.rst
+++ b/README.rst
@@ -138,9 +138,10 @@ Notes
 
 Here is the mapping of coordinates to noncoding positions:
 
-.. code-block:: text
+.. csv-table::
+   :class: table-scroll
+   :header: "Coordinate", "Position", "Offset", "Region"
 
-   Coordinate, Position, Offset, Region
    "0", "5","0", "u"
    "1", "4","0", "u"
    "2", "3","0", "u"

From 03309a8ac928bfa24c2c35b6318a75407a8cf199 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 10 Mar 2026 22:11:18 +0100
Subject: [PATCH 050/127] Refactor: crossmapper and tests for degenerate option

---
 mutalyzer_crossmapper/crossmapper.py |  68 ++--
 tests/test_crossmapper.py            | 571 ++++++++++++++++-----------
 2 files changed, 377 insertions(+), 262 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 9762598..5bc9f5c 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -69,46 +69,49 @@ def __init__(self, locations, cds, inverted=False):
 
         b0 = self._noncoding.to_position(cds[0])
         b1 = self._noncoding.to_position(cds[1])
+        e0 = self._noncoding.to_position(locations[0][0])
+        e1 = self._noncoding.to_position(locations[-1][1]-1)
 
         if self._inverted:
             self._coding = (b1["position"] + b1["offset"] + 1, b0["position"] + b0["offset"] + 1)
-            self._cds_len = (b0["position"] + b0["offset"]) - (b1["position"] + b1["offset"])
+            self._cds_len = abs((b0["position"] + b0["offset"]) - (b1["position"] + b1["offset"]))
+            self._exons_end = e0["position"]
         else:
             self._coding = (b0["position"] + b0["offset"], b1["position"] + b1["offset"])
-            self._cds_len = (b1["position"] + b1["offset"]) - (b0["position"] + b0["offset"])
+            self._cds_len = abs((b1["position"] + b1["offset"]) - (b0["position"] + b0["offset"]))
+            self._exons_end = e1["position"]
 
     def _coordinate_to_coding(self, coordinate):
         """Convert a coordinate to a coding position (c./r.).
 
         :arg int coordinate: Coordinate.
 
-        :returns tuple: Coding position (c./r.).
+        :returns dict: Coding position model (c./r.).
         """
-        noncoding_pos = self._noncoding.to_position(coordinate)
+        noncoding_pos_m = self._noncoding.to_position(coordinate)
 
-        # on top of the noncoding position model, add CDs info
-        location = noncoding_pos["position"]
-        if noncoding_pos["region"] == "":
-            if location < self._coding[0]: # before CDs
+        location = noncoding_pos_m["position"]
+        if noncoding_pos_m["region"] == "":
+            if location < self._coding[0]:
                 return {
                     "position": self._coding[0] - location,
-                    "offset": noncoding_pos["offset"],
+                    "offset": noncoding_pos_m["offset"],
                     "region": "-"
                 }
-            elif location >= self._coding[1]: # after CDs
+            elif location >= self._coding[1]:
                 return {
                     "position": location - self._coding[1] + 1,
-                    "offset": noncoding_pos["offset"],
+                    "offset": noncoding_pos_m["offset"],
                     "region": "*"
                 }
             else:
                 return {
                     "position": location - self._coding[0] + 1,
-                    "offset": noncoding_pos["offset"],
+                    "offset": noncoding_pos_m["offset"],
                     "region": ""
                 }
         else:
-            return noncoding_pos
+            return noncoding_pos_m
 
     def coordinate_to_coding(self, coordinate, degenerate=False):
         """Convert a coordinate to a coding position (c./r.).
@@ -116,57 +119,58 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
         :arg int coordinate: Coordinate.
         :arg bool degenerate: Return a degenerate position.
 
-        :returns tuple: Coding position (c./r.).
+        :returns dict: Coding position model (c./r.).
         """
-        pos = self._coordinate_to_coding(coordinate)
-        if degenerate and pos["region"] in ["u", "d"]:
-            if pos["region"] == "u":
-                pos["position"] = pos["position"] + self._coding[0]
-                pos["region"] = "-"
-            else:
-                pos["position"] = pos["position"] + self._coding[1]
-                pos["region"] = "*"
-        return pos
+        pos_m = self._coordinate_to_coding(coordinate)
+        if degenerate:
+            if pos_m["region"] == "u":
+                pos_m["position"] = pos_m["position"] + self._coding[0]
+                pos_m["region"] = "-"
+            if pos_m["region"] == "d":
+                pos_m["position"] = pos_m["position"] + self._exons_end - self._coding[1] + 1
+                pos_m["region"] = "*"
+        return pos_m
 
     def coding_to_coordinate(self, pos_m):
         """Convert a coding position (c./r.) to a coordinate.
 
-        :arg tuple position: Coding position (c./r.).
+        :arg dict pos_m: Coding position model (c./r.).
 
         :returns int: Coordinate.
         """
         region = pos_m["region"]
         if region == "u":
-            noncoding_pos = {
-                "position": abs(pos_m["position"]) + pos_m["offset"],
+            noncoding_pos_m = {
+                "position": pos_m["position"] - pos_m["offset"],
                 "offset": 0,
                 "region": "u"
             }
         elif region == "d":
-            noncoding_pos = {
-                "position": abs(pos_m["position"]) + pos_m["offset"],
+            noncoding_pos_m = {
+                "position": pos_m["position"] + pos_m["offset"],
                 "offset": 0,
                 "region": "d"
             }
         elif region == "":
-            noncoding_pos = {
+            noncoding_pos_m = {
                 "position": pos_m["position"] + self._coding[0] -1,
                 "offset": pos_m["offset"],
                 "region": ""
             }
+        # add checks for degenerate results?
         elif region == "-":
-            noncoding_pos = {
+            noncoding_pos_m = {
                 "position": self._coding[0] - pos_m["position"],
                 "offset": pos_m["offset"],
                 "region": ""
             }
         else: # *
-            noncoding_pos = {
+            noncoding_pos_m = {
                 "position": self._coding[1] + pos_m["position"] - 1,
                 "offset": pos_m["offset"],
                 "region": ""
             }
-        return self._noncoding.to_coordinate(noncoding_pos)
+        return self._noncoding.to_coordinate(noncoding_pos_m)
 
 
     def coordinate_to_protein(self, coordinate):
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 6ba2d83..dbaf87b 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -11,9 +11,17 @@ def test_Genomic():
     crossmap = Genomic()
 
     invariant(
-        crossmap.coordinate_to_genomic, 0, crossmap.genomic_to_coordinate, {"position": 1})
+        crossmap.coordinate_to_genomic,
+        0,
+        crossmap.genomic_to_coordinate,
+        {"position": 1},
+    )
     invariant(
-        crossmap.coordinate_to_genomic, 98, crossmap.genomic_to_coordinate, {"position": 99})
+        crossmap.coordinate_to_genomic,
+        98,
+        crossmap.genomic_to_coordinate,
+        {"position": 99},
+    )
 
 
 def test_NonCoding():
@@ -22,19 +30,31 @@ def test_NonCoding():
 
     # Boundary between upstream and transcript.
     invariant(
-        crossmap.coordinate_to_noncoding, 4,
-        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region":"u"})
+        crossmap.coordinate_to_noncoding,
+        4,
+        crossmap.noncoding_to_coordinate,
+        {"position": 1, "offset": 0, "region": "u"},
+    )
     invariant(
-        crossmap.coordinate_to_noncoding, 5,
-        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region": ""})
+        crossmap.coordinate_to_noncoding,
+        5,
+        crossmap.noncoding_to_coordinate,
+        {"position": 1, "offset": 0, "region": ""},
+    )
 
     # Boundary between downstream and transcript.
     invariant(
-        crossmap.coordinate_to_noncoding, 71,
-        crossmap.noncoding_to_coordinate, {"position": 22, "offset": 0, "region": ""})
+        crossmap.coordinate_to_noncoding,
+        71,
+        crossmap.noncoding_to_coordinate,
+        {"position": 22, "offset": 0, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_noncoding, 72,
-        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region": "d"})
+        crossmap.coordinate_to_noncoding,
+        72,
+        crossmap.noncoding_to_coordinate,
+        {"position": 1, "offset": 0, "region": "d"},
+    )
 
 
 def test_NonCoding_inverted():
@@ -43,19 +63,31 @@ def test_NonCoding_inverted():
 
     # Boundary between upstream and transcript.
     invariant(
-        crossmap.coordinate_to_noncoding, 72,
-        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region": "u"})
+        crossmap.coordinate_to_noncoding,
+        72,
+        crossmap.noncoding_to_coordinate,
+        {"position": 1, "offset": 0, "region": "u"},
+    )
     invariant(
-        crossmap.coordinate_to_noncoding, 71,
-        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region": ""})
+        crossmap.coordinate_to_noncoding,
+        71,
+        crossmap.noncoding_to_coordinate,
+        {"position": 1, "offset": 0, "region": ""},
+    )
 
     # Boundary between downstream and transcript.
     invariant(
-        crossmap.coordinate_to_noncoding, 5,
-        crossmap.noncoding_to_coordinate, {"position": 22, "offset": 0, "region": ""})
+        crossmap.coordinate_to_noncoding,
+        5,
+        crossmap.noncoding_to_coordinate,
+        {"position": 22, "offset": 0, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_noncoding, 4,
-        crossmap.noncoding_to_coordinate, {"position": 1, "offset": 0, "region": "d"})
+        crossmap.coordinate_to_noncoding,
+        4,
+        crossmap.noncoding_to_coordinate,
+        {"position": 1, "offset": 0, "region": "d"},
+    )
 
 
 def test_NonCoding_degenerate():
@@ -64,19 +96,23 @@ def test_NonCoding_degenerate():
 
     # Boundary between upstream and transcript.
     degenerate_equal(
-        crossmap.noncoding_to_coordinate, 4,
+        crossmap.noncoding_to_coordinate,
+        4,
         [
-            {"position": 1, "offset": 0, "region":"u"},
-            {"position": 0, "offset": -1, "region":"u"}
-            ])
+            {"position": 1, "offset": 0, "region": "u"},
+            {"position": 0, "offset": -1, "region": "u"},
+        ],
+    )
 
     # Boundary between downstream and transcript.
     degenerate_equal(
-        crossmap.noncoding_to_coordinate, 72,
+        crossmap.noncoding_to_coordinate,
+        72,
         [
             {"position": 1, "offset": 0, "region": "d"},
-            {"position": 0, "offset": 1, "region": "d"}
-            ])
+            {"position": 0, "offset": 1, "region": "d"},
+        ],
+    )
 
 
 def test_NonCoding_inverted_degenerate():
@@ -85,54 +121,50 @@ def test_NonCoding_inverted_degenerate():
 
     # Boundary between upstream and transcript.
     degenerate_equal(
-        crossmap.noncoding_to_coordinate, 72,
-        [{"position": 1, "offset": 0, "region": "u"}])
+        crossmap.noncoding_to_coordinate,
+        72,
+        [{"position": 1, "offset": 0, "region": "u"}],
+    )
 
     # Boundary between downstream and transcript.
     degenerate_equal(
-        crossmap.noncoding_to_coordinate, 4,
-        [{"position": 1 , "offset": 0, "region": "d"}])
+        crossmap.noncoding_to_coordinate,
+        4,
+        [{"position": 1, "offset": 0, "region": "d"}],
+    )
+
 
-_exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
-_cds = (32, 43)
 def test_Coding():
     """Forward oriented coding transcript."""
     crossmap = Coding(_exons, _cds)
 
     # Boundary between 5' and CDS.
     invariant(
-        crossmap.coordinate_to_coding, 31,
+        crossmap.coordinate_to_coding,
+        31,
         crossmap.coding_to_coordinate,
-        {"position": 1,
-         "offset":0,
-         "region":"-"
-        }
+        {"position": 1, "offset": 0, "region": "-"},
     )
     invariant(
-        crossmap.coordinate_to_coding, 32,
+        crossmap.coordinate_to_coding,
+        32,
         crossmap.coding_to_coordinate,
-        {"position": 1,
-         "offset":0,
-         "region":""
-        }
-        )
+        {"position": 1, "offset": 0, "region": ""},
+    )
 
     # Boundary between CDS and 3'.
     invariant(
-        crossmap.coordinate_to_coding, 42,
+        crossmap.coordinate_to_coding,
+        42,
         crossmap.coding_to_coordinate,
-        {"position": 6,
-         "offset":0,
-         "region":""
-        })
+        {"position": 6, "offset": 0, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 43,
+        crossmap.coordinate_to_coding,
+        43,
         crossmap.coding_to_coordinate,
-        {"position": 1,
-         "offset":0,
-         "region":"*"
-        }
-        )
+        {"position": 1, "offset": 0, "region": "*"},
+    )
 
 
 def test_Coding_inverted():
@@ -141,42 +173,30 @@ def test_Coding_inverted():
 
     # Boundary between 5' and CDS.
     invariant(
-        crossmap.coordinate_to_coding, 43,
+        crossmap.coordinate_to_coding,
+        43,
         crossmap.coding_to_coordinate,
-        {
-            "position": 1,
-            "offset": 0,
-            "region": "-"
-        }
+        {"position": 1, "offset": 0, "region": "-"},
     )
     invariant(
-        crossmap.coordinate_to_coding, 42,
+        crossmap.coordinate_to_coding,
+        42,
         crossmap.coding_to_coordinate,
-        {
-            "position": 1,
-            "offset": 0,
-            "region": ""
-        }
-        )
+        {"position": 1, "offset": 0, "region": ""},
+    )
 
     # Boundary between CDS and 3'.
     invariant(
-        crossmap.coordinate_to_coding, 32,
+        crossmap.coordinate_to_coding,
+        32,
         crossmap.coding_to_coordinate,
-        {
-            "position": 6,
-            "offset": 0,
-            "region": ""
-        }
-        )
+        {"position": 6, "offset": 0, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 31,
+        crossmap.coordinate_to_coding,
+        31,
         crossmap.coding_to_coordinate,
-        {
-            "position": 1,
-            "offset": 0,
-            "region": "*"
-        }
+        {"position": 1, "offset": 0, "region": "*"},
     )
 
 
@@ -186,23 +206,31 @@ def test_Coding_regions():
 
     # Upstream odd length intron between two regions.
     invariant(
-        crossmap.coordinate_to_coding, 25,
+        crossmap.coordinate_to_coding,
+        25,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 5, 'region': '-'})
+        {"position": 1, "offset": 5, "region": "-"},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 26,
+        crossmap.coordinate_to_coding,
+        26,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': -4, 'region': ''})
+        {"position": 1, "offset": -4, "region": ""},
+    )
 
     # Downstream odd length intron between two regions.
     invariant(
-        crossmap.coordinate_to_coding, 44,
+        crossmap.coordinate_to_coding,
+        44,
         crossmap.coding_to_coordinate,
-        {'position': 10, 'offset': 5, 'region': ''})
+        {"position": 10, "offset": 5, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 45,
+        crossmap.coordinate_to_coding,
+        45,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': -4, 'region': '*'})
+        {"position": 1, "offset": -4, "region": "*"},
+    )
 
 
 def test_Coding_regions_inverted():
@@ -211,23 +239,31 @@ def test_Coding_regions_inverted():
 
     # Upstream odd length intron between two regions.
     invariant(
-        crossmap.coordinate_to_coding, 44,
+        crossmap.coordinate_to_coding,
+        44,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 5, 'region': '-'})
+        {"position": 1, "offset": 5, "region": "-"},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 43,
+        crossmap.coordinate_to_coding,
+        43,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': -4, 'region': ''})
+        {"position": 1, "offset": -4, "region": ""},
+    )
 
     # Downstream odd length intron between two regions.
     invariant(
-        crossmap.coordinate_to_coding, 25,
+        crossmap.coordinate_to_coding,
+        25,
         crossmap.coding_to_coordinate,
-        {'position': 10, 'offset': 5, 'region': ''})
+        {"position": 10, "offset": 5, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 24,
+        crossmap.coordinate_to_coding,
+        24,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': -4, 'region': '*'})
+        {"position": 1, "offset": -4, "region": "*"},
+    )
 
 
 def test_Coding_no_utr5():
@@ -236,13 +272,17 @@ def test_Coding_no_utr5():
 
     # Direct transition from upstream to CDS.
     invariant(
-        crossmap.coordinate_to_coding, 9,
+        crossmap.coordinate_to_coding,
+        9,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': 'u'}) # serialize result : u1
+        {"position": 1, "offset": 0, "region": "u"},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 10,
+        crossmap.coordinate_to_coding,
+        10,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': ''}) # serialize result: 1
+        {"position": 1, "offset": 0, "region": ""},
+    )
 
 
 def test_Coding_no_utr5_inverted():
@@ -251,13 +291,17 @@ def test_Coding_no_utr5_inverted():
 
     # Direct transition from upstream to CDS.
     invariant(
-        crossmap.coordinate_to_coding, 20,
+        crossmap.coordinate_to_coding,
+        20,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': 'u'})
+        {"position": 1, "offset": 0, "region": "u"},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 19,
+        crossmap.coordinate_to_coding,
+        19,
         crossmap.coding_to_coordinate,
-        {'position': 2, 'offset': 0, 'region': '-'})
+        {"position": 2, "offset": 0, "region": "-"},
+    )
 
 
 def test_Coding_no_utr3():
@@ -265,15 +309,18 @@ def test_Coding_no_utr3():
     crossmap = Coding([(10, 20)], (15, 20))
 
     # Direct transition from CDS to downstream.
-    #TODO:
     invariant(
-        crossmap.coordinate_to_coding, 19,
+        crossmap.coordinate_to_coding,
+        19,
         crossmap.coding_to_coordinate,
-        {'position': 9, 'offset': 0, 'region': '*'})
+        {"position": 9, "offset": 0, "region": "*"},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 20,
+        crossmap.coordinate_to_coding,
+        20,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': 'd'})
+        {"position": 1, "offset": 0, "region": "d"},
+    )
 
 
 def test_Coding_no_utr3_inverted():
@@ -282,13 +329,17 @@ def test_Coding_no_utr3_inverted():
 
     # Direct transition from CDS to downstream.
     invariant(
-        crossmap.coordinate_to_coding, 10,
+        crossmap.coordinate_to_coding,
+        10,
         crossmap.coding_to_coordinate,
-        {'position': 5, 'offset': 0, 'region': ''})
+        {"position": 5, "offset": 0, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 9,
+        crossmap.coordinate_to_coding,
+        9,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': 'd'})
+        {"position": 1, "offset": 0, "region": "d"},
+    )
 
 
 def test_Coding_small_utr5():
@@ -297,18 +348,23 @@ def test_Coding_small_utr5():
 
     # Transition from upstream to 5' UTR to CDS.
     invariant(
-        crossmap.coordinate_to_coding, 9,
+        crossmap.coordinate_to_coding,
+        9,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': 'u'})
+        {"position": 1, "offset": 0, "region": "u"},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 10,
+        crossmap.coordinate_to_coding,
+        10,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': '-'}
+        {"position": 1, "offset": 0, "region": "-"},
     )
     invariant(
-        crossmap.coordinate_to_coding, 11,
+        crossmap.coordinate_to_coding,
+        11,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': ''})
+        {"position": 1, "offset": 0, "region": ""},
+    )
 
 
 def test_Coding_small_utr5_inverted():
@@ -317,17 +373,23 @@ def test_Coding_small_utr5_inverted():
 
     # Transition from upstream to 5' UTR to CDS.
     invariant(
-        crossmap.coordinate_to_coding, 20,
-        crossmap.coding_to_coordinate,# (-1, -1, -1, -1)
-        {'position': 1, 'offset': 0, 'region': 'u'})
+        crossmap.coordinate_to_coding,
+        20,
+        crossmap.coding_to_coordinate,
+        {"position": 1, "offset": 0, "region": "u"},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 19,
-        crossmap.coding_to_coordinate, #(-1, 0, -1, 0))
-        {'position': 1, 'offset': 0, 'region': '-'})
+        crossmap.coordinate_to_coding,
+        19,
+        crossmap.coding_to_coordinate,
+        {"position": 1, "offset": 0, "region": "-"},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 18,
+        crossmap.coordinate_to_coding,
+        18,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': ''})
+        {"position": 1, "offset": 0, "region": ""},
+    )
 
 
 def test_Coding_small_utr3():
@@ -336,17 +398,23 @@ def test_Coding_small_utr3():
 
     # Transition from CDS to 3' UTR to downstream.
     invariant(
-        crossmap.coordinate_to_coding, 18,
+        crossmap.coordinate_to_coding,
+        18,
         crossmap.coding_to_coordinate,
-        {'position': 4, 'offset': 0, 'region': ''})
+        {"position": 4, "offset": 0, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 19,
-        crossmap.coding_to_coordinate, #(1, 0, 1, 0)
-        {'position': 1, 'offset': 0, 'region': '*'})
+        crossmap.coordinate_to_coding,
+        19,
+        crossmap.coding_to_coordinate,
+        {"position": 1, "offset": 0, "region": "*"},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 20,
-        crossmap.coding_to_coordinate, #(1, 1, 1, 1))
-        {'position': 1, 'offset': 0, 'region': 'd'})
+        crossmap.coordinate_to_coding,
+        20,
+        crossmap.coding_to_coordinate,
+        {"position": 1, "offset": 0, "region": "d"},
+    )
 
 
 def test_Coding_small_utr3_inverted():
@@ -355,17 +423,23 @@ def test_Coding_small_utr3_inverted():
 
     # Transition from CDS to 3' UTR to downstream.
     invariant(
-        crossmap.coordinate_to_coding, 11,
+        crossmap.coordinate_to_coding,
+        11,
         crossmap.coding_to_coordinate,
-        {'position': 4, 'offset': 0, 'region': ''})
+        {"position": 4, "offset": 0, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 10,
+        crossmap.coordinate_to_coding,
+        10,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': '*'})
+        {"position": 1, "offset": 0, "region": "*"},
+    )
     invariant(
-        crossmap.coordinate_to_coding, 9,
+        crossmap.coordinate_to_coding,
+        9,
         crossmap.coding_to_coordinate,
-        {'position': 1, 'offset': 0, 'region': 'd'})
+        {"position": 1, "offset": 0, "region": "d"},
+    )
 
 
 def test_Coding_degenerate():
@@ -373,57 +447,45 @@ def test_Coding_degenerate():
     crossmap = Coding([(10, 20)], (11, 19))
 
     degenerate_equal(
-        crossmap.coding_to_coordinate, 9,
+        crossmap.coding_to_coordinate,
+        9,
         [
-            {'position': 1, 'offset': 0, 'region': 'u'},
-            {'position': 2, 'offset': 1, 'region': 'u'},
-            {'position': 0, 'offset': -1, 'region': 'u'},
-            {'position': 1, 'offset': -1, 'region': '-'},
-            {'position': 2, 'offset': 0, 'region': '-'},
-            {'position': 1, 'offset': -2, 'region': ''},
-        ])
+            {"position": 1, "offset": 0, "region": "u"},
+            {"position": 2, "offset": 1, "region": "u"},
+            {"position": 0, "offset": -1, "region": "u"},
+        ],
+    )
     degenerate_equal(
-        crossmap.coding_to_coordinate, 20,
+        crossmap.coding_to_coordinate,
+        20,
         [
-            {'position': 1, 'offset': 0, 'region': 'd'},
-            {'position': 8, 'offset': -7, 'region': 'd'},
-            {'position': 0, 'offset': -1, 'region': 'd'},
-            {'position': 2, 'offset': 0, 'region': '*'},
-            {'position': 1, 'offset': 1, 'region': '*'},
-            {'position': 8, 'offset': 2, 'region': ''},
-        ]
+            {"position": 1, "offset": 0, "region": "d"},
+            {"position": 8, "offset": -7, "region": "d"},
+            {"position": 0, "offset": -1, "region": "d"},
+        ],
     )
 
 
-#TODO: Add tests for silently degenerate,
-#   position value <= 0
-#   offset value > intron length
-
-
 def test_Coding_inverted_degenerate():
     """Degenerate upstream and downstream positions are silently corrected."""
     crossmap = Coding([(10, 20)], (11, 19), True)
 
     degenerate_equal(
-        crossmap.coding_to_coordinate, 20,
+        crossmap.coding_to_coordinate,
+        20,
         [
-            {'position': 1, 'offset': 0, 'region': 'u'},
-            {'position': 2, 'offset': 1, 'region': 'u'},
-            {'position': 0, 'offset': -1, 'region': 'u'},
-            {'position': 1, 'offset': -2, 'region': ''},
-            {'position': 1, 'offset': -1, 'region': '-'},
-            {'position': 2, 'offset': 0, 'region': '-'}
-        ]
+            {"position": 1, "offset": 0, "region": "u"},
+            {"position": 2, "offset": 1, "region": "u"},
+            {"position": 0, "offset": -1, "region": "u"},
+        ],
     )
     degenerate_equal(
-        crossmap.coding_to_coordinate, 9,
+        crossmap.coding_to_coordinate,
+        9,
         [
-            {'position': 1, 'offset': 0, 'region': 'd'},
-            {'position': 2, 'offset': -1, 'region': 'd'},
-            {'position': 1, 'offset': 1, 'region': '*'},
-            {'position': 1, 'offset': 1, 'region': '*'},
-            {'position': 10, 'offset': 0, 'region': ''},
-        ]
+            {"position": 1, "offset": 0, "region": "d"},
+            {"position": 2, "offset": -1, "region": "d"},
+        ],
     )
 
 
@@ -431,37 +493,50 @@ def test_Coding_degenerate_return():
     """Degenerate upstream and downstream positions may be returned."""
     crossmap = Coding([(10, 20)], (11, 19))
 
-    for i in range(0, 30):
-        print(i, crossmap.coordinate_to_coding(i), crossmap.coordinate_to_coding(i, True))
-
-    assert crossmap.coordinate_to_coding(9, True) == {'position': 2, 'offset': 0, 'region': '-'}
-    assert crossmap.coordinate_to_coding(20, True) == {'position': 2, 'offset': 0, 'region': '*'}
+    assert crossmap.coordinate_to_coding(9, True) == {
+        "position": 2,
+        "offset": 0,
+        "region": "-",
+    }
+    assert crossmap.coordinate_to_coding(20, True) == {
+        "position": 2,
+        "offset": 0,
+        "region": "*",
+    }
 
 
 def test_Coding_inverted_degenerate_return():
     """Degenerate upstream and downstream positions may be returned."""
     crossmap = Coding([(10, 20)], (11, 19), True)
     for i in range(0, 30):
-        print(i, crossmap.coordinate_to_coding(i), crossmap.coordinate_to_coding(i, True))
+        print(
+            i, crossmap.coordinate_to_coding(i), crossmap.coordinate_to_coding(i, True)
+        )
 
-    assert crossmap.coordinate_to_coding(20, True) == {'position': 2, 'offset': 0, 'region': '-'}
-    assert crossmap.coordinate_to_coding(9, True) == {'position': 2, 'offset': 0, 'region': '*'}
+    assert crossmap.coordinate_to_coding(20, True) == {
+        "position": 2,
+        "offset": 0,
+        "region": "-",
+    }
+    assert crossmap.coordinate_to_coding(9, True) == {
+        "position": 2,
+        "offset": 0,
+        "region": "*",
+    }
 
 
 def test_Coding_degenerate_no_return():
     """Degenerate internal positions do not exist."""
     crossmap = Coding([(10, 20), (30, 40)], (10, 40))
 
-    assert (crossmap.coordinate_to_coding(25) ==
-            crossmap.coordinate_to_coding(25, True))
+    assert crossmap.coordinate_to_coding(25) == crossmap.coordinate_to_coding(25, True)
 
 
 def test_Coding_inverted_degenerate_no_return():
     """Degenerate internal positions do not exist."""
     crossmap = Coding([(10, 20), (30, 40)], (10, 40), True)
 
-    assert (crossmap.coordinate_to_coding(25) ==
-            crossmap.coordinate_to_coding(25, True))
+    assert crossmap.coordinate_to_coding(25) == crossmap.coordinate_to_coding(25, True)
 
 
 def test_Coding_no_utr_degenerate():
@@ -469,45 +544,45 @@ def test_Coding_no_utr_degenerate():
     crossmap = Coding([(10, 11)], (10, 11))
 
     degenerate_equal(
-        crossmap.coding_to_coordinate, 9,
+        crossmap.coding_to_coordinate,
+        9,
         [
-            {'position': 1, 'offset': 0, 'region': '-'},
-            {'position': 1, 'offset': 0, 'region': 'u'},
-            {'position': 1, 'offset': -1, 'region': ''},
-        ]
+            {"position": 2, "offset": 1, "region": "u"},
+            {"position": 1, "offset": 0, "region": "u"},
+        ],
     )
     degenerate_equal(
-        crossmap.coding_to_coordinate, 11,
+        crossmap.coding_to_coordinate,
+        11,
         [
-            {'position': 1, 'offset': 0, 'region': '*'},
-            {'position': 1, 'offset': 0, 'region': 'd'},
-            {'position': 1, 'offset': 1, 'region': ''}
-        ]
+            {"position": 1, "offset": 0, "region": "d"},
+            {"position": 2, "offset": -1, "region": "d"},
+        ],
     )
 
+
 def test_Coding_inverted_no_utr_degenerate():
     """UTRs may be missing."""
     crossmap = Coding([(10, 11)], (10, 11), True)
 
-        # [(1, -1, 0, -1), (-1, 0, -1, -1), (1, -2, 1, -1)])
     degenerate_equal(
-        crossmap.coding_to_coordinate, 11,
+        crossmap.coding_to_coordinate,
+        11,
         [
-            {'position': 1, 'offset': 0, 'region': 'u'},
-            {'position': 2, 'offset': 1, 'region': 'u'},
-            {'position': 1, 'offset': 0, 'region': '-'},
-            {'position': 1, 'offset': 0, 'region': '*'},
-        ]
-)
+            {"position": 1, "offset": 0, "region": "u"},
+            {"position": 2, "offset": 1, "region": "u"},
+        ],
+    )
     degenerate_equal(
-        crossmap.coding_to_coordinate, 9,
+        crossmap.coding_to_coordinate,
+        9,
         [
-            {'position': 1, 'offset': 0, 'region': 'd'},
-            {'position': 1, 'offset': 0, 'region': '*'},
-            {'position': 1, 'offset': -1, 'region': ''},
-        ]
+            {"position": 1, "offset": 0, "region": "d"},
+            {"position": 2, "offset": -1, "region": "d"},
+        ],
     )
 
+
 def test_Coding_no_utr_degenerate_return():
     """UTRs may be missing."""
     crossmap = Coding([(10, 11)], (10, 11))
@@ -515,50 +590,86 @@ def test_Coding_no_utr_degenerate_return():
     print(crossmap.coordinate_to_coding(11), crossmap.coordinate_to_coding(11, True))
     print(crossmap.coordinate_to_coding(12), crossmap.coordinate_to_coding(12, True))
 
-    assert crossmap.coordinate_to_coding(8, True) == {'position': 2, 'offset': 0, 'region': '-'}#(-2, 0, -1, -2)
-    assert crossmap.coordinate_to_coding(9, True) == {'position': 1, 'offset': 0, 'region': '-'}#(-1, 0, -1, -1)
-    assert crossmap.coordinate_to_coding(11, True) == {'position': 1, 'offset': 0, 'region': '*'}#(1, 0, 1, 1)
-    assert crossmap.coordinate_to_coding(12, True) == {'position': 2, 'offset': 0, 'region': '*'}#(2, 0, 1, 2)
+    assert crossmap.coordinate_to_coding(8, True) == {
+        "position": 2,
+        "offset": 0,
+        "region": "-",
+    }
+    assert crossmap.coordinate_to_coding(9, True) == {
+        "position": 1,
+        "offset": 0,
+        "region": "-",
+    }
+    assert crossmap.coordinate_to_coding(11, True) == {
+        "position": 1,
+        "offset": 0,
+        "region": "*",
+    }
+    assert crossmap.coordinate_to_coding(12, True) == {
+        "position": 2,
+        "offset": 0,
+        "region": "*",
+    }
 
 
 def test_Coding_inverted_no_utr_degenerate_return():
     """UTRs may be missing."""
     crossmap = Coding([(10, 11)], (10, 11), True)
 
-    assert crossmap.coordinate_to_coding(11, True) == (-1, 0, -1, -1)
-    assert crossmap.coordinate_to_coding(9, True) == (1, 0, 1, 1)
+    assert crossmap.coordinate_to_coding(11, True) == {
+        "position": 3,
+        "offset": 0,
+        "region": "-",
+    }
+    assert crossmap.coordinate_to_coding(9, True) == {
+        "position": 1,
+        "offset": 0,
+        "region": "*",
+    }
 
 
 def test_Coding_protein():
     """Protein positions."""
     crossmap = Coding(_exons, _cds)
 
-    # Boundary between 5' UTR and CDS.
+    # Boundary between 5' UTR and CDS
     invariant(
-        crossmap.coordinate_to_protein, 31,
+        crossmap.coordinate_to_protein,
+        31,
         crossmap.protein_to_coordinate,
-        {'position': 1, "position_in_codon": 1, 'offset': 0, 'region': '-'})
+        {"position": 1, "position_in_codon": 1, "offset": 0, "region": "-"},
+    )
     invariant(
-        crossmap.coordinate_to_protein, 32,
+        crossmap.coordinate_to_protein,
+        32,
         crossmap.protein_to_coordinate,
-        {'position': 1, "position_in_codon": 1, 'offset': 0, 'region': ''})
+        {"position": 1, "position_in_codon": 1, "offset": 0, "region": ""},
+    )
 
     # Intron boundary.
     invariant(
-        crossmap.coordinate_to_protein, 34,
+        crossmap.coordinate_to_protein,
+        34,
         crossmap.protein_to_coordinate,
-        {'position': 1, "position_in_codon": 3, 'offset': 0, 'region': ''})
+        {"position": 1, "position_in_codon": 3, "offset": 0, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_protein, 35,
+        crossmap.coordinate_to_protein,
+        35,
         crossmap.protein_to_coordinate,
-        {'position': 1, "position_in_codon": 3, 'offset': 1, 'region': ''})
+        {"position": 1, "position_in_codon": 3, "offset": 1, "region": ""},
+    )
 
     # Boundary between CDS and 3' UTR.
     invariant(
-        crossmap.coordinate_to_protein, 42,
+        crossmap.coordinate_to_protein,
+        42,
         crossmap.protein_to_coordinate,
-        {'position': 2, "position_in_codon": 3, 'offset': 0, 'region': ''})
+        {"position": 2, "position_in_codon": 3, "offset": 0, "region": ""},
+    )
     invariant(
-        crossmap.coordinate_to_protein, 43,
+        crossmap.coordinate_to_protein,
+        43,
         crossmap.protein_to_coordinate,
-        {'position': 1, "position_in_codon": 1, 'offset': 0, 'region': '*'})
+        {"position": 1, "position_in_codon": 1, "offset": 0, "region": "*"},
+    )

From fccc27555324864800126ea59c7b178ada24b68c Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 11 Mar 2026 08:53:11 +0100
Subject: [PATCH 051/127] Add surpport for degenerate position model as input

---
 mutalyzer_crossmapper/crossmapper.py | 55 +++++++++++++++++++---------
 tests/test_crossmapper.py            | 13 +++----
 2 files changed, 44 insertions(+), 24 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 5bc9f5c..65b07d9 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -68,18 +68,20 @@ def __init__(self, locations, cds, inverted=False):
         NonCoding.__init__(self, locations, inverted)
 
         b0 = self._noncoding.to_position(cds[0])
-        b1 = self._noncoding.to_position(cds[1])
+        b1 = self._noncoding.to_position(cds[1]-1)
         e0 = self._noncoding.to_position(locations[0][0])
         e1 = self._noncoding.to_position(locations[-1][1]-1)
 
         if self._inverted:
-            self._coding = (b1["position"] + b1["offset"] + 1, b0["position"] + b0["offset"] + 1)
+            self._coding = (b1["position"] + b1["offset"], b0["position"] + b0["offset"] + 1)
             self._cds_len = abs((b0["position"] + b0["offset"]) - (b1["position"] + b1["offset"]))
-            self._exons_end = e0["position"]
+            self._exons_end = e1["position"]
+            self._exons_start = e0["position"]
         else:
-            self._coding = (b0["position"] + b0["offset"], b1["position"] + b1["offset"])
+            self._coding = (b0["position"] + b0["offset"], b1["position"] + b1["offset"] +1)
             self._cds_len = abs((b1["position"] + b1["offset"]) - (b0["position"] + b0["offset"]))
             self._exons_end = e1["position"]
+            self._exons_start = e0["position"]
 
     def _coordinate_to_coding(self, coordinate):
         """Convert a coordinate to a coding position (c./r.).
@@ -89,7 +91,6 @@ def _coordinate_to_coding(self, coordinate):
         :returns dict: Coding position model (c./r.).
         """
         noncoding_pos_m = self._noncoding.to_position(coordinate)
-
         location = noncoding_pos_m["position"]
         if noncoding_pos_m["region"] == "":
             if location < self._coding[0]:
@@ -124,10 +125,16 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
         pos_m = self._coordinate_to_coding(coordinate)
         if degenerate:
             if pos_m["region"] == "u":
-                pos_m["position"] = pos_m["position"] + self._coding[0]
+                if self._inverted:
+                    pos_m["position"] = pos_m["position"] + self._exons_start - self._coding[1] + 1
+                else:
+                    pos_m["position"] = pos_m["position"] + self._coding[0]
                 pos_m["region"] = "-"
             if pos_m["region"] == "d":
-                pos_m["position"] = pos_m["position"] + self._exons_end - self._coding[1] + 1
+                if self._inverted:
+                    pos_m["position"] = pos_m["position"] + self._coding[0]
+                else:
+                    pos_m["position"] = pos_m["position"] + self._exons_end - self._coding[1] + 1
                 pos_m["region"] = "*"
         return pos_m
 
@@ -159,17 +166,31 @@ def coding_to_coordinate(self, pos_m):
             }
         # add checks for degenerate results?
         elif region == "-":
-            noncoding_pos_m = {
-                "position": self._coding[0] - pos_m["position"],
-                "offset": pos_m["offset"],
-                "region": ""
-            }
+            if pos_m["position"] > self._coding[0]: #degenerate result
+                noncoding_pos_m = {
+                    "position": pos_m["position"] - self._coding[0],
+                    "offset": pos_m["offset"],
+                    "region": "u"
+                }
+            else:
+                noncoding_pos_m = {
+                    "position": self._coding[0] - pos_m["position"],
+                    "offset": pos_m["offset"],
+                    "region": ""
+                }
         else: # *
-            noncoding_pos_m = {
-                "position": self._coding[1] + pos_m["position"] - 1,
-                "offset": pos_m["offset"],
-                "region": ""
-            }
+            if pos_m["position"] > self._coding[1]:
+                noncoding_pos_m = {
+                    "position": pos_m["position"] - self._coding[1],
+                    "offset": pos_m["offset"],
+                    "region": "d"
+                }
+            else:
+                noncoding_pos_m = {
+                    "position": self._coding[1] + pos_m["position"] - 1,
+                    "offset": pos_m["offset"],
+                    "region": ""
+                }
         return self._noncoding.to_coordinate(noncoding_pos_m)
 
 
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index dbaf87b..e2cccbe 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -300,7 +300,7 @@ def test_Coding_no_utr5_inverted():
         crossmap.coordinate_to_coding,
         19,
         crossmap.coding_to_coordinate,
-        {"position": 2, "offset": 0, "region": "-"},
+        {"position": 1 , "offset": 0, "region": ""},
     )
 
 
@@ -313,7 +313,7 @@ def test_Coding_no_utr3():
         crossmap.coordinate_to_coding,
         19,
         crossmap.coding_to_coordinate,
-        {"position": 9, "offset": 0, "region": "*"},
+        {"position": 5, "offset": 0, "region": ""},
     )
     invariant(
         crossmap.coordinate_to_coding,
@@ -508,10 +508,7 @@ def test_Coding_degenerate_return():
 def test_Coding_inverted_degenerate_return():
     """Degenerate upstream and downstream positions may be returned."""
     crossmap = Coding([(10, 20)], (11, 19), True)
-    for i in range(0, 30):
-        print(
-            i, crossmap.coordinate_to_coding(i), crossmap.coordinate_to_coding(i, True)
-        )
+
 
     assert crossmap.coordinate_to_coding(20, True) == {
         "position": 2,
@@ -571,6 +568,8 @@ def test_Coding_inverted_no_utr_degenerate():
         [
             {"position": 1, "offset": 0, "region": "u"},
             {"position": 2, "offset": 1, "region": "u"},
+            {"position": 1, "offset": 0, "region": "-"},
+
         ],
     )
     degenerate_equal(
@@ -617,7 +616,7 @@ def test_Coding_inverted_no_utr_degenerate_return():
     crossmap = Coding([(10, 11)], (10, 11), True)
 
     assert crossmap.coordinate_to_coding(11, True) == {
-        "position": 3,
+        "position": 1,
         "offset": 0,
         "region": "-",
     }

From 00e98bdc7df4643ac3eef909555e5338f8edf7b8 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 11 Mar 2026 09:17:46 +0100
Subject: [PATCH 052/127] Add degenerate tests

---
 tests/test_crossmapper.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index e2cccbe..788863b 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -477,6 +477,7 @@ def test_Coding_inverted_degenerate():
             {"position": 1, "offset": 0, "region": "u"},
             {"position": 2, "offset": 1, "region": "u"},
             {"position": 0, "offset": -1, "region": "u"},
+            {"position": 2, "offset": 0, "region": "-"},
         ],
     )
     degenerate_equal(
@@ -485,6 +486,7 @@ def test_Coding_inverted_degenerate():
         [
             {"position": 1, "offset": 0, "region": "d"},
             {"position": 2, "offset": -1, "region": "d"},
+            {"position": 2, "offset": 0, "region": "*"},
         ],
     )
 
@@ -546,6 +548,7 @@ def test_Coding_no_utr_degenerate():
         [
             {"position": 2, "offset": 1, "region": "u"},
             {"position": 1, "offset": 0, "region": "u"},
+            {"position": 1, "offset": 0, "region": "-"},
         ],
     )
     degenerate_equal(
@@ -554,6 +557,7 @@ def test_Coding_no_utr_degenerate():
         [
             {"position": 1, "offset": 0, "region": "d"},
             {"position": 2, "offset": -1, "region": "d"},
+            {"position": 1, "offset": 0, "region": "*"},
         ],
     )
 
@@ -578,6 +582,8 @@ def test_Coding_inverted_no_utr_degenerate():
         [
             {"position": 1, "offset": 0, "region": "d"},
             {"position": 2, "offset": -1, "region": "d"},
+            {"position": 1, "offset": 0, "region": "*"},
+            {"position": 1, "offset": 1, "region": ""},
         ],
     )
 
@@ -586,9 +592,6 @@ def test_Coding_no_utr_degenerate_return():
     """UTRs may be missing."""
     crossmap = Coding([(10, 11)], (10, 11))
 
-    print(crossmap.coordinate_to_coding(11), crossmap.coordinate_to_coding(11, True))
-    print(crossmap.coordinate_to_coding(12), crossmap.coordinate_to_coding(12, True))
-
     assert crossmap.coordinate_to_coding(8, True) == {
         "position": 2,
         "offset": 0,

From e281d6423fc2b62f71b7a3ff55d961bb96417fb0 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 11 Mar 2026 09:51:59 +0100
Subject: [PATCH 053/127] Cleanup

---
 mutalyzer_crossmapper/crossmapper.py | 31 +++++++++++++++-------------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 65b07d9..ff2369a 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -146,49 +146,52 @@ def coding_to_coordinate(self, pos_m):
         :returns int: Coordinate.
         """
         region = pos_m["region"]
+        position = pos_m["position"]
+        offset = pos_m["offset"]
+
         if region == "u":
             noncoding_pos_m = {
-                "position": pos_m["position"] - pos_m["offset"],
+                "position": position - offset,
                 "offset": 0,
                 "region": "u"
             }
         elif region == "d":
             noncoding_pos_m = {
-                "position": pos_m["position"] + pos_m["offset"],
+                "position": position + offset,
                 "offset": 0,
                 "region": "d"
             }
         elif region == "":
             noncoding_pos_m = {
-                "position": pos_m["position"] + self._coding[0] -1,
-                "offset": pos_m["offset"],
+                "position": position + self._coding[0] -1,
+                "offset": offset,
                 "region": ""
             }
         # add checks for degenerate results?
         elif region == "-":
-            if pos_m["position"] > self._coding[0]: #degenerate result
+            if position > self._coding[0]:
                 noncoding_pos_m = {
-                    "position": pos_m["position"] - self._coding[0],
-                    "offset": pos_m["offset"],
+                    "position": position - self._coding[0],
+                    "offset": offset,
                     "region": "u"
                 }
             else:
                 noncoding_pos_m = {
-                    "position": self._coding[0] - pos_m["position"],
-                    "offset": pos_m["offset"],
+                    "position": self._coding[0] - position,
+                    "offset": offset,
                     "region": ""
                 }
         else: # *
-            if pos_m["position"] > self._coding[1]:
+            if position > self._coding[1]:
                 noncoding_pos_m = {
-                    "position": pos_m["position"] - self._coding[1],
-                    "offset": pos_m["offset"],
+                    "position": position - self._coding[1],
+                    "offset": offset,
                     "region": "d"
                 }
             else:
                 noncoding_pos_m = {
-                    "position": self._coding[1] + pos_m["position"] - 1,
-                    "offset": pos_m["offset"],
+                    "position": self._coding[1] + position - 1,
+                    "offset": offset,
                     "region": ""
                 }
         return self._noncoding.to_coordinate(noncoding_pos_m)

From 925cb568c0af9e44cd59a9bccb9eed145432498e Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 11 Mar 2026 09:54:13 +0100
Subject: [PATCH 054/127] Cleanup

---
 mutalyzer_crossmapper/crossmapper.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index ff2369a..c16fdf7 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -74,12 +74,12 @@ def __init__(self, locations, cds, inverted=False):
 
         if self._inverted:
             self._coding = (b1["position"] + b1["offset"], b0["position"] + b0["offset"] + 1)
-            self._cds_len = abs((b0["position"] + b0["offset"]) - (b1["position"] + b1["offset"]))
+            self._cds_len = (b0["position"] + b0["offset"]) - (b1["position"] + b1["offset"])
             self._exons_end = e1["position"]
             self._exons_start = e0["position"]
         else:
             self._coding = (b0["position"] + b0["offset"], b1["position"] + b1["offset"] +1)
-            self._cds_len = abs((b1["position"] + b1["offset"]) - (b0["position"] + b0["offset"]))
+            self._cds_len = (b1["position"] + b1["offset"]) - (b0["position"] + b0["offset"])
             self._exons_end = e1["position"]
             self._exons_start = e0["position"]
 
@@ -202,7 +202,7 @@ def coordinate_to_protein(self, coordinate):
 
         :arg int coordinate: Coordinate.
 
-        :returns tuple: Protein position (p.).
+        :returns dict: Protein position model(p.).
         """
         pos = self.coordinate_to_coding(coordinate)
 
@@ -216,20 +216,20 @@ def coordinate_to_protein(self, coordinate):
                 "position_in_codon": (pos["position"]+2) % 3 + 1,
                 **{k: v for k, v in pos.items() if k != "position"}}
 
-    def protein_to_coordinate(self, position):
+    def protein_to_coordinate(self, pos_m):
         """Convert a protein position (p.) to a coordinate.
 
-        :arg tuple position: Protein position (p.).
+        :arg dict position: Protein position model(p.).
 
         :returns int: Coordinate.
         """
-        if position["region"] in ["-", "*"]:
+        if pos_m["region"] in ["-", "*"]:
             return self.coding_to_coordinate(
-                {"position": 3 * position["position"] + position["position_in_codon"] - 3,
-                 "offset": position["offset"],
-                 "region": position["region"]})
+                {"position": 3 * pos_m["position"] + pos_m["position_in_codon"] - 3,
+                 "offset": pos_m["offset"],
+                 "region": pos_m["region"]})
 
         return self.coding_to_coordinate(
-                {"position": 3 * position["position"] + position["position_in_codon"] - 3,
-                 "offset": position["offset"],
-                 "region": position["region"]})
+                {"position": 3 * pos_m["position"] + pos_m["position_in_codon"] - 3,
+                 "offset": pos_m["offset"],
+                 "region": pos_m["region"]})

From 5f2bef7a142ebe0d1bad23dcd437d861719dd09f Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 11 Mar 2026 11:55:38 +0100
Subject: [PATCH 055/127] Local copy before checkout

---
 tests/helper.py           | 19 +++++++++++++++----
 tests/test_crossmapper.py |  6 ++++++
 2 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/tests/helper.py b/tests/helper.py
index a17b119..9e51367 100644
--- a/tests/helper.py
+++ b/tests/helper.py
@@ -2,8 +2,19 @@ def invariant(f, x, f_i, y):
     assert f(x) == y
     assert f_i(y) == x
 
-
 def degenerate_equal(f, coordinate, locations):
-    assert f(locations[0]) == coordinate
-    assert len(
-        set(map(f, locations))) == 1
+    results = [f(loc) for loc in locations]
+
+    # First condition: first maps correctly
+    assert results[0] == coordinate, (
+        f"\nFirst location: {locations[0]}"
+        f"\nExpected:       {coordinate}"
+        f"\nGot:            {results[0]}"
+    )
+
+    # Second condition: all map to same coordinate
+    assert len(set(results)) == 1, (
+        f"\nLocations: {locations}"
+        f"\nResults:   {results}"
+        f"\nExpected all to map to the same coordinate"
+    )
\ No newline at end of file
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 788863b..d22715b 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -29,6 +29,12 @@ def test_NonCoding():
     crossmap = NonCoding(_exons)
 
     # Boundary between upstream and transcript.
+    invariant(
+        crossmap.coordinate_to_noncoding,
+        3,
+        crossmap.noncoding_to_coordinate,
+        {"position": 2, "offset": 0, "region": "u"},
+    )
     invariant(
         crossmap.coordinate_to_noncoding,
         4,

From 55fe7979a8f353a2cdee9d7792adda36619a099c Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Wed, 11 Mar 2026 15:41:39 +0100
Subject: [PATCH 056/127] Update table for Genomic and NonCoding classes in
 document

---
 README.rst | 129 ++++++++++-------------------------------------------
 1 file changed, 24 insertions(+), 105 deletions(-)

diff --git a/README.rst b/README.rst
index afeb981..6559526 100644
--- a/README.rst
+++ b/README.rst
@@ -60,17 +60,17 @@ The ``Genomic`` class provides an interface for conversions between genomic posi
 Genomic Position Model
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-Genomic positions follow the HGVS ``g`` coordinate system. They are represented as dictionaries:
+Genomic positions follow the HGVS ``g`` coordinate system. They are represented as dictionaries. Below is an example of `g.1` in HGVS.
 
 .. code-block:: json
 
     {
-        "position": int
+        "position": 1
     }
 
 Where:
 
-- **position**: a positive integer
+- **position**: a positive integer(>0)
 
 Genomic Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -83,17 +83,6 @@ Genomic Position Conversion
     {"position": 1}
     >>> crossmap.genomic_to_coordinate({"position": 1})
     0
-Here is the mapping of coordinates to genomic positions:
-
-.. csv-table:: Coordinate to Genomic Position (0-4)
-   :header: "Coordinate", "Position"
-
-   0, 1
-   1, 2
-   2, 3
-   3, 4
-   4, 5
-   ...
 
 NonCoding Class
 ---------------
@@ -103,21 +92,21 @@ The ``NonCoding`` class provides conversions between noncoding positions and coo
 NonCoding Position Model
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-Noncoding positions follow the HGVS ``n`` coordinate system. They are represented as dictionaries:
+Noncoding positions follow the HGVS ``n`` coordinate system. They are represented as dictionaries. Below is an example of ``n.14+1`` in HGVS.
 
 .. code-block:: json
 
     {
-        "position": int,
-        "offset": int,
-        "region": str
+        "position": 10,
+        "offset": -5,
+        "region": ''
     }
 
 Where:
 
-- **position**: a positive integer
+- **position**: a positive integer (>0)
 - **offset**: an integer indicating the offset relative to the position (negative for upstream, positive for downstream)
-- **region**: a string describing the region type (``""`` for standard, ``"u"`` for upstream, ``"d"`` for downstream)
+- **region**: a string describing the region type (``''`` for standard, ``'u'`` for upstream, ``'d'`` for downstream)
 
 NonCoding Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -126,10 +115,10 @@ NonCoding Position Conversion
 
     >>> from mutalyzer_crossmapper import NonCoding
     >>> crossmap = NonCoding(_exons)
-    >>> crossmap.coordinate_to_noncoding(35)
-    {"position": 14, "offset": 1, "region": ""}
-    >>> crossmap.noncoding_to_coordinate({"position": 14, "offset": 1, "region": ""})
-    35
+    >>> crossmap.coordinate_to_noncoding(25)
+    {"position": 10, "offset": -5, "region": ""}
+    >>> crossmap.noncoding_to_coordinate({"position": 10, "offset": -5, "region": ''})
+    25
 
 Notes
 ~~~~~
@@ -140,88 +129,18 @@ Here is the mapping of coordinates to noncoding positions:
 
 .. csv-table::
    :class: table-scroll
-   :header: "Coordinate", "Position", "Offset", "Region"
+   :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
 
-   "0", "5","0", "u"
-   "1", "4","0", "u"
-   "2", "3","0", "u"
-   "3", "2","0", "u"
-   "4", "1","0", "u"
-   "5", "1","0", ""
-   "6", "2","0", ""
-   "7", "3","0", ""
-   "8", "3","1", ""
-   "9", "3","2", ""
-   "10", "3","3", ""
-   "11", "4","-3", ""
-   "12", "4","-2", ""
-   "13", "4","-1", ""
-   "14", "4","0", ""
-   "15", "5","0", ""
-   "16", "6","0", ""
-   "17", "7","0", ""
-   "18", "8","0", ""
-   "19", "9","0", ""
-   "20", "9","1", ""
-   "21", "9","2", ""
-   "22", "9","3", ""
-   "23", "9","4", ""
-   "24", "9","5", ""
-   "25", "10","-5", ""
-   "26", "10","-4", ""
-   "27", "10","-3", ""
-   "28", "10","-2", ""
-   "29", "10","-1", ""
-   "30", "10","0", ""
-   "31", "11","0", ""
-   "32", "12","0", ""
-   "33", "13","0", ""
-   "34", "14","0", ""
-   "35", "14","1", ""
-   "36", "14","2", ""
-   "37", "14","3", ""
-   "38", "15","-2", ""
-   "39", "15","-1", ""
-   "40", "15","0", ""
-   "41", "16","0", ""
-   "42", "17","0", ""
-   "43", "18","0", ""
-   "44", "18","1", ""
-   "45", "18","2", ""
-   "46", "18","3", ""
-   "47", "19","-3", ""
-   "48", "19","-2", ""
-   "49", "19","-1", ""
-   "50", "19","0", ""
-   "51", "20","0", ""
-   "52", "20","1", ""
-   "53", "20","2", ""
-   "54", "20","3", ""
-   "55", "20","4", ""
-   "56", "20","5", ""
-   "57", "20","6", ""
-   "58", "20","7", ""
-   "59", "20","8", ""
-   "60", "20","9", ""
-   "61", "21","-9", ""
-   "62", "21","-8", ""
-   "63", "21","-7", ""
-   "64", "21","-6", ""
-   "65", "21","-5", ""
-   "66", "21","-4", ""
-   "67", "21","-3", ""
-   "68", "21","-2", ""
-   "69", "21","-1", ""
-   "70", "21","0", ""
-   "71", "22","0", ""
-   "72", "1","0", "d"
-   "73", "2","0", "d"
-   "74", "3","0", "d"
-   "75", "4","0", "d"
-   "76", "5","0", "d"
-   "77", "6","0", "d"
-   "78", "7","0", "d"
-   "79", "8","0", "d"
+   "4", "1","0", "u", "n.u1"
+   "5", "1","0", "", "n.1"
+   ...
+   "24", "9","5", "", "n.9+5"
+   "25", "10","-5", "", "n.10-5"
+   ...
+   "71", "22","0", "", "n.22"
+   "72", "1","0", "d", "n.d1"
+   ...
+   "79", "8","0", "d", "n.d8"
 
 
 

From a2003b362a95c9834d3a8c004483bf0344c0d403 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Wed, 11 Mar 2026 15:52:12 +0100
Subject: [PATCH 057/127] Update table for Coding class in document

---
 README.rst | 89 ++++++------------------------------------------------
 1 file changed, 10 insertions(+), 79 deletions(-)

diff --git a/README.rst b/README.rst
index 6559526..ece04cf 100644
--- a/README.rst
+++ b/README.rst
@@ -133,13 +133,10 @@ Here is the mapping of coordinates to noncoding positions:
 
    "4", "1","0", "u", "n.u1"
    "5", "1","0", "", "n.1"
-   ...
    "24", "9","5", "", "n.9+5"
    "25", "10","-5", "", "n.10-5"
-   ...
    "71", "22","0", "", "n.22"
    "72", "1","0", "d", "n.d1"
-   ...
    "79", "8","0", "d", "n.d8"
 
 
@@ -152,14 +149,14 @@ The ``Coding`` class provides conversions between coding positions and coordinat
 Coding Position Model
 ~~~~~~~~~~~~~~~~~~~~
 
-Coding positions follow the HGVS ``c`` coordinate system. They are represented as dictionaries:
+Coding positions follow the HGVS ``c`` coordinate system. They are represented as dictionaries. Here is an example of ``c.*1+3``.
 
 .. code-block:: json
 
     {
-        "position": int,
-        "offset": int,
-        "region": str
+        "position": 1,
+        "offset": 3,
+        "region": '*'
     }
 
 Where:
@@ -175,10 +172,10 @@ Coding Position Conversion
 
     >>> from mutalyzer_crossmapper import Coding
     >>> crossmap = Coding(_exons, _cds)
-    >>> crossmap.coordinate_to_coding(31)
-    {"position": -1, "offset": 0, "region": '-'}
-    >>> crossmap.coding_to_coordinate({"position": -1, "offset": 0, "region": '-'})
-    31
+    >>> crossmap.coordinate_to_coding(46)
+    {"position": 1, "offset": 3, "region": '*'}
+    >>> crossmap.coding_to_coordinate({"position": 1, "offset": 3, "region": '*'})
+    46
 
 Notes
 ~~~~~
@@ -189,88 +186,22 @@ Here is the mapping of coordinates to coding positions:
 
 .. csv-table::
    :class: table-scroll
-   :header: "Coordinate", "Position", "Offset", "Region"
+   :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
 
-   "0", "5","0", "u"
-   "1", "4","0", "u"
-   "2", "3","0", "u"
-   "3", "2","0", "u"
    "4", "1","0", "u"
    "5", "11","0", '-'
-   "6", "10","0", '-'
-   "7", "9","0", '-'
-   "8", "9","1", '-'
-   "9", "9","2", '-'
-   "10", "9","3", '-'
-   "11", "8","-3", '-'
-   "12", "8","-2", '-'
-   "13", "8","-1", '-'
-   "14", "8","0", '-'
-   "15", "7","0", '-'
-   "16", "6","0", '-'
-   "17", "5","0", '-'
-   "18", "4","0", '-'
-   "19", "3","0", '-'
-   "20", "3","1", '-'
-   "21", "3","2", '-'
-   "22", "3","3", '-'
-   "23", "3","4", '-'
    "24", "3","5", '-'
    "25", "2","-5", '-'
-   "26", "2","-4", '-'
-   "27", "2","-3", '-'
-   "28", "2","-2", '-'
-   "29", "2","-1", '-'
-   "30", "2","0", '-'
    "31", "1","0", '-'
    "32", "1","0", ""
-   "33", "2","0", ""
-   "34", "3","0", ""
-   "35", "3","1", ""
-   "36", "3","2", ""
    "37", "3","3", ""
    "38", "4","-2", ""
-   "39", "4","-1", ""
-   "40", "4","0", ""
-   "41", "5","0", ""
-   "42", "6","0", ""
    "43", "1","0", '*'
-   "44", "1","1", '*'
-   "45", "1","2", '*'
-   "46", "1","3", '*'
-   "47", "2","-3", '*'
-   "48", "2","-2", '*'
-   "49", "2","-1", '*'
-   "50", "2","0", '*'
-   "51", "3","0", '*'
-   "52", "3","1", '*'
-   "53", "3","2", '*'
-   "54", "3","3", '*'
-   "55", "3","4", '*'
-   "56", "3","5", '*'
-   "57", "3","6", '*'
-   "58", "3","7", '*'
-   "59", "3","8", '*'
    "60", "3","9", '*'
    "61", "4","-9", '*'
-   "62", "4","-8", '*'
-   "63", "4","-7", '*'
-   "64", "4","-6", '*'
-   "65", "4","-5", '*'
-   "66", "4","-4", '*'
-   "67", "4","-3", '*'
-   "68", "4","-2", '*'
-   "69", "4","-1", '*'
-   "70", "4","0", '*'
    "71", "5","0", '*'
    "72", "1","0", "d"
-   "73", "2","0", "d"
-   "74", "3","0", "d"
-   "75", "4","0", "d"
-   "76", "5","0", "d"
-   "77", "6","0", "d"
-   "78", "7","0", "d"
-   "79", "8","0", "d"
+
 
 
 

From 4d9089a500e500e8a52c6194490ac72350c61051 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Wed, 11 Mar 2026 15:58:54 +0100
Subject: [PATCH 058/127] Add HGVS column in coding table

---
 README.rst | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/README.rst b/README.rst
index ece04cf..f316b9f 100644
--- a/README.rst
+++ b/README.rst
@@ -188,19 +188,19 @@ Here is the mapping of coordinates to coding positions:
    :class: table-scroll
    :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
 
-   "4", "1","0", "u"
-   "5", "11","0", '-'
-   "24", "3","5", '-'
-   "25", "2","-5", '-'
-   "31", "1","0", '-'
-   "32", "1","0", ""
-   "37", "3","3", ""
-   "38", "4","-2", ""
-   "43", "1","0", '*'
-   "60", "3","9", '*'
-   "61", "4","-9", '*'
-   "71", "5","0", '*'
-   "72", "1","0", "d"
+   "4", "1","0", "u", "c.u1"
+   "5", "11","0", '-', "c.-11"
+   "24", "3","5", '-', "c.-3+5"
+   "25", "2","-5", '-', "c.-2-5"
+   "31", "1","0", '-', "c.-1"
+   "32", "1","0", "", "c.1"
+   "37", "3","3", "", "c.3+3"
+   "38", "4","-2", "", "c.4-2"
+   "43", "1","0", '*', "c.*1"
+   "60", "3","9", '*', "c.*3+9"
+   "61", "4","-9", '*', "c.*4+9"
+   "71", "5","0", '*', "c.*5"
+   "79", "8","0", "d", "c.d8"
 
 
 

From 15428949bea49d2dcab35cefa27b0a20aa680a72 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Wed, 11 Mar 2026 16:06:51 +0100
Subject: [PATCH 059/127] Fix sytax

---
 README.rst | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/README.rst b/README.rst
index f316b9f..86ccdb0 100644
--- a/README.rst
+++ b/README.rst
@@ -116,7 +116,7 @@ NonCoding Position Conversion
     >>> from mutalyzer_crossmapper import NonCoding
     >>> crossmap = NonCoding(_exons)
     >>> crossmap.coordinate_to_noncoding(25)
-    {"position": 10, "offset": -5, "region": ""}
+    {"position": 10, "offset": -5, "region": ''}
     >>> crossmap.noncoding_to_coordinate({"position": 10, "offset": -5, "region": ''})
     25
 
@@ -131,13 +131,13 @@ Here is the mapping of coordinates to noncoding positions:
    :class: table-scroll
    :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
 
-   "4", "1","0", "u", "n.u1"
-   "5", "1","0", "", "n.1"
-   "24", "9","5", "", "n.9+5"
-   "25", "10","-5", "", "n.10-5"
-   "71", "22","0", "", "n.22"
-   "72", "1","0", "d", "n.d1"
-   "79", "8","0", "d", "n.d8"
+   "4", "1","0", "'u'", "n.u1"
+   "5", "1","0", "''", "n.1"
+   "24", "9","5", "''", "n.9+5"
+   "25", "10","-5", "''", "n.10-5"
+   "71", "22","0", "''", "n.22"
+   "72", "1","0", "'d'", "n.d1"
+   "79", "8","0", "'d'", "n.d8"
 
 
 
@@ -188,19 +188,19 @@ Here is the mapping of coordinates to coding positions:
    :class: table-scroll
    :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
 
-   "4", "1","0", "u", "c.u1"
+   "4", "1","0", "'u'", "c.u1"
    "5", "11","0", '-', "c.-11"
    "24", "3","5", '-', "c.-3+5"
    "25", "2","-5", '-', "c.-2-5"
    "31", "1","0", '-', "c.-1"
-   "32", "1","0", "", "c.1"
-   "37", "3","3", "", "c.3+3"
-   "38", "4","-2", "", "c.4-2"
+   "32", "1","0", "''", "c.1"
+   "37", "3","3", "''", "c.3+3"
+   "38", "4","-2", "''", "c.4-2"
    "43", "1","0", '*', "c.*1"
    "60", "3","9", '*', "c.*3+9"
    "61", "4","-9", '*', "c.*4+9"
    "71", "5","0", '*', "c.*5"
-   "79", "8","0", "d", "c.d8"
+   "79", "8","0", "'d'", "c.d8"
 
 
 

From 75a5cba52247e006eb42e013d1c66427bc8059de Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Wed, 11 Mar 2026 16:14:22 +0100
Subject: [PATCH 060/127] Update protein example in document

---
 README.rst | 24 +++++++++++-------------
 1 file changed, 11 insertions(+), 13 deletions(-)

diff --git a/README.rst b/README.rst
index 86ccdb0..b1749f1 100644
--- a/README.rst
+++ b/README.rst
@@ -64,9 +64,7 @@ Genomic positions follow the HGVS ``g`` coordinate system. They are represented
 
 .. code-block:: json
 
-    {
-        "position": 1
-    }
+    {"position": 1}
 
 Where:
 
@@ -211,15 +209,15 @@ Protein
 Protein Position Model
 ~~~~~~~~~~~~~~~~~~~~~~
 
-Protein positions follow the HGVS ``p`` coordinate system. They are represented as dictionaries:
+Protein positions follow the HGVS ``p`` coordinate system. They are represented as dictionaries. Here is an example of ``p.1`` in HGVS.
 
 .. code-block:: json
 
     {
-        "position": int,
-        "position_in_codon": int,
-        "offset": int,
-        "region": str
+        "position": 1,
+        "position_in_codon": 3,
+        "offset": 3,
+        "region": ''
     }
 
 Where:
@@ -227,7 +225,7 @@ Where:
 - **position**: the amino acid position (1-based)
 - **position_in_codon**: the codon nucleotide index (1, 2, or 3)
 - **offset**: an integer indicating offset relative to the codon
-- **region**: a string describing the region type (``""`` for standard positions)
+- **region**: a string describing the region type (``''`` for standard positions)
 
 Protein Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -236,10 +234,10 @@ Conversions between protein positions and coordinates:
 
 .. code-block:: python
 
-    >>> crossmap.coordinate_to_protein(41)
-    {"position": 2, "position_in_codon": 2, "offset": 1, "region": ""}
-    >>> crossmap.protein_to_coordinate({"position": 2, "position_in_codon": 2, "offset": 1, "region": ""})
-    41
+    >>> crossmap.coordinate_to_protein(37)
+    {"position": 1, "position_in_codon": 3, "offset": 3, "region": ""}
+    >>> crossmap.protein_to_coordinate({"position": 1, "position_in_codon": 3, "offset": 3, "region": ""})
+    37
 
 
 .. _numbering: http://varnomen.hgvs.org/bg-material/numbering/

From b0ed66feeceab9cf802f59d7960a5c4253f18690 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Thu, 12 Mar 2026 17:14:42 +0100
Subject: [PATCH 061/127] Add protein table in document

---
 README.rst | 25 +++++++++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/README.rst b/README.rst
index b1749f1..a31322f 100644
--- a/README.rst
+++ b/README.rst
@@ -97,7 +97,7 @@ Noncoding positions follow the HGVS ``n`` coordinate system. They are represente
     {
         "position": 10,
         "offset": -5,
-        "region": ''
+        "region": ""
     }
 
 Where:
@@ -217,7 +217,7 @@ Protein positions follow the HGVS ``p`` coordinate system. They are represented
         "position": 1,
         "position_in_codon": 3,
         "offset": 3,
-        "region": ''
+        "region": ""
     }
 
 Where:
@@ -240,5 +240,26 @@ Conversions between protein positions and coordinates:
     37
 
 
+Here is the mapping of coordinates to coding positions:
+
+.. csv-table::
+   :class: table-scroll
+   :header: "Coordinate", "Position", "position_in_codon", "Offset", "Region", "HGVS" 
+
+   "0", "4", "2", "0", "'u'", 
+   "4", "4", "2", "0", "'u'",
+   "5", "4", "2", "0", '-',
+   "6", "4", "3", "0", '-',
+   "7", "3", "1", "0", '-',
+   "31", "1", "3", "0", '-',
+   "32", "1", "1", "0", "''", "p.1"
+   "42", "2", "3", "0", "''", "p.2"
+   "43", "1", "1", "0", '*',
+   "44", "1", "1", "1", '*',
+   "79", "2", "2", "0", "'d'",
+
+
+
+
 .. _numbering: http://varnomen.hgvs.org/bg-material/numbering/
 .. _ReadTheDocs: https://mutalyzer-crossmapper.readthedocs.io

From 16e9a62261606689df9f3336d6f22bd3ed59d680 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Thu, 12 Mar 2026 17:15:33 +0100
Subject: [PATCH 062/127] Fix typo

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index a31322f..29f15d1 100644
--- a/README.rst
+++ b/README.rst
@@ -240,7 +240,7 @@ Conversions between protein positions and coordinates:
     37
 
 
-Here is the mapping of coordinates to coding positions:
+Here is the mapping of coordinates to protein positions:
 
 .. csv-table::
    :class: table-scroll

From d6c868d168ed855ed98eb755c69285a7b95ee2e1 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 13 Mar 2026 09:17:35 +0100
Subject: [PATCH 063/127] Add tests

---
 tests/test_crossmapper.py | 31 +++++++++++++++++++++++++++----
 1 file changed, 27 insertions(+), 4 deletions(-)

diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index d22715b..40546b8 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -107,6 +107,7 @@ def test_NonCoding_degenerate():
         [
             {"position": 1, "offset": 0, "region": "u"},
             {"position": 0, "offset": -1, "region": "u"},
+            {"position": 1, "offset": -1, "region": ""},
         ],
     )
 
@@ -117,6 +118,7 @@ def test_NonCoding_degenerate():
         [
             {"position": 1, "offset": 0, "region": "d"},
             {"position": 0, "offset": 1, "region": "d"},
+            {"position": 22, "offset": 1, "region": ""},
         ],
     )
 
@@ -129,14 +131,18 @@ def test_NonCoding_inverted_degenerate():
     degenerate_equal(
         crossmap.noncoding_to_coordinate,
         72,
-        [{"position": 1, "offset": 0, "region": "u"}],
+        [
+            {"position": 1, "offset": 0, "region": "u"},
+            {"position": 1, "offset": -1, "region": ""},],
     )
 
     # Boundary between downstream and transcript.
     degenerate_equal(
         crossmap.noncoding_to_coordinate,
         4,
-        [{"position": 1, "offset": 0, "region": "d"}],
+        [
+            {"position": 1, "offset": 0, "region": "d"},
+            {"position": 22, "offset": 1, "region": ""},],
     )
 
 
@@ -459,6 +465,8 @@ def test_Coding_degenerate():
             {"position": 1, "offset": 0, "region": "u"},
             {"position": 2, "offset": 1, "region": "u"},
             {"position": 0, "offset": -1, "region": "u"},
+            {"position": 1, "offset": -1, "region": "-"},
+            {"position": 1, "offset": -2, "region": ""},
         ],
     )
     degenerate_equal(
@@ -468,6 +476,9 @@ def test_Coding_degenerate():
             {"position": 1, "offset": 0, "region": "d"},
             {"position": 8, "offset": -7, "region": "d"},
             {"position": 0, "offset": -1, "region": "d"},
+            {"position": 8, "offset": 2, "region": ""},
+            {"position": 2, "offset": 0, "region": "*"},
+            {"position": 1, "offset": 1, "region": "*"},
         ],
     )
 
@@ -483,7 +494,10 @@ def test_Coding_inverted_degenerate():
             {"position": 1, "offset": 0, "region": "u"},
             {"position": 2, "offset": 1, "region": "u"},
             {"position": 0, "offset": -1, "region": "u"},
+            {"position": 1, "offset": -2, "region": ""},
+            {"position": 2, "offset": -3, "region": ""},
             {"position": 2, "offset": 0, "region": "-"},
+            {"position": 1, "offset": -1, "region": "-"},
         ],
     )
     degenerate_equal(
@@ -492,6 +506,8 @@ def test_Coding_inverted_degenerate():
         [
             {"position": 1, "offset": 0, "region": "d"},
             {"position": 2, "offset": -1, "region": "d"},
+            {"position": 8, "offset": 2, "region": ""},
+            {"position": 7, "offset": 3, "region": ""},
             {"position": 2, "offset": 0, "region": "*"},
         ],
     )
@@ -555,6 +571,9 @@ def test_Coding_no_utr_degenerate():
             {"position": 2, "offset": 1, "region": "u"},
             {"position": 1, "offset": 0, "region": "u"},
             {"position": 1, "offset": 0, "region": "-"},
+            {"position": 2, "offset": 1, "region": "-"},
+            {"position": 1, "offset": -1, "region": ""},
+            {"position": 2, "offset": -2, "region": ""},
         ],
     )
     degenerate_equal(
@@ -564,6 +583,9 @@ def test_Coding_no_utr_degenerate():
             {"position": 1, "offset": 0, "region": "d"},
             {"position": 2, "offset": -1, "region": "d"},
             {"position": 1, "offset": 0, "region": "*"},
+            {"position": 2, "offset": -1, "region": "*"},
+            {"position": 3, "offset": -2, "region": "*"},
+            {"position": 1, "offset": 1, "region": ""},
         ],
     )
 
@@ -579,7 +601,8 @@ def test_Coding_inverted_no_utr_degenerate():
             {"position": 1, "offset": 0, "region": "u"},
             {"position": 2, "offset": 1, "region": "u"},
             {"position": 1, "offset": 0, "region": "-"},
-
+            {"position": 2, "offset": 1, "region": "-"},
+            {"position": 1, "offset": -1, "region": ""},
         ],
     )
     degenerate_equal(
@@ -645,7 +668,7 @@ def test_Coding_protein():
         crossmap.coordinate_to_protein,
         31,
         crossmap.protein_to_coordinate,
-        {"position": 1, "position_in_codon": 1, "offset": 0, "region": "-"},
+        {"position": 1, "position_in_codon": 3, "offset": 0, "region": "-"},
     )
     invariant(
         crossmap.coordinate_to_protein,

From 41bd3d5939a758ca057c7f941a1d7ad72236f23d Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 13 Mar 2026 09:26:18 +0100
Subject: [PATCH 064/127] Refactor crossmap

---
 mutalyzer_crossmapper/crossmapper.py | 50 ++++++++++++++++++++--------
 1 file changed, 37 insertions(+), 13 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index c16fdf7..a714902 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -75,12 +75,12 @@ def __init__(self, locations, cds, inverted=False):
         if self._inverted:
             self._coding = (b1["position"] + b1["offset"], b0["position"] + b0["offset"] + 1)
             self._cds_len = (b0["position"] + b0["offset"]) - (b1["position"] + b1["offset"])
-            self._exons_end = e1["position"]
+            self._exons = (e1["position"], e0["position"])
             self._exons_start = e0["position"]
         else:
             self._coding = (b0["position"] + b0["offset"], b1["position"] + b1["offset"] +1)
             self._cds_len = (b1["position"] + b1["offset"]) - (b0["position"] + b0["offset"])
-            self._exons_end = e1["position"]
+            self._exons = (e0["position"], e1["position"])
             self._exons_start = e0["position"]
 
     def _coordinate_to_coding(self, coordinate):
@@ -126,7 +126,7 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
         if degenerate:
             if pos_m["region"] == "u":
                 if self._inverted:
-                    pos_m["position"] = pos_m["position"] + self._exons_start - self._coding[1] + 1
+                    pos_m["position"] = pos_m["position"] + self._exons[1] - self._coding[1] + 1
                 else:
                     pos_m["position"] = pos_m["position"] + self._coding[0]
                 pos_m["region"] = "-"
@@ -134,7 +134,7 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
                 if self._inverted:
                     pos_m["position"] = pos_m["position"] + self._coding[0]
                 else:
-                    pos_m["position"] = pos_m["position"] + self._exons_end - self._coding[1] + 1
+                    pos_m["position"] = pos_m["position"] + self._exons[1]- self._coding[1] + 1
                 pos_m["region"] = "*"
         return pos_m
 
@@ -171,8 +171,8 @@ def coding_to_coordinate(self, pos_m):
         elif region == "-":
             if position > self._coding[0]:
                 noncoding_pos_m = {
-                    "position": position - self._coding[0],
-                    "offset": offset,
+                    "position": position - self._coding[0] - offset,
+                    "offset": 0,
                     "region": "u"
                 }
             else:
@@ -182,10 +182,10 @@ def coding_to_coordinate(self, pos_m):
                     "region": ""
                 }
         else: # *
-            if position > self._coding[1]:
+            if position > self._coding[0]:
                 noncoding_pos_m = {
-                    "position": position - self._coding[1],
-                    "offset": offset,
+                    "position": position - self._coding[0] + offset,
+                    "offset": 0,
                     "region": "d"
                 }
             else:
@@ -206,10 +206,30 @@ def coordinate_to_protein(self, coordinate):
         """
         pos = self.coordinate_to_coding(coordinate)
 
-        if pos["region"] in ["-", "*"]:
+        if pos["region"] == "u":
+            pos = self.coordinate_to_coding(coordinate + pos["position"])
             return {
                 "position": pos["position"] // 3 + 1,
                 "position_in_codon": pos["position"] % 3,
+                "region": "u",
+                **{k: v for k, v in pos.items() if k not in ["position", "region"]}}
+        elif pos["region"] == "d":
+            pos = self.coordinate_to_coding(coordinate - pos["position"])
+            return {
+                "position": pos["position"] // 3 + 1,
+                "position_in_codon": pos["position"] % 3,
+                "region": "d",
+                **{k: v for k, v in pos.items() if k not in ["position", "region"]}}
+
+        if pos["region"] == "-":
+            return {
+                "position": (pos["position"]+2) // 3,
+                "position_in_codon": -pos["position"] % 3 + 1,
+                **{k: v for k, v in pos.items() if k != "position"}}
+        if pos["region"] == "*":
+            return {
+                "position": (pos["position"]+2)// 3,
+                "position_in_codon": (pos["position"] + 2) % 3 + 1,
                 **{k: v for k, v in pos.items() if k != "position"}}
         return {
                 "position": (pos["position"]+2) // 3,
@@ -223,12 +243,16 @@ def protein_to_coordinate(self, pos_m):
 
         :returns int: Coordinate.
         """
-        if pos_m["region"] in ["-", "*"]:
+        if pos_m["region"] == "-":
             return self.coding_to_coordinate(
-                {"position": 3 * pos_m["position"] + pos_m["position_in_codon"] - 3,
+                {"position": 3 * pos_m["position"] - pos_m["position_in_codon"] + 1,
                  "offset": pos_m["offset"],
                  "region": pos_m["region"]})
-
+        if pos_m["region"] == "*":
+                    return self.coding_to_coordinate(
+                        {"position": 3 * pos_m["position"] + pos_m["position_in_codon"] - 3,
+                        "offset": pos_m["offset"],
+                        "region": pos_m["region"]})
         return self.coding_to_coordinate(
                 {"position": 3 * pos_m["position"] + pos_m["position_in_codon"] - 3,
                  "offset": pos_m["offset"],

From 17523633f4aa100272199aa37f49aedc6af94a21 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 13 Mar 2026 09:44:30 +0100
Subject: [PATCH 065/127] Cleanup

---
 mutalyzer_crossmapper/crossmapper.py | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index a714902..dfdb23d 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -92,6 +92,7 @@ def _coordinate_to_coding(self, coordinate):
         """
         noncoding_pos_m = self._noncoding.to_position(coordinate)
         location = noncoding_pos_m["position"]
+
         if noncoding_pos_m["region"] == "":
             if location < self._coding[0]:
                 return {
@@ -123,18 +124,21 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
         :returns dict: Coding position model (c./r.).
         """
         pos_m = self._coordinate_to_coding(coordinate)
+        region = pos_m["region"]
+        position = pos_m["position"]
+
         if degenerate:
-            if pos_m["region"] == "u":
+            if region == "u":
                 if self._inverted:
-                    pos_m["position"] = pos_m["position"] + self._exons[1] - self._coding[1] + 1
+                    pos_m["position"] = position + self._exons[1] - self._coding[1] + 1
                 else:
-                    pos_m["position"] = pos_m["position"] + self._coding[0]
+                    pos_m["position"] = position + self._coding[0]
                 pos_m["region"] = "-"
-            if pos_m["region"] == "d":
+            if region == "d":
                 if self._inverted:
-                    pos_m["position"] = pos_m["position"] + self._coding[0]
+                    pos_m["position"] = position + self._coding[0]
                 else:
-                    pos_m["position"] = pos_m["position"] + self._exons[1]- self._coding[1] + 1
+                    pos_m["position"] = position + self._exons[1]- self._coding[1] + 1
                 pos_m["region"] = "*"
         return pos_m
 
@@ -167,9 +171,8 @@ def coding_to_coordinate(self, pos_m):
                 "offset": offset,
                 "region": ""
             }
-        # add checks for degenerate results?
         elif region == "-":
-            if position > self._coding[0]:
+            if position > self._coding[0]: # correct it to 'u'
                 noncoding_pos_m = {
                     "position": position - self._coding[0] - offset,
                     "offset": 0,
@@ -182,7 +185,7 @@ def coding_to_coordinate(self, pos_m):
                     "region": ""
                 }
         else: # *
-            if position > self._coding[0]:
+            if position > self._coding[0]: # correct it to 'd'
                 noncoding_pos_m = {
                     "position": position - self._coding[0] + offset,
                     "offset": 0,
@@ -213,7 +216,8 @@ def coordinate_to_protein(self, coordinate):
                 "position_in_codon": pos["position"] % 3,
                 "region": "u",
                 **{k: v for k, v in pos.items() if k not in ["position", "region"]}}
-        elif pos["region"] == "d":
+
+        if pos["region"] == "d":
             pos = self.coordinate_to_coding(coordinate - pos["position"])
             return {
                 "position": pos["position"] // 3 + 1,
@@ -226,11 +230,13 @@ def coordinate_to_protein(self, coordinate):
                 "position": (pos["position"]+2) // 3,
                 "position_in_codon": -pos["position"] % 3 + 1,
                 **{k: v for k, v in pos.items() if k != "position"}}
+
         if pos["region"] == "*":
             return {
                 "position": (pos["position"]+2)// 3,
                 "position_in_codon": (pos["position"] + 2) % 3 + 1,
                 **{k: v for k, v in pos.items() if k != "position"}}
+
         return {
                 "position": (pos["position"]+2) // 3,
                 "position_in_codon": (pos["position"]+2) % 3 + 1,

From 31f483adcf45b41823693aa4c5adad8fdcb8f668 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 13 Mar 2026 09:46:06 +0100
Subject: [PATCH 066/127] Cleanup

---
 mutalyzer_crossmapper/crossmapper.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index dfdb23d..cf751da 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -76,12 +76,10 @@ def __init__(self, locations, cds, inverted=False):
             self._coding = (b1["position"] + b1["offset"], b0["position"] + b0["offset"] + 1)
             self._cds_len = (b0["position"] + b0["offset"]) - (b1["position"] + b1["offset"])
             self._exons = (e1["position"], e0["position"])
-            self._exons_start = e0["position"]
         else:
             self._coding = (b0["position"] + b0["offset"], b1["position"] + b1["offset"] +1)
             self._cds_len = (b1["position"] + b1["offset"]) - (b0["position"] + b0["offset"])
             self._exons = (e0["position"], e1["position"])
-            self._exons_start = e0["position"]
 
     def _coordinate_to_coding(self, coordinate):
         """Convert a coordinate to a coding position (c./r.).

From eeacf85fac8dab54e1cf9bcf4d55eafb46c46e9a Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 13 Mar 2026 09:47:34 +0100
Subject: [PATCH 067/127] Cleanup

---
 mutalyzer_crossmapper/crossmapper.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index cf751da..d1a4cec 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -104,12 +104,11 @@ def _coordinate_to_coding(self, coordinate):
                     "offset": noncoding_pos_m["offset"],
                     "region": "*"
                 }
-            else:
-                return {
-                    "position": location - self._coding[0] + 1,
-                    "offset": noncoding_pos_m["offset"],
-                    "region": ""
-                }
+            return {
+                "position": location - self._coding[0] + 1,
+                "offset": noncoding_pos_m["offset"],
+                "region": ""
+            }
         else:
             return noncoding_pos_m
 

From bb8ee668620aa8be644ad412a10031d52d9493e6 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 13 Mar 2026 09:50:57 +0100
Subject: [PATCH 068/127] Cleanup

---
 mutalyzer_crossmapper/crossmapper.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index d1a4cec..31de6c6 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -251,11 +251,6 @@ def protein_to_coordinate(self, pos_m):
                 {"position": 3 * pos_m["position"] - pos_m["position_in_codon"] + 1,
                  "offset": pos_m["offset"],
                  "region": pos_m["region"]})
-        if pos_m["region"] == "*":
-                    return self.coding_to_coordinate(
-                        {"position": 3 * pos_m["position"] + pos_m["position_in_codon"] - 3,
-                        "offset": pos_m["offset"],
-                        "region": pos_m["region"]})
         return self.coding_to_coordinate(
                 {"position": 3 * pos_m["position"] + pos_m["position_in_codon"] - 3,
                  "offset": pos_m["offset"],

From 87f507d0b8916c5764d448ad467d74dd89d82fda Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 13 Mar 2026 11:38:43 +0100
Subject: [PATCH 069/127] Add missing tests

---
 tests/test_crossmapper.py | 21 ++++++++-------------
 1 file changed, 8 insertions(+), 13 deletions(-)

diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 40546b8..00caa14 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -106,7 +106,6 @@ def test_NonCoding_degenerate():
         4,
         [
             {"position": 1, "offset": 0, "region": "u"},
-            {"position": 0, "offset": -1, "region": "u"},
             {"position": 1, "offset": -1, "region": ""},
         ],
     )
@@ -117,8 +116,7 @@ def test_NonCoding_degenerate():
         72,
         [
             {"position": 1, "offset": 0, "region": "d"},
-            {"position": 0, "offset": 1, "region": "d"},
-            {"position": 22, "offset": 1, "region": ""},
+            {"position": 23, "offset": 0, "region": ""},
         ],
     )
 
@@ -132,8 +130,8 @@ def test_NonCoding_inverted_degenerate():
         crossmap.noncoding_to_coordinate,
         72,
         [
-            {"position": 1, "offset": 0, "region": "u"},
-            {"position": 1, "offset": -1, "region": ""},],
+            {"position": 1, "offset": -1, "region": ""},
+            {"position": 1, "offset": 0, "region": "u"},],
     )
 
     # Boundary between downstream and transcript.
@@ -463,22 +461,19 @@ def test_Coding_degenerate():
         9,
         [
             {"position": 1, "offset": 0, "region": "u"},
-            {"position": 2, "offset": 1, "region": "u"},
-            {"position": 0, "offset": -1, "region": "u"},
-            {"position": 1, "offset": -1, "region": "-"},
+            {"position": 2, "offset": 0, "region": "-"},
             {"position": 1, "offset": -2, "region": ""},
+            {"position": 1, "offset": -10, "region": "*"},
         ],
     )
     degenerate_equal(
         crossmap.coding_to_coordinate,
         20,
         [
-            {"position": 1, "offset": 0, "region": "d"},
-            {"position": 8, "offset": -7, "region": "d"},
-            {"position": 0, "offset": -1, "region": "d"},
-            {"position": 8, "offset": 2, "region": ""},
-            {"position": 2, "offset": 0, "region": "*"},
             {"position": 1, "offset": 1, "region": "*"},
+            {"position": 2, "offset": 0, "region": "*"},
+            {"position": 8, "offset": 2, "region": ""},
+            {"position": 1, "offset": 10, "region": "-"},
         ],
     )
 

From e5d734252aa7fef41bd3eebf6f60f2187653abeb Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 13 Mar 2026 13:18:51 +0100
Subject: [PATCH 070/127] Add missing tests

---
 tests/test_crossmapper.py | 30 +++++++++---------------------
 1 file changed, 9 insertions(+), 21 deletions(-)

diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 00caa14..55a9a92 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -487,12 +487,9 @@ def test_Coding_inverted_degenerate():
         20,
         [
             {"position": 1, "offset": 0, "region": "u"},
-            {"position": 2, "offset": 1, "region": "u"},
-            {"position": 0, "offset": -1, "region": "u"},
-            {"position": 1, "offset": -2, "region": ""},
-            {"position": 2, "offset": -3, "region": ""},
             {"position": 2, "offset": 0, "region": "-"},
-            {"position": 1, "offset": -1, "region": "-"},
+            {"position": 1, "offset": -2, "region": ""},
+            {"position": 1, "offset": -10, "region": "*"},
         ],
     )
     degenerate_equal(
@@ -500,10 +497,10 @@ def test_Coding_inverted_degenerate():
         9,
         [
             {"position": 1, "offset": 0, "region": "d"},
-            {"position": 2, "offset": -1, "region": "d"},
-            {"position": 8, "offset": 2, "region": ""},
-            {"position": 7, "offset": 3, "region": ""},
             {"position": 2, "offset": 0, "region": "*"},
+            {"position": 8, "offset": 2, "region": ""},
+            {"position": 1, "offset": 10, "region": "-"},
+
         ],
     )
 
@@ -563,12 +560,9 @@ def test_Coding_no_utr_degenerate():
         crossmap.coding_to_coordinate,
         9,
         [
-            {"position": 2, "offset": 1, "region": "u"},
             {"position": 1, "offset": 0, "region": "u"},
             {"position": 1, "offset": 0, "region": "-"},
-            {"position": 2, "offset": 1, "region": "-"},
-            {"position": 1, "offset": -1, "region": ""},
-            {"position": 2, "offset": -2, "region": ""},
+            {"position": 1, "offset": -2, "region": "*"},
         ],
     )
     degenerate_equal(
@@ -576,11 +570,8 @@ def test_Coding_no_utr_degenerate():
         11,
         [
             {"position": 1, "offset": 0, "region": "d"},
-            {"position": 2, "offset": -1, "region": "d"},
             {"position": 1, "offset": 0, "region": "*"},
-            {"position": 2, "offset": -1, "region": "*"},
-            {"position": 3, "offset": -2, "region": "*"},
-            {"position": 1, "offset": 1, "region": ""},
+            {"position": 1, "offset": 2, "region": "-"},
         ],
     )
 
@@ -594,10 +585,8 @@ def test_Coding_inverted_no_utr_degenerate():
         11,
         [
             {"position": 1, "offset": 0, "region": "u"},
-            {"position": 2, "offset": 1, "region": "u"},
             {"position": 1, "offset": 0, "region": "-"},
-            {"position": 2, "offset": 1, "region": "-"},
-            {"position": 1, "offset": -1, "region": ""},
+            {"position": 1, "offset": -2, "region": "*"},
         ],
     )
     degenerate_equal(
@@ -605,9 +594,8 @@ def test_Coding_inverted_no_utr_degenerate():
         9,
         [
             {"position": 1, "offset": 0, "region": "d"},
-            {"position": 2, "offset": -1, "region": "d"},
             {"position": 1, "offset": 0, "region": "*"},
-            {"position": 1, "offset": 1, "region": ""},
+            {"position": 1, "offset": 2, "region": "-"},
         ],
     )
 

From 53954d3bc26c4ec6feccd61d9504901ff45fc6ce Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 13 Mar 2026 13:21:48 +0100
Subject: [PATCH 071/127] Refactor

---
 mutalyzer_crossmapper/crossmapper.py | 14 ++------------
 1 file changed, 2 insertions(+), 12 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 31de6c6..a334dd3 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -150,18 +150,8 @@ def coding_to_coordinate(self, pos_m):
         position = pos_m["position"]
         offset = pos_m["offset"]
 
-        if region == "u":
-            noncoding_pos_m = {
-                "position": position - offset,
-                "offset": 0,
-                "region": "u"
-            }
-        elif region == "d":
-            noncoding_pos_m = {
-                "position": position + offset,
-                "offset": 0,
-                "region": "d"
-            }
+        if region in ["u", "d"]:
+            return self._noncoding.to_coordinate(pos_m)
         elif region == "":
             noncoding_pos_m = {
                 "position": position + self._coding[0] -1,

From 6cb7d3238e83b7285403d71c820c966d055498d5 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Mar 2026 09:34:25 +0100
Subject: [PATCH 072/127] Cleanup

---
 mutalyzer_crossmapper/multi_locus.py | 32 +++++++---------------------
 tests/test_multi_locus.py            |  1 -
 2 files changed, 8 insertions(+), 25 deletions(-)

diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 2853ee6..861e5cd 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -68,24 +68,10 @@ def to_position(self, coordinate:int):
                 "region": region
             }
 
-        if location["offset"] == 0:
-            return {
-                "position": location["position"] + self._offsets[self._direction(index)],
-                "offset": 0,
-                "region": ""
-            }
-
-        if location["offset"] < 0:
-            return {
-                "position": self._offsets[self._direction(index)],
-                "offset": location["offset"],
-                "region": ""
-            }
-
-        return{
+        return {
             "position": location["position"] + self._offsets[self._direction(index)],
             "offset": location["offset"],
-            "region": ""
+            "region": region
         }
 
     def to_coordinate(self, pos_m:dict):
@@ -97,13 +83,11 @@ def to_coordinate(self, pos_m:dict):
         """
         region = pos_m["region"]
 
-        if region == "u":
-            if self._inverted:
-                return abs(pos_m["position"]) + self._locations[-1][1] + pos_m["offset"] - 1
-            return self._locations[0][0] - abs(pos_m["position"]) + pos_m["offset"]
-
-        if region == "d":
+        if pos_m["region"] in ("u", "d"):
+            is_upstream = region == "u"
             if self._inverted:
+                is_upstream = not is_upstream
+            if is_upstream:
                 return self._locations[0][0] - abs(pos_m["position"]) + pos_m["offset"]
             return abs(pos_m["position"]) + self._locations[-1][1] + pos_m["offset"] - 1
 
@@ -111,5 +95,5 @@ def to_coordinate(self, pos_m:dict):
             len(self._offsets),
             max(0, bisect_right(self._offsets, pos_m["position"]) - 1)
         )
-        pos_m["position"] = pos_m["position"] - self._offsets[index]
-        return self._loci[self._direction(index)].to_coordinate(pos_m)
+        locus_pos_m = {**pos_m, "position": pos_m["position"] - self._offsets[index]}
+        return self._loci[self._direction(index)].to_coordinate(locus_pos_m)
diff --git a/tests/test_multi_locus.py b/tests/test_multi_locus.py
index c08ff7f..3434a62 100644
--- a/tests/test_multi_locus.py
+++ b/tests/test_multi_locus.py
@@ -321,6 +321,5 @@ def test_MultiLocus_inverted_degenerate():
         [
             {"position": 0, "offset": -1, "region": "d"},
             {"position": 1, "offset": 0, "region": "d"},
-            {"position": 2, "offset": 1, "region": "d"},
         ],
     )

From 3e32bb96e258a0e6f02f5886bdebc5579f173300 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Mar 2026 09:35:05 +0100
Subject: [PATCH 073/127] Cleanup and add tests

---
 mutalyzer_crossmapper/crossmapper.py | 189 +++++++++++++--------------
 tests/test_crossmapper.py            |  29 +++-
 2 files changed, 119 insertions(+), 99 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index a334dd3..0fd0c09 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -52,9 +52,10 @@ def noncoding_to_coordinate(self, pos_m):
 
         :returns int: Coordinate.
         """
+        multilocus_pos_m = {**pos_m}
         if pos_m["region"] == "":
-            pos_m["position"] = pos_m["position"] - 1
-        return self._noncoding.to_coordinate(pos_m)
+            multilocus_pos_m["position"] = pos_m["position"] - 1
+        return self._noncoding.to_coordinate(multilocus_pos_m)
 
 
 class Coding(NonCoding):
@@ -74,13 +75,52 @@ def __init__(self, locations, cds, inverted=False):
 
         if self._inverted:
             self._coding = (b1["position"] + b1["offset"], b0["position"] + b0["offset"] + 1)
-            self._cds_len = (b0["position"] + b0["offset"]) - (b1["position"] + b1["offset"])
             self._exons = (e1["position"], e0["position"])
         else:
             self._coding = (b0["position"] + b0["offset"], b1["position"] + b1["offset"] +1)
-            self._cds_len = (b1["position"] + b1["offset"]) - (b0["position"] + b0["offset"])
             self._exons = (e0["position"], e1["position"])
 
+    def _degenerate_position(self, pos_m):
+        """Degenerate a coding position model (c./r.).
+
+        :arg dict pos_m: Coding position model.
+
+        :returns dict: a generate coding position model.
+        """
+        region = pos_m["region"]
+        position = pos_m["position"]
+
+        degenerated_pos_m = {"offset": pos_m["offset"]}
+
+        if region == "u":
+            if self._inverted:
+                degenerated_pos_m["position"] = position + self._exons[1] - self._coding[1] + 1
+            else:
+                degenerated_pos_m["position"] = position + self._coding[0]
+            degenerated_pos_m["region"] = "-"
+        if region == "d":
+            if self._inverted:
+                degenerated_pos_m["position"] = position + self._coding[0]
+            else:
+                degenerated_pos_m["position"] = position + self._exons[1]- self._coding[1] + 1
+            degenerated_pos_m["region"] = "*"
+        return degenerated_pos_m
+
+    def _normalize_position(self, pos_m):
+        """Normalize a coding position model (c./r.).
+
+        :arg dict pos_m: Coding position model.
+
+        :returns dict: a normalized coding postion model.
+        """
+        initial_pos = {**pos_m, "offset": 0}
+        coordinate = self._coding_to_coordinate(initial_pos)
+        if self._inverted:
+            coordinate = coordinate - pos_m["offset"]
+        else:
+            coordinate = coordinate + pos_m["offset"]
+        return self.coordinate_to_coding(coordinate)
+
     def _coordinate_to_coding(self, coordinate):
         """Convert a coordinate to a coding position (c./r.).
 
@@ -89,28 +129,29 @@ def _coordinate_to_coding(self, coordinate):
         :returns dict: Coding position model (c./r.).
         """
         noncoding_pos_m = self._noncoding.to_position(coordinate)
-        location = noncoding_pos_m["position"]
 
-        if noncoding_pos_m["region"] == "":
-            if location < self._coding[0]:
-                return {
-                    "position": self._coding[0] - location,
-                    "offset": noncoding_pos_m["offset"],
-                    "region": "-"
-                }
-            elif location >= self._coding[1]:
-                return {
-                    "position": location - self._coding[1] + 1,
-                    "offset": noncoding_pos_m["offset"],
-                    "region": "*"
-                }
+        if noncoding_pos_m["region"] in ["u", "d"]:
+            return noncoding_pos_m
+
+        location = noncoding_pos_m["position"]
+        offset = noncoding_pos_m["offset"]
+        if location < self._coding[0]:
+            return {
+                "position": self._coding[0] - location,
+                "offset": offset,
+                "region": "-"
+            }
+        if location >= self._coding[1]:
             return {
-                "position": location - self._coding[0] + 1,
-                "offset": noncoding_pos_m["offset"],
-                "region": ""
+                "position": location - self._coding[1] + 1,
+                "offset": offset,
+                "region": "*"
             }
-        else:
-            return noncoding_pos_m
+        return {
+            "position": location - self._coding[0] + 1,
+            "offset": offset,
+            "region": ""
+        }
 
     def coordinate_to_coding(self, coordinate, degenerate=False):
         """Convert a coordinate to a coding position (c./r.).
@@ -121,71 +162,45 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
         :returns dict: Coding position model (c./r.).
         """
         pos_m = self._coordinate_to_coding(coordinate)
-        region = pos_m["region"]
-        position = pos_m["position"]
 
-        if degenerate:
-            if region == "u":
-                if self._inverted:
-                    pos_m["position"] = position + self._exons[1] - self._coding[1] + 1
-                else:
-                    pos_m["position"] = position + self._coding[0]
-                pos_m["region"] = "-"
-            if region == "d":
-                if self._inverted:
-                    pos_m["position"] = position + self._coding[0]
-                else:
-                    pos_m["position"] = position + self._exons[1]- self._coding[1] + 1
-                pos_m["region"] = "*"
+        if degenerate and pos_m["region"] in ("u", "d"):
+            pos_m = self._degenerate_position(pos_m)
+
         return pos_m
 
-    def coding_to_coordinate(self, pos_m):
+    def _coding_to_coordinate(self, pos_m):
         """Convert a coding position (c./r.) to a coordinate.
 
         :arg dict pos_m: Coding position model (c./r.).
 
         :returns int: Coordinate.
         """
-        region = pos_m["region"]
         position = pos_m["position"]
-        offset = pos_m["offset"]
+        region = pos_m["region"]
 
         if region in ["u", "d"]:
             return self._noncoding.to_coordinate(pos_m)
-        elif region == "":
-            noncoding_pos_m = {
-                "position": position + self._coding[0] -1,
-                "offset": offset,
-                "region": ""
-            }
+
+        noncoding_pos_m = {"offset": pos_m["offset"], "region": ""}
+        if region == "":
+            noncoding_pos_m["position"] = position + self._coding[0] - 1
         elif region == "-":
-            if position > self._coding[0]: # correct it to 'u'
-                noncoding_pos_m = {
-                    "position": position - self._coding[0] - offset,
-                    "offset": 0,
-                    "region": "u"
-                }
-            else:
-                noncoding_pos_m = {
-                    "position": self._coding[0] - position,
-                    "offset": offset,
-                    "region": ""
-                }
-        else: # *
-            if position > self._coding[0]: # correct it to 'd'
-                noncoding_pos_m = {
-                    "position": position - self._coding[0] + offset,
-                    "offset": 0,
-                    "region": "d"
-                }
-            else:
-                noncoding_pos_m = {
-                    "position": self._coding[1] + position - 1,
-                    "offset": offset,
-                    "region": ""
-                }
+            noncoding_pos_m["position"] = self._coding[0] - position
+        else:
+            noncoding_pos_m["position"] = self._coding[1] + position - 1
+
         return self._noncoding.to_coordinate(noncoding_pos_m)
 
+    def coding_to_coordinate(self, pos_m):
+        """Convert a coding position (c./r.) to a coordinate.
+
+        :arg dict pos_m: Coding position model (c./r.).
+
+        :returns int: Coordinate.
+        """
+        normalized_pos_m = self._normalize_position(pos_m)
+
+        return self._coding_to_coordinate(normalized_pos_m)
 
     def coordinate_to_protein(self, coordinate):
         """Convert a coordinate to a protein position (p.).
@@ -198,35 +213,18 @@ def coordinate_to_protein(self, coordinate):
 
         if pos["region"] == "u":
             pos = self.coordinate_to_coding(coordinate + pos["position"])
-            return {
-                "position": pos["position"] // 3 + 1,
-                "position_in_codon": pos["position"] % 3,
-                "region": "u",
-                **{k: v for k, v in pos.items() if k not in ["position", "region"]}}
-
-        if pos["region"] == "d":
+        elif pos["region"] == "d":
             pos = self.coordinate_to_coding(coordinate - pos["position"])
-            return {
-                "position": pos["position"] // 3 + 1,
-                "position_in_codon": pos["position"] % 3,
-                "region": "d",
-                **{k: v for k, v in pos.items() if k not in ["position", "region"]}}
 
+        position = pos["position"]
         if pos["region"] == "-":
             return {
-                "position": (pos["position"]+2) // 3,
-                "position_in_codon": -pos["position"] % 3 + 1,
+                "position": abs(-position // 3),
+                "position_in_codon": -position % 3 + 1,
                 **{k: v for k, v in pos.items() if k != "position"}}
-
-        if pos["region"] == "*":
-            return {
-                "position": (pos["position"]+2)// 3,
-                "position_in_codon": (pos["position"] + 2) % 3 + 1,
-                **{k: v for k, v in pos.items() if k != "position"}}
-
         return {
-                "position": (pos["position"]+2) // 3,
-                "position_in_codon": (pos["position"]+2) % 3 + 1,
+                "position": (position + 2) // 3,
+                "position_in_codon": (position + 2) % 3 + 1,
                 **{k: v for k, v in pos.items() if k != "position"}}
 
     def protein_to_coordinate(self, pos_m):
@@ -241,6 +239,7 @@ def protein_to_coordinate(self, pos_m):
                 {"position": 3 * pos_m["position"] - pos_m["position_in_codon"] + 1,
                  "offset": pos_m["offset"],
                  "region": pos_m["region"]})
+
         return self.coding_to_coordinate(
                 {"position": 3 * pos_m["position"] + pos_m["position_in_codon"] - 3,
                  "offset": pos_m["offset"],
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 55a9a92..a3bc5f7 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -105,8 +105,8 @@ def test_NonCoding_degenerate():
         crossmap.noncoding_to_coordinate,
         4,
         [
-            {"position": 1, "offset": 0, "region": "u"},
             {"position": 1, "offset": -1, "region": ""},
+            {"position": 1, "offset": 0, "region": "u"},
         ],
     )
 
@@ -116,6 +116,7 @@ def test_NonCoding_degenerate():
         72,
         [
             {"position": 1, "offset": 0, "region": "d"},
+            {"position": 22, "offset": 1, "region": ""},
             {"position": 23, "offset": 0, "region": ""},
         ],
     )
@@ -131,7 +132,8 @@ def test_NonCoding_inverted_degenerate():
         72,
         [
             {"position": 1, "offset": -1, "region": ""},
-            {"position": 1, "offset": 0, "region": "u"},],
+            {"position": 1, "offset": 0, "region": "u"},
+        ],
     )
 
     # Boundary between downstream and transcript.
@@ -140,7 +142,9 @@ def test_NonCoding_inverted_degenerate():
         4,
         [
             {"position": 1, "offset": 0, "region": "d"},
-            {"position": 22, "offset": 1, "region": ""},],
+            {"position": 23, "offset": 0, "region": ""},
+            {"position": 22, "offset": 1, "region": ""},
+        ],
     )
 
 
@@ -464,16 +468,21 @@ def test_Coding_degenerate():
             {"position": 2, "offset": 0, "region": "-"},
             {"position": 1, "offset": -2, "region": ""},
             {"position": 1, "offset": -10, "region": "*"},
+            {"position": 2, "offset": -11, "region": "*"},
+            {"position": 3, "offset": 1, "region": "-"},
+            {"position": 4, "offset": 2, "region": "-"},
         ],
     )
     degenerate_equal(
         crossmap.coding_to_coordinate,
         20,
         [
-            {"position": 1, "offset": 1, "region": "*"},
+            {"position": 1, "offset": 0, "region": "d"},
             {"position": 2, "offset": 0, "region": "*"},
             {"position": 8, "offset": 2, "region": ""},
             {"position": 1, "offset": 10, "region": "-"},
+            {"position": 2, "offset": 11, "region": "-"},
+            {"position": 7, "offset": 3, "region": ""},
         ],
     )
 
@@ -490,6 +499,8 @@ def test_Coding_inverted_degenerate():
             {"position": 2, "offset": 0, "region": "-"},
             {"position": 1, "offset": -2, "region": ""},
             {"position": 1, "offset": -10, "region": "*"},
+            {"position": 1, "offset": -11, "region": "d"},
+            {"position": 2, "offset": -3, "region": ""},
         ],
     )
     degenerate_equal(
@@ -500,6 +511,8 @@ def test_Coding_inverted_degenerate():
             {"position": 2, "offset": 0, "region": "*"},
             {"position": 8, "offset": 2, "region": ""},
             {"position": 1, "offset": 10, "region": "-"},
+            {"position": 1, "offset": 11, "region": "u"},
+            {"position": 2, "offset": 12, "region": "u"},
 
         ],
     )
@@ -563,6 +576,8 @@ def test_Coding_no_utr_degenerate():
             {"position": 1, "offset": 0, "region": "u"},
             {"position": 1, "offset": 0, "region": "-"},
             {"position": 1, "offset": -2, "region": "*"},
+            {"position": 1, "offset": -1, "region": ""},
+            {"position": 1, "offset": -2, "region": "d"},
         ],
     )
     degenerate_equal(
@@ -572,6 +587,8 @@ def test_Coding_no_utr_degenerate():
             {"position": 1, "offset": 0, "region": "d"},
             {"position": 1, "offset": 0, "region": "*"},
             {"position": 1, "offset": 2, "region": "-"},
+            {"position": 1, "offset": 1, "region": ""},
+            {"position": 1, "offset": 2, "region": "u"},
         ],
     )
 
@@ -587,6 +604,8 @@ def test_Coding_inverted_no_utr_degenerate():
             {"position": 1, "offset": 0, "region": "u"},
             {"position": 1, "offset": 0, "region": "-"},
             {"position": 1, "offset": -2, "region": "*"},
+            {"position": 1, "offset": -1, "region": ""},
+            {"position": 1, "offset": -2, "region": "d"},
         ],
     )
     degenerate_equal(
@@ -596,6 +615,8 @@ def test_Coding_inverted_no_utr_degenerate():
             {"position": 1, "offset": 0, "region": "d"},
             {"position": 1, "offset": 0, "region": "*"},
             {"position": 1, "offset": 2, "region": "-"},
+            {"position": 1, "offset": 1, "region": ""},
+            {"position": 1, "offset": 2, "region": "u"},
         ],
     )
 

From 186e2a69c0029e73b0e5a0b5f171cfa09dd05686 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 09:52:55 +0100
Subject: [PATCH 074/127] Update tables in documentation

---
 README.rst | 70 ++++++++++++++++++++++++++++--------------------------
 1 file changed, 36 insertions(+), 34 deletions(-)

diff --git a/README.rst b/README.rst
index 29f15d1..cc007b2 100644
--- a/README.rst
+++ b/README.rst
@@ -129,13 +129,14 @@ Here is the mapping of coordinates to noncoding positions:
    :class: table-scroll
    :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
 
-   "4", "1","0", "'u'", "n.u1"
-   "5", "1","0", "''", "n.1"
-   "24", "9","5", "''", "n.9+5"
-   "25", "10","-5", "''", "n.10-5"
-   "71", "22","0", "''", "n.22"
-   "72", "1","0", "'d'", "n.d1"
-   "79", "8","0", "'d'", "n.d8"
+   "0", "5", "0", "u", "c.u5"
+   "4", "1", "0", "u", "n.u1"
+   "5", "1", "0", "", "n.1"
+   "24", "9", "5", "", "n.9+5"
+   "25", "10", "-5", "", "n.10-5"
+   "71", "22", "0", "", "n.22"
+   "72", "1", "0", "d", "n.d1"
+   "79", "8", "0", "d", "n.d8"
 
 
 
@@ -154,7 +155,7 @@ Coding positions follow the HGVS ``c`` coordinate system. They are represented a
     {
         "position": 1,
         "offset": 3,
-        "region": '*'
+        "region": "*"
     }
 
 Where:
@@ -186,19 +187,20 @@ Here is the mapping of coordinates to coding positions:
    :class: table-scroll
    :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
 
-   "4", "1","0", "'u'", "c.u1"
-   "5", "11","0", '-', "c.-11"
-   "24", "3","5", '-', "c.-3+5"
-   "25", "2","-5", '-', "c.-2-5"
-   "31", "1","0", '-', "c.-1"
-   "32", "1","0", "''", "c.1"
-   "37", "3","3", "''", "c.3+3"
-   "38", "4","-2", "''", "c.4-2"
-   "43", "1","0", '*', "c.*1"
-   "60", "3","9", '*', "c.*3+9"
-   "61", "4","-9", '*', "c.*4+9"
-   "71", "5","0", '*', "c.*5"
-   "79", "8","0", "'d'", "c.d8"
+   "0", "5", "0", "u", "c.u5"
+   "4", "1", "0", "u", "c.u1"
+   "5", "11", "0", "\-", "c.-11"
+   "24", "3", "5", "\-", "c.-3+5"
+   "25", "2", "-5", "\-", "c.-2-5"
+   "31", "1", "0", "\-", "c.-1"
+   "32", "1", "0", "", "c.1"
+   "37", "3", "3", "", "c.3+3"
+   "38", "4", "-2", "", "c.4-2"
+   "43", "1", "0", "\*", "c.*1"
+   "60", "3", "9", "\*", "c.*3+9"
+   "61", "4", "-9", "\*", "c.*4+9"
+   "71", "5", "0", "\*", "c.*5"
+   "79", "8", "0", "d", "c.d8"
 
 
 
@@ -244,19 +246,19 @@ Here is the mapping of coordinates to protein positions:
 
 .. csv-table::
    :class: table-scroll
-   :header: "Coordinate", "Position", "position_in_codon", "Offset", "Region", "HGVS" 
-
-   "0", "4", "2", "0", "'u'", 
-   "4", "4", "2", "0", "'u'",
-   "5", "4", "2", "0", '-',
-   "6", "4", "3", "0", '-',
-   "7", "3", "1", "0", '-',
-   "31", "1", "3", "0", '-',
-   "32", "1", "1", "0", "''", "p.1"
-   "42", "2", "3", "0", "''", "p.2"
-   "43", "1", "1", "0", '*',
-   "44", "1", "1", "1", '*',
-   "79", "2", "2", "0", "'d'",
+   :header: "Coordinate", "Position", "position_in_codon", "Offset", "Region", "HGVS"
+
+   "0", "4", "2", "0", "u",
+   "4", "4", "2", "0", "u",
+   "5", "4", "2", "0", "\-",
+   "6", "4", "3", "0", "\-",
+   "7", "3", "1", "0", "\-",
+   "31", "1", "3", "0", "\-",
+   "32", "1", "1", "0", "", "p.1"
+   "42", "2", "3", "0", "", "p.2"
+   "43", "1", "1", "0", "\*",
+   "44", "1", "1", "1", "\*",
+   "79", "2", "2", "0", "d",
 
 
 

From 617b126d548c540d369d36ceea919474ec1ed2dc Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 09:54:28 +0100
Subject: [PATCH 075/127] Update README.rst

---
 README.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.rst b/README.rst
index cc007b2..79e9c48 100644
--- a/README.rst
+++ b/README.rst
@@ -115,7 +115,7 @@ NonCoding Position Conversion
     >>> crossmap = NonCoding(_exons)
     >>> crossmap.coordinate_to_noncoding(25)
     {"position": 10, "offset": -5, "region": ''}
-    >>> crossmap.noncoding_to_coordinate({"position": 10, "offset": -5, "region": ''})
+    >>> crossmap.noncoding_to_coordinate({"position": 10, "offset": -5, "region": ""})
     25
 
 Notes
@@ -173,7 +173,7 @@ Coding Position Conversion
     >>> crossmap = Coding(_exons, _cds)
     >>> crossmap.coordinate_to_coding(46)
     {"position": 1, "offset": 3, "region": '*'}
-    >>> crossmap.coding_to_coordinate({"position": 1, "offset": 3, "region": '*'})
+    >>> crossmap.coding_to_coordinate({"position": 1, "offset": 3, "region": "*"})
     46
 
 Notes

From 4fddbc316100af52b75e570b6de9aa15f89569db Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Mar 2026 10:47:40 +0100
Subject: [PATCH 076/127] Use single quate for dictionary

---
 mutalyzer_crossmapper/crossmapper.py | 130 +++++++++++++--------------
 1 file changed, 65 insertions(+), 65 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 0fd0c09..3994271 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -10,7 +10,7 @@ def coordinate_to_genomic(self, coordinate):
 
         :returns dict: Genomic position model.
         """
-        return {"position": coordinate + 1}
+        return {'position': coordinate + 1}
 
     def genomic_to_coordinate(self, pos_m):
         """Convert a genomic position (g./m./o.) to a coordinate.
@@ -19,7 +19,7 @@ def genomic_to_coordinate(self, pos_m):
 
         :returns int: Coordinate.
         """
-        return pos_m["position"] - 1
+        return pos_m['position'] - 1
 
 
 class NonCoding(Genomic):
@@ -41,8 +41,8 @@ def coordinate_to_noncoding(self, coordinate):
         :returns dict: Noncoding position model.
         """
         pos_m = self._noncoding.to_position(coordinate)
-        if pos_m["region"] == "":
-            pos_m["position"] = pos_m["position"] + 1
+        if pos_m['region'] == '':
+            pos_m['position'] = pos_m['position'] + 1
         return pos_m
 
     def noncoding_to_coordinate(self, pos_m):
@@ -53,8 +53,8 @@ def noncoding_to_coordinate(self, pos_m):
         :returns int: Coordinate.
         """
         multilocus_pos_m = {**pos_m}
-        if pos_m["region"] == "":
-            multilocus_pos_m["position"] = pos_m["position"] - 1
+        if pos_m['region'] == '':
+            multilocus_pos_m['position'] = pos_m['position'] - 1
         return self._noncoding.to_coordinate(multilocus_pos_m)
 
 
@@ -74,11 +74,11 @@ def __init__(self, locations, cds, inverted=False):
         e1 = self._noncoding.to_position(locations[-1][1]-1)
 
         if self._inverted:
-            self._coding = (b1["position"] + b1["offset"], b0["position"] + b0["offset"] + 1)
-            self._exons = (e1["position"], e0["position"])
+            self._coding = (b1['position'] + b1['offset'], b0['position'] + b0['offset'] + 1)
+            self._exons = (e1['position'], e0['position'])
         else:
-            self._coding = (b0["position"] + b0["offset"], b1["position"] + b1["offset"] +1)
-            self._exons = (e0["position"], e1["position"])
+            self._coding = (b0['position'] + b0['offset'], b1['position'] + b1['offset'] +1)
+            self._exons = (e0['position'], e1['position'])
 
     def _degenerate_position(self, pos_m):
         """Degenerate a coding position model (c./r.).
@@ -87,23 +87,23 @@ def _degenerate_position(self, pos_m):
 
         :returns dict: a generate coding position model.
         """
-        region = pos_m["region"]
-        position = pos_m["position"]
+        region = pos_m['region']
+        position = pos_m['position']
 
-        degenerated_pos_m = {"offset": pos_m["offset"]}
+        degenerated_pos_m = {'offset': pos_m['offset']}
 
-        if region == "u":
+        if region == 'u':
             if self._inverted:
-                degenerated_pos_m["position"] = position + self._exons[1] - self._coding[1] + 1
+                degenerated_pos_m['position'] = position + self._exons[1] - self._coding[1] + 1
             else:
-                degenerated_pos_m["position"] = position + self._coding[0]
-            degenerated_pos_m["region"] = "-"
-        if region == "d":
+                degenerated_pos_m['position'] = position + self._coding[0]
+            degenerated_pos_m['region'] = '-'
+        if region == 'd':
             if self._inverted:
-                degenerated_pos_m["position"] = position + self._coding[0]
+                degenerated_pos_m['position'] = position + self._coding[0]
             else:
-                degenerated_pos_m["position"] = position + self._exons[1]- self._coding[1] + 1
-            degenerated_pos_m["region"] = "*"
+                degenerated_pos_m['position'] = position + self._exons[1]- self._coding[1] + 1
+            degenerated_pos_m['region'] = '*'
         return degenerated_pos_m
 
     def _normalize_position(self, pos_m):
@@ -113,12 +113,12 @@ def _normalize_position(self, pos_m):
 
         :returns dict: a normalized coding postion model.
         """
-        initial_pos = {**pos_m, "offset": 0}
+        initial_pos = {**pos_m, 'offset': 0}
         coordinate = self._coding_to_coordinate(initial_pos)
         if self._inverted:
-            coordinate = coordinate - pos_m["offset"]
+            coordinate = coordinate - pos_m['offset']
         else:
-            coordinate = coordinate + pos_m["offset"]
+            coordinate = coordinate + pos_m['offset']
         return self.coordinate_to_coding(coordinate)
 
     def _coordinate_to_coding(self, coordinate):
@@ -130,27 +130,27 @@ def _coordinate_to_coding(self, coordinate):
         """
         noncoding_pos_m = self._noncoding.to_position(coordinate)
 
-        if noncoding_pos_m["region"] in ["u", "d"]:
+        if noncoding_pos_m['region'] in ['u', 'd']:
             return noncoding_pos_m
 
-        location = noncoding_pos_m["position"]
-        offset = noncoding_pos_m["offset"]
+        location = noncoding_pos_m['position']
+        offset = noncoding_pos_m['offset']
         if location < self._coding[0]:
             return {
-                "position": self._coding[0] - location,
-                "offset": offset,
-                "region": "-"
+                'position': self._coding[0] - location,
+                'offset': offset,
+                'region': '-'
             }
         if location >= self._coding[1]:
             return {
-                "position": location - self._coding[1] + 1,
-                "offset": offset,
-                "region": "*"
+                'position': location - self._coding[1] + 1,
+                'offset': offset,
+                'region': '*'
             }
         return {
-            "position": location - self._coding[0] + 1,
-            "offset": offset,
-            "region": ""
+            'position': location - self._coding[0] + 1,
+            'offset': offset,
+            'region': ''
         }
 
     def coordinate_to_coding(self, coordinate, degenerate=False):
@@ -163,7 +163,7 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
         """
         pos_m = self._coordinate_to_coding(coordinate)
 
-        if degenerate and pos_m["region"] in ("u", "d"):
+        if degenerate and pos_m['region'] in ('u', 'd'):
             pos_m = self._degenerate_position(pos_m)
 
         return pos_m
@@ -175,19 +175,19 @@ def _coding_to_coordinate(self, pos_m):
 
         :returns int: Coordinate.
         """
-        position = pos_m["position"]
-        region = pos_m["region"]
+        position = pos_m['position']
+        region = pos_m['region']
 
-        if region in ["u", "d"]:
+        if region in ['u', 'd']:
             return self._noncoding.to_coordinate(pos_m)
 
-        noncoding_pos_m = {"offset": pos_m["offset"], "region": ""}
-        if region == "":
-            noncoding_pos_m["position"] = position + self._coding[0] - 1
-        elif region == "-":
-            noncoding_pos_m["position"] = self._coding[0] - position
+        noncoding_pos_m = {'offset': pos_m['offset'], 'region': ''}
+        if region == '':
+            noncoding_pos_m['position'] = position + self._coding[0] - 1
+        elif region == '-':
+            noncoding_pos_m['position'] = self._coding[0] - position
         else:
-            noncoding_pos_m["position"] = self._coding[1] + position - 1
+            noncoding_pos_m['position'] = self._coding[1] + position - 1
 
         return self._noncoding.to_coordinate(noncoding_pos_m)
 
@@ -211,21 +211,21 @@ def coordinate_to_protein(self, coordinate):
         """
         pos = self.coordinate_to_coding(coordinate)
 
-        if pos["region"] == "u":
-            pos = self.coordinate_to_coding(coordinate + pos["position"])
-        elif pos["region"] == "d":
-            pos = self.coordinate_to_coding(coordinate - pos["position"])
+        if pos['region'] == 'u':
+            pos = self.coordinate_to_coding(coordinate + pos['position'])
+        elif pos['region'] == 'd':
+            pos = self.coordinate_to_coding(coordinate - pos['position'])
 
-        position = pos["position"]
-        if pos["region"] == "-":
+        position = pos['position']
+        if pos['region'] == '-':
             return {
-                "position": abs(-position // 3),
-                "position_in_codon": -position % 3 + 1,
-                **{k: v for k, v in pos.items() if k != "position"}}
+                'position': abs(-position // 3),
+                'position_in_codon': -position % 3 + 1,
+                **{k: v for k, v in pos.items() if k != 'position'}}
         return {
-                "position": (position + 2) // 3,
-                "position_in_codon": (position + 2) % 3 + 1,
-                **{k: v for k, v in pos.items() if k != "position"}}
+                'position': (position + 2) // 3,
+                'position_in_codon': (position + 2) % 3 + 1,
+                **{k: v for k, v in pos.items() if k != 'position'}}
 
     def protein_to_coordinate(self, pos_m):
         """Convert a protein position (p.) to a coordinate.
@@ -234,13 +234,13 @@ def protein_to_coordinate(self, pos_m):
 
         :returns int: Coordinate.
         """
-        if pos_m["region"] == "-":
+        if pos_m['region'] == '-':
             return self.coding_to_coordinate(
-                {"position": 3 * pos_m["position"] - pos_m["position_in_codon"] + 1,
-                 "offset": pos_m["offset"],
-                 "region": pos_m["region"]})
+                {'position': 3 * pos_m['position'] - pos_m['position_in_codon'] + 1,
+                 'offset': pos_m['offset'],
+                 'region': pos_m['region']})
 
         return self.coding_to_coordinate(
-                {"position": 3 * pos_m["position"] + pos_m["position_in_codon"] - 3,
-                 "offset": pos_m["offset"],
-                 "region": pos_m["region"]})
+                {'position': 3 * pos_m['position'] + pos_m['position_in_codon'] - 3,
+                 'offset': pos_m['offset'],
+                 'region': pos_m['region']})

From f85b25f5a73e588fd07d887ac8e2082b6161c206 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 10:59:20 +0100
Subject: [PATCH 077/127] Delete table

---
 README.rst | 251 ++++++++++-------------------------------------------
 1 file changed, 45 insertions(+), 206 deletions(-)

diff --git a/README.rst b/README.rst
index 79e9c48..d398402 100644
--- a/README.rst
+++ b/README.rst
@@ -27,239 +27,78 @@ HGVS position crossmapper
 This library provides an interface to convert (cross map) between different
 HGVS numbering_ systems.
 
-Converting between the transcript oriented c. or n. and the genomic oriented g.
+Converting between the transcript oriented ``c.`` or ``n.`` and the genomic oriented ``g.``
 numbering systems can be difficult, especially when the transcript in question
-resides on the complement strand.
+resides on the complement strand. This library provides functions to convert between any HGVS
+numbering system to standard (0-based) coordinates and vice versa.
 
 **Features:**
 
-- Support for genomic positions to standard coordinates and vice versa.
-- Support for noncoding positions to standard coordinates and vice versa.
-- Support for coding positions to standard coordinates and vice versa.
-- Support for protein positions to standard coordinates and vice versa.
-- Basic classes for loci that can be used for genomic loci other than genes.
+- Support for genomic (``g.``, ``m.``, ``o.``) positions to standard coordinates and vice versa.
+- Support for noncoding (``n.``, ``r.``) positions to standard coordinates and vice versa.
+- Support for coding (``c.``, ``r.``) positions to standard coordinates and vice versa.
+- Support for protein (``p.``) positions to standard coordinates and vice versa.
+- Basic classes that can be used for loci other than genes or transcripts.
 
 Please see ReadTheDocs_ for the latest documentation.
 
-Quick Start
-===========
+Quick start
+-----------
 
-An example below uses the following transcript data:
+The ``Genomic`` class provides an interface to conversions between genomic
+positions and coordinates.
 
-.. code-block:: python
-
-    >>>_exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
-    >>>_cds = (32, 43)
-
-
-Genomic Class
--------------
-
-The ``Genomic`` class provides an interface for conversions between genomic positions and coordinates.
-
-Genomic Position Model
-~~~~~~~~~~~~~~~~~~~~~~~
-
-Genomic positions follow the HGVS ``g`` coordinate system. They are represented as dictionaries. Below is an example of `g.1` in HGVS.
-
-.. code-block:: json
-
-    {"position": 1}
-
-Where:
-
-- **position**: a positive integer(>0)
-
-Genomic Position Conversion
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. code-block:: python
+.. code:: python
 
     >>> from mutalyzer_crossmapper import Genomic
     >>> crossmap = Genomic()
     >>> crossmap.coordinate_to_genomic(0)
-    {"position": 1}
-    >>> crossmap.genomic_to_coordinate({"position": 1})
+    1
+    >>> crossmap.genomic_to_coordinate({'position': 1})
     0
 
-NonCoding Class
----------------
-
-The ``NonCoding`` class provides conversions between noncoding positions and coordinates.
-
-NonCoding Position Model
-~~~~~~~~~~~~~~~~~~~~~~~
+On top of the functionality provided by the ``Genomic`` class, the
+``NonCoding`` class provides an interface to conversions between noncoding
+positions and coordinates.
 
-Noncoding positions follow the HGVS ``n`` coordinate system. They are represented as dictionaries. Below is an example of ``n.14+1`` in HGVS.
-
-.. code-block:: json
-
-    {
-        "position": 10,
-        "offset": -5,
-        "region": ""
-    }
-
-Where:
-
-- **position**: a positive integer (>0)
-- **offset**: an integer indicating the offset relative to the position (negative for upstream, positive for downstream)
-- **region**: a string describing the region type (``''`` for standard, ``'u'`` for upstream, ``'d'`` for downstream)
-
-NonCoding Position Conversion
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. code-block:: python
+.. code:: python
 
     >>> from mutalyzer_crossmapper import NonCoding
-    >>> crossmap = NonCoding(_exons)
-    >>> crossmap.coordinate_to_noncoding(25)
-    {"position": 10, "offset": -5, "region": ''}
-    >>> crossmap.noncoding_to_coordinate({"position": 10, "offset": -5, "region": ""})
-    25
-
-Notes
-~~~~~
-
-- Add the flag ``inverted=True`` to the constructor when the transcript resides on the reverse complement strand.
-
-Here is the mapping of coordinates to noncoding positions:
-
-.. csv-table::
-   :class: table-scroll
-   :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
-
-   "0", "5", "0", "u", "c.u5"
-   "4", "1", "0", "u", "n.u1"
-   "5", "1", "0", "", "n.1"
-   "24", "9", "5", "", "n.9+5"
-   "25", "10", "-5", "", "n.10-5"
-   "71", "22", "0", "", "n.22"
-   "72", "1", "0", "d", "n.d1"
-   "79", "8", "0", "d", "n.d8"
-
-
+    >>> exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
+    >>> crossmap = NonCoding(exons)
+    >>> crossmap.coordinate_to_noncoding(35)
+    {'position':14, 'offset':1, 'region':''}
+    >>> crossmap.noncoding_to_coordinate({'position':14, 'offset':1, 'region':''})
+    35
 
-Coding Class
-------------
+Add the flag ``inverted=True`` to the constructor when the transcript resides
+on the reverse complement strand.
 
-The ``Coding`` class provides conversions between coding positions and coordinates, as well as protein positions.
+On top of the functionality provided by the ``NonCoding`` class, the ``Coding``
+class provides an interface to conversions between coding positions and
+coordinates as well as conversions between protein positions and coordinates.
 
-Coding Position Model
-~~~~~~~~~~~~~~~~~~~~
-
-Coding positions follow the HGVS ``c`` coordinate system. They are represented as dictionaries. Here is an example of ``c.*1+3``.
-
-.. code-block:: json
-
-    {
-        "position": 1,
-        "offset": 3,
-        "region": "*"
-    }
-
-Where:
-
-- **position**: a positive integer
-- **offset**: an integer indicating the offset relative to the position
-- **region**: a string describing the region type (`""` for standard coding positions, `'-'` for 5' UTR, `'*'` for 3' UTR, `'u'` for upstream and ``"d"`` for downstream)
-
-Coding Position Conversion
-~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. code-block:: python
+.. code:: python
 
     >>> from mutalyzer_crossmapper import Coding
-    >>> crossmap = Coding(_exons, _cds)
-    >>> crossmap.coordinate_to_coding(46)
-    {"position": 1, "offset": 3, "region": '*'}
-    >>> crossmap.coding_to_coordinate({"position": 1, "offset": 3, "region": "*"})
-    46
-
-Notes
-~~~~~
-
-- The flag ``inverted=True`` can be used for transcripts on the reverse complement strand.
-
-Here is the mapping of coordinates to coding positions:
-
-.. csv-table::
-   :class: table-scroll
-   :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
-
-   "0", "5", "0", "u", "c.u5"
-   "4", "1", "0", "u", "c.u1"
-   "5", "11", "0", "\-", "c.-11"
-   "24", "3", "5", "\-", "c.-3+5"
-   "25", "2", "-5", "\-", "c.-2-5"
-   "31", "1", "0", "\-", "c.-1"
-   "32", "1", "0", "", "c.1"
-   "37", "3", "3", "", "c.3+3"
-   "38", "4", "-2", "", "c.4-2"
-   "43", "1", "0", "\*", "c.*1"
-   "60", "3", "9", "\*", "c.*3+9"
-   "61", "4", "-9", "\*", "c.*4+9"
-   "71", "5", "0", "\*", "c.*5"
-   "79", "8", "0", "d", "c.d8"
-
-
-
-
-Protein
--------
-
-Protein Position Model
-~~~~~~~~~~~~~~~~~~~~~~
-
-Protein positions follow the HGVS ``p`` coordinate system. They are represented as dictionaries. Here is an example of ``p.1`` in HGVS.
-
-.. code-block:: json
-
-    {
-        "position": 1,
-        "position_in_codon": 3,
-        "offset": 3,
-        "region": ""
-    }
-
-Where:
-
-- **position**: the amino acid position (1-based)
-- **position_in_codon**: the codon nucleotide index (1, 2, or 3)
-- **offset**: an integer indicating offset relative to the codon
-- **region**: a string describing the region type (``''`` for standard positions)
-
-Protein Position Conversion
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Conversions between protein positions and coordinates:
-
-.. code-block:: python
-
-    >>> crossmap.coordinate_to_protein(37)
-    {"position": 1, "position_in_codon": 3, "offset": 3, "region": ""}
-    >>> crossmap.protein_to_coordinate({"position": 1, "position_in_codon": 3, "offset": 3, "region": ""})
-    37
-
+    >>> cds = (32, 43)
+    >>> crossmap = Coding(exons, cds)
+    >>> crossmap.coordinate_to_coding(31)
+    {'position':1, 'offset':0, 'region':'-'}
+    >>> crossmap.coding_to_coordinate({'position':1, 'offset':0, 'region':'-'})
+    31
 
-Here is the mapping of coordinates to protein positions:
+Again, the flag ``inverted=True`` can be used for transcripts that reside on
+the reverse complement strand.
 
-.. csv-table::
-   :class: table-scroll
-   :header: "Coordinate", "Position", "position_in_codon", "Offset", "Region", "HGVS"
+Conversions between protein positions and coordinates are done as follows.
 
-   "0", "4", "2", "0", "u",
-   "4", "4", "2", "0", "u",
-   "5", "4", "2", "0", "\-",
-   "6", "4", "3", "0", "\-",
-   "7", "3", "1", "0", "\-",
-   "31", "1", "3", "0", "\-",
-   "32", "1", "1", "0", "", "p.1"
-   "42", "2", "3", "0", "", "p.2"
-   "43", "1", "1", "0", "\*",
-   "44", "1", "1", "1", "\*",
-   "79", "2", "2", "0", "d",
+.. code:: python
 
+    >>> crossmap.coordinate_to_protein(41)
+    {'position':2, 'position_in_codon': 2, 'offset':0, 'region':''}
+    >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon': 2, 'offset':0, 'region':''})
+    41
 
 
 

From ca4379ef865138c0d66a9436f102497b1f91dbf5 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 11:32:56 +0100
Subject: [PATCH 078/127] Update README.rst

---
 README.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.rst b/README.rst
index d398402..fd0308c 100644
--- a/README.rst
+++ b/README.rst
@@ -54,7 +54,7 @@ positions and coordinates.
     >>> crossmap = Genomic()
     >>> crossmap.coordinate_to_genomic(0)
     1
-    >>> crossmap.genomic_to_coordinate({'position': 1})
+    >>> crossmap.genomic_to_coordinate({'position':1})
     0
 
 On top of the functionality provided by the ``Genomic`` class, the
@@ -97,7 +97,7 @@ Conversions between protein positions and coordinates are done as follows.
 
     >>> crossmap.coordinate_to_protein(41)
     {'position':2, 'position_in_codon': 2, 'offset':0, 'region':''}
-    >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon': 2, 'offset':0, 'region':''})
+    >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon':2, 'offset':0, 'region':''})
     41
 
 

From 072719d7dd1a1c27b7be8adb1e234dca56d7cc78 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Mar 2026 13:32:07 +0100
Subject: [PATCH 079/127] Update library, replace tuple with dictionary

---
 docs/library.rst | 308 ++++++++++++++++++++++++++---------------------
 1 file changed, 173 insertions(+), 135 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 6ef095a..032b5c8 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -8,7 +8,24 @@ The ``Genomic`` class
 ---------------------
 
 The ``Genomic`` class provides an interface to conversions between genomic
-positions and coordinates.
+(``g.``, ``m``, ``n``) positions and coordinates.
+
+Genomic Position Model
+~~~~~~~~~~~~~~~~~~~~~~~
+
+Genomic positions follow the HGVS genomic coordinate system.
+They are represented as 1-key dictionaries. Below is an example of `g.1` in HGVS.
+
+.. code-block:: json
+
+    {'position':1}
+
+Where:
+
+- **position**: a positive integer(>0)
+
+Genomic Position Conversion
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code:: python
 
@@ -22,7 +39,7 @@ used to convert to and from genomic positions.
 
     >>> crossmap.coordinate_to_genomic(0)
     1
-    >>> crossmap.genomic_to_coordinate(1)
+    >>> crossmap.genomic_to_coordinate({'position':1})
     0
 
 See section :doc:`api/crossmap` for a detailed description.
@@ -32,8 +49,33 @@ The ``NonCoding`` class
 
 On top of the functionality provided by the ``Genomic`` class, the
 ``NonCoding`` class provides an interface to conversions between noncoding
-positions and coordinates. Conversions between positioning systems should be
-done via a coordinate.
+(``n.``, ``r.``) positions and coordinates. Conversions between positioning
+systems should be done via a coordinate.
+
+NonCoding Position Model
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+Noncoding positions follow the HGVS ``n`` coordinate system. They are represented
+as 3-key dictionaries. Below is an example of ``n.14+1`` in HGVS.
+
+.. code-block:: json
+
+    {
+        'position': 14,
+        'offset': 1,
+        'region': ''
+    }
+
+Where:
+
+- **position**: an interger representing a transcript position (>0)
+- **offset**: an integer indicating the offset relative to the position (negative for upstream,
+  positive for downstream)
+- **region**: a string describing the region type (``''`` for standard, ``'u'`` for upstream,
+  ``'d'`` for downstream)
+
+NonCoding Position Conversion
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code:: python
 
@@ -41,22 +83,8 @@ done via a coordinate.
     >>> exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
     >>> crossmap = NonCoding(exons)
 
-Now the functions ``coordinate_to_noncoding()`` and
-``noncoding_to_coordinate()`` can be used. These functions use a 3-tuple to
-represent a noncoding position.
-
-.. _table_noncoding:
-.. list-table:: Noncoding positions.
-   :header-rows: 1
-
-   * - index
-     - description
-   * - 0
-     - Transcript position.
-   * - 1
-     - Offset.
-   * - 2
-     - Upstream or downstream offset.
+Now the functions ``coordinate_to_noncoding()`` and ``noncoding_to_coordinate()``
+can be used.
 
 In our example, the HGVS position "g.36" (coordinate ``35``) is equivalent to
 position "n.14+1". We can convert between these two as follows.
@@ -64,25 +92,24 @@ position "n.14+1". We can convert between these two as follows.
 .. code:: python
 
     >>> crossmap.coordinate_to_noncoding(35)
-    (14, 1, 0)
+    {'position':14, 'offset':1, 'region':''}
+    >>> crossmap.noncoding_to_coordinate({'position':14, 'offset':1, 'region':''})
+    {'position':14, 'offset':1, 'region':''}
 
-When the coordinate is upstream or downstream of the transcript, the last
-element of the tuple denotes the offset with respect to the transcript. This
-makes it possible to distinguish between intronic positions and those outside
-of the transcript.
+When the coordinate is upstream or downstream of the transcript,  we use ``'u`` to
+present upstream and ``'d'`` to present downstream.
 
 .. code:: python
 
     >>> crossmap.coordinate_to_noncoding(2)
-    (1, -3, -3)
+    {'position':3, 'offset':0, 'region':'u'}
+    >>> crossmap.noncoding_to_coordinate({'position':3, 'offset':0, 'region':'u'})
+    2
     >>> crossmap.coordinate_to_noncoding(73)
-    (22, 2, 2)
+    {'position':2, 'offset':0, 'region':'d'}
+    >>> crossmap.noncoding_to_coordinate({'position':2, 'offset':0, 'region':'d'})
+    73
 
-Note that this last element is optional (and ignored) when a conversion to a
-coordinate is requested.
-
-    >>> crossmap.noncoding_to_coordinate((14, 1))
-    35
 
 For transcripts that reside on the reverse complement strand, the ``inverted``
 parameter should be set to ``True``. In our example, HGVS position "g.36"
@@ -92,18 +119,55 @@ parameter should be set to ``True``. In our example, HGVS position "g.36"
 
     >>> crossmap = NonCoding(exons, inverted=True)
     >>> crossmap.coordinate_to_noncoding(35)
-    (9, -1, 0)
-    >>> crossmap.noncoding_to_coordinate((9, -1))
+    {'position':9, 'offset':-1, 'region':''}
+    >>> crossmap.noncoding_to_coordinate({'position':9, 'offset':-1, 'region':''})
     35
 
+In the following table, we show a number of annotated examples.
+.. csv-table::
+   :class: table-scroll
+   :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
+
+   "0", "5", "0", `u`, `n.u5`
+   "4", "1", "0", `u`, `n.u1`
+   "5", "1", "0", `""`, `n.1`
+   "24", "9", "5", `""`, `n.9+5`
+   "25", "10", "-5", `""`, `n.10-5`
+   "71", "22", "0", `""`, `n.22`
+   "72", "1", "0", `d`, `n.d1`
+   "79", "8", "0", `d`, `n.d8`
+
 See section :doc:`api/crossmap` for a detailed description.
 
 The ``Coding`` class
 --------------------
 
 The ``Coding`` class provides an interface to all conversions between
-positioning systems and coordinates. Conversions between positioning systems
-should be done via a coordinate.
+coding (``c.``, ``r.``) rpositioning systems and coordinates. Conversions between
+positioning systems should be done via a coordinate.
+
+Coding Position Model
+~~~~~~~~~~~~~~~~~~~~~
+Coding positions follow the HGVS ``c`` coordinate system. They are
+represented as 3-key dictionaries. Here is an example of ``c.*1+3``.
+
+.. code-block:: json
+
+    {
+        'position': 1,
+        'offset': 3,
+        'region': '*'
+    }
+
+Where:
+
+- **position**: an interger representing a transcript position (>0)
+- **offset**: an integer indicating the offset relative to the position
+- **region**: a string describing the region type (`''` for standard coding positions,
+  `'-'` for 5' UTR, `'*'` for 3' UTR, `'u'` for upstream and ``'d'`` for downstream)
+
+Coding Position Conversion
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code:: python
 
@@ -114,40 +178,7 @@ should be done via a coordinate.
 
 On top of the functionality provided by the ``NonCoding`` class, the functions
 ``coordinate_to_coding()`` and ``coding_to_coordinate()`` can be used. These
-functions use a 4-tuple to represent a coding position.
-
-.. list-table:: Coding positions.
-   :header-rows: 1
-
-   * - index
-     - description
-   * - 0
-     - Transcript position.
-   * - 1
-     - Offset.
-   * - 2
-     - Region.
-   * - 3
-     - Upstream or downstream offset.
-
-The region denotes the location of the position with respect to the CDS. This
-is needed in order to work with the HGVS "-" and "*" positions.
-
-.. list-table:: Coding position regions.
-   :header-rows: 1
-
-   * - value
-     - description
-     - HGVS example
-   * - ``-1``
-     - Upstream of the CDS.
-     - "c.-10"
-   * - ``0``
-     - In the CDS.
-     - "c.1"
-   * - ``1``
-     - Downstream of the CDS.
-     - "c.*10"
+functions use a 3-key dictionary to represent a coding position.
 
 In our example, the HGVS position "g.32" (coordinate ``31``) is equivalent to
 position "c.-1". We can convert between these two as follows.
@@ -155,40 +186,64 @@ position "c.-1". We can convert between these two as follows.
 .. code:: python
 
     >>> crossmap.coordinate_to_coding(31)
-    (-1, 0, -1, 0)
-    >>> crossmap.coding_to_coordinate((-1, 0, -1))
+    {'position':1, 'offset':0, 'region':'-'}
+    >>> crossmap.coding_to_coordinate({'position':1, 'offset':0, 'region':'-'})
     31
 
 The ``coordinate_to_coding()`` function accepts an optional ``degenerate``
 argument. When set to ``True``, positions outside of the transcript are no
-longer described using the offset notation.
+longer described using the ``'u'`` or ``'d'`` notation.
 
 .. code:: python
 
     >>> crossmap.coordinate_to_coding(4)
-    (-11, -1, -1, -1)
+    {'position':1, 'offset':0, 'region':'u'}
     >>> crossmap.coordinate_to_coding(4, True)
-    (-12, 0, -1, -1)
+    {'position':12, 'offset':0, 'region':'-'}
+
+In the following table, we show a number of annotated examples.
+
+.. csv-table::
+   :class:
+   :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
+
+   "0", "5", "0", `u`, `c.u5`
+   "4", "1", "0", `u`, `c.u1`
+   "5", "11", "0", `-`, `c.-11`
+   "24", "3", "5", `-`, `c.-3+5`
+   "31", "1", "0", `-`, `c.-1`
+   "32", "1", "0", `""`, `c.1`
+   "37", "3", "3", `""`, `c.3+3`
+   "38", "4", "-2", `""`, `c.4-2`
+   "43", "1", "0", `*`, `c.*1`
+   "61", "4", "-9", `*`, `c.*4+9`
+   "71", "5", "0", `*`, `c.*5`
+   "79", "8", "0", `d`, `c.d8`
+
+
+Protein
+-------
 
 Additionally, the functions ``coordinate_to_protein()`` and
-``protein_to_coordinate()`` can be used. These functions use a 5-tuple to
-represent a protein position.
-
-.. list-table:: Protein positions.
-   :header-rows: 1
-
-   * - index
-     - description
-   * - 0
-     - Protein position.
-   * - 1
-     - Codon position.
-   * - 2
-     - Offset.
-   * - 3
-     - Region.
-   * - 4
-     - Upstream or downstream offset.
+``protein_to_coordinate()`` can be used. These functions use a 4-key dictionary
+to represent a protein position. Here is an example of ``p.1`` in HGVS.
+
+.. code-block:: json
+
+    {
+        'position': 1,
+        'position_in_codon': 3,
+        'offset': 3,
+        'region': ''
+    }
+
+Where:
+
+- **position**: an interger representing the protein position (>0)
+- **position_in_codon**: an integer indicating the nucleotide index within the codon (1, 2, or 3)
+- **offset**: an integer indicating offset relative to the codon
+- **region**: a string describing the region type (``''`` for standard positions)
+
 
 In our example the HGVS position "g.42" (coordinate ``41``) corresponds with
 position "p.2". We can convert between these to as follows.
@@ -196,49 +251,32 @@ position "p.2". We can convert between these to as follows.
 .. code:: python
 
     >>> crossmap.coordinate_to_protein(41)
-    (2, 2, 0, 0, 0)
-    >>> crossmap.protein_to_coordinate((2, 2, 0, 0))
+    {'position':2, 'position_in_codon':2, 'offset':0, 'region':''}
+    >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon':2, offset':0, 'region':''})
     41
 
 Note that the protein position only corresponds with the HGVS "p." notation
 when the offset equals ``0`` and the region equals ``1``. In the following
 table, we show a number of annotated examples.
 
-.. list-table:: Protein positions examples.
-   :header-rows: 1
-
-   * - coordinate
-     - protein position
-     - description
-     - HGVS position
-   * - ``4``
-     - ``(-4, 2, -1, -1, -1)``
-     - Upstream position.
-     - invalid
-   * - ``31``
-     - ``(-1, 3, 0, -1, 0)``
-     - 5' UTR position.
-     - invalid
-   * - ``36``
-     - ``(1, 3, 2, 0, 0)``
-     - Intronic position.
-     - invalid
-   * - ``40``
-     - ``(2, 1, 0, 0, 0)``
-     - Second amino acid, first nucleotide.
-     - "p.2"
-   * - ``41``
-     - ``(2, 2, 0, 0, 0)``
-     - Second amino acid, second nucleotide.
-     - "p.2"
-   * - ``43``
-     - ``(1, 1, 0, 1, 0)``
-     - 3' UTR position.
-     - invalid
-   * - ``43``
-     - ``(2, 2, 2, 1, 2)``
-     - Downstream position.
-     - invalid
+.. csv-table::
+   :class: table-scroll
+   :header: "Coordinate", "Position", "position_in_codon", "Offset", "Region", "HGVS"
+
+   "0", "4", "2", "0", `u`, ``
+   "4", "4", "2", "0", `u`, ``
+   "5", "4", "2", "0", `-`, ``
+   "6", "4", "3", "0", `-`, ``
+   "7", "3", "1", "0", `-`, ``
+   "31", "1", "3", "0", `-`, ``
+   "32", "1", "1", "0", ``, `p.1`
+   "33", "1", "2", "0", ``, `p.1`
+   "42", "2", "3", "0", ``, `p.2`
+   "43", "1", "1", "0", `*`, ``
+   "44", "1", "1", "1", `*`, ``
+   "79", "2", "2", "0", `d`, ``
+
+
 
 See section :doc:`api/crossmap` for a detailed description.
 
@@ -279,7 +317,7 @@ The ``Locus`` class
 ^^^^^^^^^^^^^^^^^^^
 
 The ``Locus`` class is used to deal with offsets with respect to a single
-locus. 
+locus.
 
 .. code:: python
 
@@ -288,13 +326,13 @@ locus.
 
 This class provides the functions ``to_position()`` and ``to_coordinate()`` for
 converting from a locus position to a coordinate and vice versa. These
-functions work with a 2-tuple, see the section about `The NonCoding class`_
+functions work with a 2-key dictionary, see the section about `The NonCoding class`_
 for the semantics.
 
 .. code:: python
 
     >>> locus.to_position(9)
-    (1, -1)
+    {'position':1, 'offset':-1}
 
 For loci that reside on the reverse complement strand, the optional
 ``inverted`` constructor parameter should be set to ``True``.
@@ -317,8 +355,8 @@ The interface to this class is similar to that of the ``Locus`` class.
 .. code:: python
 
     >>> multilocus.to_position(22)
-    (10, 3)
+    {'position':10, 'offset':3, 'region':''}
     >>> multilocus.to_position(38)
-    (11, -2)
+    {'position':11, 'offset':-2, 'region':''}
 
 See section :doc:`api/multi_locus` for a detailed description.

From fba6b95312134da10a4b5b41c0e74c9829dbe2c8 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 14:16:35 +0100
Subject: [PATCH 080/127] Use python code block in library.rst

---
 docs/library.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/library.rst b/docs/library.rst
index 032b5c8..263d463 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -16,7 +16,7 @@ Genomic Position Model
 Genomic positions follow the HGVS genomic coordinate system.
 They are represented as 1-key dictionaries. Below is an example of `g.1` in HGVS.
 
-.. code-block:: json
+.. code-block:: python
 
     {'position':1}
 

From ca45f679b380a4b658d1896532eddd93a766bc7e Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 14:17:47 +0100
Subject: [PATCH 081/127] Update library.rst

---
 docs/library.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 263d463..5d84c9e 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -58,7 +58,7 @@ NonCoding Position Model
 Noncoding positions follow the HGVS ``n`` coordinate system. They are represented
 as 3-key dictionaries. Below is an example of ``n.14+1`` in HGVS.
 
-.. code-block:: json
+.. code-block:: python
 
     {
         'position': 14,
@@ -151,7 +151,7 @@ Coding Position Model
 Coding positions follow the HGVS ``c`` coordinate system. They are
 represented as 3-key dictionaries. Here is an example of ``c.*1+3``.
 
-.. code-block:: json
+.. code-block:: python
 
     {
         'position': 1,
@@ -228,7 +228,7 @@ Additionally, the functions ``coordinate_to_protein()`` and
 ``protein_to_coordinate()`` can be used. These functions use a 4-key dictionary
 to represent a protein position. Here is an example of ``p.1`` in HGVS.
 
-.. code-block:: json
+.. code-block:: python
 
     {
         'position': 1,

From e4e1642cd379323feba882e4ac75ecfdb7ed80de Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 14:32:24 +0100
Subject: [PATCH 082/127] Update library.rst

---
 docs/library.rst | 244 ++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 200 insertions(+), 44 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 5d84c9e..1f5ac9a 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -124,18 +124,56 @@ parameter should be set to ``True``. In our example, HGVS position "g.36"
     35
 
 In the following table, we show a number of annotated examples.
-.. csv-table::
-   :class: table-scroll
-   :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
-
-   "0", "5", "0", `u`, `n.u5`
-   "4", "1", "0", `u`, `n.u1`
-   "5", "1", "0", `""`, `n.1`
-   "24", "9", "5", `""`, `n.9+5`
-   "25", "10", "-5", `""`, `n.10-5`
-   "71", "22", "0", `""`, `n.22`
-   "72", "1", "0", `d`, `n.d1`
-   "79", "8", "0", `d`, `n.d8`
+
+.. _table_noncoding:
+.. list-table:: Coordinates to Noncoding Positions mapping.
+   :header-rows: 1
+
+   * - Coordinate
+     - Position
+     - Offset
+     - Region
+     - HGVS
+   * - 0
+     - 5
+     - 0
+     - ``u``
+     - ``n.u5``
+   * - 4
+     - 1
+     - 0
+     - ``u``
+     - ``n.u1``
+   * - 5
+     - 1
+     - 0
+     - ``
+     - ``n.1``
+   * - 24
+     - 9
+     - 5
+     - ````
+     - ``n.9+5``
+   * - 25
+     - 10
+     - -5
+     - ````
+     - ``n.10-5``
+   * - 71
+     - 22
+     - 0
+     - ````
+     - ``n.22``
+   * - 72
+     - 1
+     - 0
+     - ``d``
+     - ``n.d1``
+   * - 79
+     - 8
+     - 0
+     - ``d``
+     - ``n.d8``
 
 See section :doc:`api/crossmap` for a detailed description.
 
@@ -203,22 +241,75 @@ longer described using the ``'u'`` or ``'d'`` notation.
 
 In the following table, we show a number of annotated examples.
 
-.. csv-table::
-   :class:
-   :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
-
-   "0", "5", "0", `u`, `c.u5`
-   "4", "1", "0", `u`, `c.u1`
-   "5", "11", "0", `-`, `c.-11`
-   "24", "3", "5", `-`, `c.-3+5`
-   "31", "1", "0", `-`, `c.-1`
-   "32", "1", "0", `""`, `c.1`
-   "37", "3", "3", `""`, `c.3+3`
-   "38", "4", "-2", `""`, `c.4-2`
-   "43", "1", "0", `*`, `c.*1`
-   "61", "4", "-9", `*`, `c.*4+9`
-   "71", "5", "0", `*`, `c.*5`
-   "79", "8", "0", `d`, `c.d8`
+.. _table_coding:
+.. list-table:: Coordinates to Coding Positions mapping
+   :header-rows: 1
+
+   * - Coordinate
+     - Position
+     - Offset
+     - Region
+     - HGVS
+   * - 0
+     - 5
+     - 0
+     - ``u``
+     - ``c.u5``
+   * - 4
+     - 1
+     - 0
+     - ``u``
+     - ``c.u1``
+   * - 5
+     - 11
+     - 0
+     - ``-``
+     - ``c.-11``
+   * - 24
+     - 3
+     - 5
+     - ``-``
+     - ``c.-3+5``
+   * - 31
+     - 1
+     - 0
+     - ``-``
+     - ``c.-1``
+   * - 32
+     - 1
+     - 0
+     - ``
+     - ``c.1``
+   * - 37
+     - 3
+     - 3
+     - ``
+     - ``c.3+3``
+   * - 38
+     - 4
+     - -2
+     - ``
+     - ``c.4-2``
+   * - 43
+     - 1
+     - 0
+     - ``*``
+     - ``c.*1``
+   * - 61
+     - 4
+     - -9
+     - ``*``
+     - ``c.*4+9``
+   * - 71
+     - 5
+     - 0
+     - ``*``
+     - ``c.*5``
+   * - 79
+     - 8
+     - 0
+     - ``d``
+     - ``c.d8``
 
 
 Protein
@@ -259,22 +350,87 @@ Note that the protein position only corresponds with the HGVS "p." notation
 when the offset equals ``0`` and the region equals ``1``. In the following
 table, we show a number of annotated examples.
 
-.. csv-table::
-   :class: table-scroll
-   :header: "Coordinate", "Position", "position_in_codon", "Offset", "Region", "HGVS"
-
-   "0", "4", "2", "0", `u`, ``
-   "4", "4", "2", "0", `u`, ``
-   "5", "4", "2", "0", `-`, ``
-   "6", "4", "3", "0", `-`, ``
-   "7", "3", "1", "0", `-`, ``
-   "31", "1", "3", "0", `-`, ``
-   "32", "1", "1", "0", ``, `p.1`
-   "33", "1", "2", "0", ``, `p.1`
-   "42", "2", "3", "0", ``, `p.2`
-   "43", "1", "1", "0", `*`, ``
-   "44", "1", "1", "1", `*`, ``
-   "79", "2", "2", "0", `d`, ``
+.. list-table::Coordinates to Protein Positions mapping
+   :header-rows: 1
+
+   * - Coordinate
+     - Position
+     - position_in_codon
+     - Offset
+     - Region
+     - HGVS
+   * - 0
+     - 4
+     - 2
+     - 0
+     - ``u``
+     - ``
+   * - 4
+     - 4
+     - 2
+     - 0
+     - ``u``
+     - ``
+   * - 5
+     - 4
+     - 2
+     - 0
+     - ``-``
+     - ``
+   * - 6
+     - 4
+     - 3
+     - 0
+     - ``-``
+     - ``
+   * - 7
+     - 3
+     - 1
+     - 0
+     - ``-``
+     - ``
+   * - 31
+     - 1
+     - 3
+     - 0
+     - ``-``
+     - ``
+   * - 32
+     - 1
+     - 1
+     - 0
+     - ``
+     - ``p.1``
+   * - 33
+     - 1
+     - 2
+     - 0
+     - ``
+     - ``p.1``
+   * - 42
+     - 2
+     - 3
+     - 0
+     - ``
+     - ``p.2``
+   * - 43
+     - 1
+     - 1
+     - 0
+     - ``*``
+     - ``
+   * - 44
+     - 1
+     - 1
+     - 1
+     - ``*``
+     - ``
+   * - 79
+     - 2
+     - 2
+     - 0
+     - ``d``
+     - ``
 
 
 

From b630851a155488efbd369bf7b0ec942b9007404d Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 14:38:56 +0100
Subject: [PATCH 083/127] Update library.rst

---
 docs/library.rst | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 1f5ac9a..6d103a9 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -96,7 +96,7 @@ position "n.14+1". We can convert between these two as follows.
     >>> crossmap.noncoding_to_coordinate({'position':14, 'offset':1, 'region':''})
     {'position':14, 'offset':1, 'region':''}
 
-When the coordinate is upstream or downstream of the transcript,  we use ``'u`` to
+When the coordinate is upstream or downstream of the transcript,  we use ``'u'`` to
 present upstream and ``'d'`` to present downstream.
 
 .. code:: python
@@ -152,17 +152,17 @@ In the following table, we show a number of annotated examples.
    * - 24
      - 9
      - 5
-     - ````
+     - ``
      - ``n.9+5``
    * - 25
      - 10
      - -5
-     - ````
+     - ``
      - ``n.10-5``
    * - 71
      - 22
      - 0
-     - ````
+     - ``
      - ``n.22``
    * - 72
      - 1

From a0514c8ad17b2de550272be1e9bdd4e70cb8e56b Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 14:44:22 +0100
Subject: [PATCH 084/127] Update library.rst

---
 docs/library.rst | 132 +++++++++++++++++++++++------------------------
 1 file changed, 66 insertions(+), 66 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 6d103a9..4e84d7e 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -137,43 +137,43 @@ In the following table, we show a number of annotated examples.
    * - 0
      - 5
      - 0
-     - ``u``
-     - ``n.u5``
+     - u``
+     - n.u5``
    * - 4
      - 1
      - 0
-     - ``u``
-     - ``n.u1``
+     - u``
+     - n.u1``
    * - 5
      - 1
      - 0
-     - ``
-     - ``n.1``
+     - 
+     - n.1``
    * - 24
      - 9
      - 5
-     - ``
-     - ``n.9+5``
+     - 
+     - n.9+5``
    * - 25
      - 10
      - -5
-     - ``
-     - ``n.10-5``
+     - 
+     - n.10-5``
    * - 71
      - 22
      - 0
-     - ``
-     - ``n.22``
+     - 
+     - n.22``
    * - 72
      - 1
      - 0
-     - ``d``
-     - ``n.d1``
+     - d``
+     - n.d1``
    * - 79
      - 8
      - 0
-     - ``d``
-     - ``n.d8``
+     - d``
+     - n.d8``
 
 See section :doc:`api/crossmap` for a detailed description.
 
@@ -253,63 +253,63 @@ In the following table, we show a number of annotated examples.
    * - 0
      - 5
      - 0
-     - ``u``
-     - ``c.u5``
+     - u``
+     - c.u5``
    * - 4
      - 1
      - 0
-     - ``u``
-     - ``c.u1``
+     - u``
+     - c.u1``
    * - 5
      - 11
      - 0
-     - ``-``
-     - ``c.-11``
+     - -``
+     - c.-11``
    * - 24
      - 3
      - 5
-     - ``-``
-     - ``c.-3+5``
+     - -``
+     - c.-3+5``
    * - 31
      - 1
      - 0
-     - ``-``
-     - ``c.-1``
+     - -``
+     - c.-1``
    * - 32
      - 1
      - 0
-     - ``
-     - ``c.1``
+     - 
+     - c.1``
    * - 37
      - 3
      - 3
-     - ``
-     - ``c.3+3``
+     - 
+     - c.3+3``
    * - 38
      - 4
      - -2
-     - ``
-     - ``c.4-2``
+     - 
+     - c.4-2``
    * - 43
      - 1
      - 0
-     - ``*``
-     - ``c.*1``
+     - *``
+     - c.*1``
    * - 61
      - 4
      - -9
-     - ``*``
-     - ``c.*4+9``
+     - *``
+     - c.*4+9``
    * - 71
      - 5
      - 0
-     - ``*``
-     - ``c.*5``
+     - *``
+     - c.*5``
    * - 79
      - 8
      - 0
-     - ``d``
-     - ``c.d8``
+     - d``
+     - c.d8``
 
 
 Protein
@@ -343,14 +343,14 @@ position "p.2". We can convert between these to as follows.
 
     >>> crossmap.coordinate_to_protein(41)
     {'position':2, 'position_in_codon':2, 'offset':0, 'region':''}
-    >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon':2, offset':0, 'region':''})
+    >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon':2, 'offset':0, 'region':''})
     41
 
 Note that the protein position only corresponds with the HGVS "p." notation
 when the offset equals ``0`` and the region equals ``1``. In the following
 table, we show a number of annotated examples.
 
-.. list-table::Coordinates to Protein Positions mapping
+.. list-table:: Coordinates to Protein Positions mapping
    :header-rows: 1
 
    * - Coordinate
@@ -363,74 +363,74 @@ table, we show a number of annotated examples.
      - 4
      - 2
      - 0
-     - ``u``
-     - ``
+     - u``
+     - 
    * - 4
      - 4
      - 2
      - 0
-     - ``u``
-     - ``
+     - u``
+     - 
    * - 5
      - 4
      - 2
      - 0
-     - ``-``
-     - ``
+     - -``
+     - 
    * - 6
      - 4
      - 3
      - 0
-     - ``-``
-     - ``
+     - -``
+     - 
    * - 7
      - 3
      - 1
      - 0
-     - ``-``
-     - ``
+     - -``
+     - 
    * - 31
      - 1
      - 3
      - 0
-     - ``-``
-     - ``
+     - -``
+     - 
    * - 32
      - 1
      - 1
      - 0
-     - ``
-     - ``p.1``
+     - 
+     - p.1``
    * - 33
      - 1
      - 2
      - 0
-     - ``
-     - ``p.1``
+     - 
+     - p.1``
    * - 42
      - 2
      - 3
      - 0
-     - ``
-     - ``p.2``
+     - 
+     - p.2``
    * - 43
      - 1
      - 1
      - 0
-     - ``*``
-     - ``
+     - *``
+     - 
    * - 44
      - 1
      - 1
      - 1
-     - ``*``
-     - ``
+     - *``
+     - 
    * - 79
      - 2
      - 2
      - 0
-     - ``d``
-     - ``
+     - d``
+     - 
 
 
 

From 21ce8dd377781aa13fad3edb238c9f1b853d6f28 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 14:50:25 +0100
Subject: [PATCH 085/127] Update library.rst

---
 docs/library.rst | 84 ++++++++++++++++++++++++------------------------
 1 file changed, 42 insertions(+), 42 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 4e84d7e..4884f84 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -137,23 +137,23 @@ In the following table, we show a number of annotated examples.
    * - 0
      - 5
      - 0
-     - u``
-     - n.u5``
+     - ``u``
+     - ``n.u5``
    * - 4
      - 1
      - 0
-     - u``
-     - n.u1``
+     - ``u``
+     - ``n.u1``
    * - 5
      - 1
      - 0
      - 
-     - n.1``
+     - ``n.1``
    * - 24
      - 9
      - 5
      - 
-     - n.9+5``
+     - ``n.9+5``
    * - 25
      - 10
      - -5
@@ -163,17 +163,17 @@ In the following table, we show a number of annotated examples.
      - 22
      - 0
      - 
-     - n.22``
+     - ``n.22``
    * - 72
      - 1
      - 0
-     - d``
-     - n.d1``
+     - ``d``
+     - ``n.d1``
    * - 79
      - 8
      - 0
-     - d``
-     - n.d8``
+     - ``d``
+     - ``n.d8``
 
 See section :doc:`api/crossmap` for a detailed description.
 
@@ -253,43 +253,43 @@ In the following table, we show a number of annotated examples.
    * - 0
      - 5
      - 0
-     - u``
-     - c.u5``
+     - ``u``
+     - ``c.u5``
    * - 4
      - 1
      - 0
-     - u``
-     - c.u1``
+     - ``u``
+     - ``c.u1``
    * - 5
      - 11
      - 0
-     - -``
-     - c.-11``
+     - ``-``
+     - ``c.-11``
    * - 24
      - 3
      - 5
-     - -``
-     - c.-3+5``
+     - ``-``
+     - ``c.-3+5``
    * - 31
      - 1
      - 0
-     - -``
-     - c.-1``
+     - ``-``
+     - ``c.-1``
    * - 32
      - 1
      - 0
      - 
-     - c.1``
+     - ``c.1``
    * - 37
      - 3
      - 3
      - 
-     - c.3+3``
+     - ``c.3+3``
    * - 38
      - 4
      - -2
      - 
-     - c.4-2``
+     - ``c.4-2``
    * - 43
      - 1
      - 0
@@ -298,18 +298,18 @@ In the following table, we show a number of annotated examples.
    * - 61
      - 4
      - -9
-     - *``
-     - c.*4+9``
+     - ``*``
+     - ``c.*4+9``
    * - 71
      - 5
      - 0
-     - *``
-     - c.*5``
+     - ``*``
+     - ``c.*5``
    * - 79
      - 8
      - 0
-     - d``
-     - c.d8``
+     - ``d``
+     - ``c.d8``
 
 
 Protein
@@ -363,73 +363,73 @@ table, we show a number of annotated examples.
      - 4
      - 2
      - 0
-     - u``
+     - ``u``
      - 
    * - 4
      - 4
      - 2
      - 0
-     - u``
+     - ``u``
      - 
    * - 5
      - 4
      - 2
      - 0
-     - -``
+     - ``-``
      - 
    * - 6
      - 4
      - 3
      - 0
-     - -``
+     - ``-``
      - 
    * - 7
      - 3
      - 1
      - 0
-     - -``
+     - ``-``
      - 
    * - 31
      - 1
      - 3
      - 0
-     - -``
+     - ``-``
      - 
    * - 32
      - 1
      - 1
      - 0
      - 
-     - p.1``
+     - ``p.1``
    * - 33
      - 1
      - 2
      - 0
      - 
-     - p.1``
+     - ``p.1``
    * - 42
      - 2
      - 3
      - 0
      - 
-     - p.2``
+     - ``p.2``
    * - 43
      - 1
      - 1
      - 0
-     - *``
+     - ``*``
      - 
    * - 44
      - 1
      - 1
      - 1
-     - *``
+     - ``*``
      - 
    * - 79
      - 2
      - 2
      - 0
-     - d``
+     - ``d``
      - 
 
 

From 6fc7709b76452125225decc66f463879d79d7b0b Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 14:59:11 +0100
Subject: [PATCH 086/127] Update library.rst

---
 docs/library.rst | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 4884f84..ab46719 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -158,7 +158,7 @@ In the following table, we show a number of annotated examples.
      - 10
      - -5
      - 
-     - n.10-5``
+     - ``n.10-5``
    * - 71
      - 22
      - 0
@@ -293,8 +293,8 @@ In the following table, we show a number of annotated examples.
    * - 43
      - 1
      - 0
-     - *``
-     - c.*1``
+     - ``*``
+     - ``c.*1``
    * - 61
      - 4
      - -9
@@ -350,6 +350,7 @@ Note that the protein position only corresponds with the HGVS "p." notation
 when the offset equals ``0`` and the region equals ``1``. In the following
 table, we show a number of annotated examples.
 
+.. _table_protein:
 .. list-table:: Coordinates to Protein Positions mapping
    :header-rows: 1
 

From 1693bab2ede6ade8964a9e9e6c0ca2414ed44fd0 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 20 Mar 2026 15:43:35 +0100
Subject: [PATCH 087/127] Update library.rst

---
 docs/library.rst | 41 ++++++++++++++++++++---------------------
 1 file changed, 20 insertions(+), 21 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index ab46719..102dbb2 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -147,22 +147,22 @@ In the following table, we show a number of annotated examples.
    * - 5
      - 1
      - 0
-     - 
+     -
      - ``n.1``
    * - 24
      - 9
      - 5
-     - 
+     -
      - ``n.9+5``
    * - 25
      - 10
      - -5
-     - 
+     -
      - ``n.10-5``
    * - 71
      - 22
      - 0
-     - 
+     -
      - ``n.22``
    * - 72
      - 1
@@ -278,17 +278,17 @@ In the following table, we show a number of annotated examples.
    * - 32
      - 1
      - 0
-     - 
+     -
      - ``c.1``
    * - 37
      - 3
      - 3
-     - 
+     -
      - ``c.3+3``
    * - 38
      - 4
      - -2
-     - 
+     -
      - ``c.4-2``
    * - 43
      - 1
@@ -365,74 +365,73 @@ table, we show a number of annotated examples.
      - 2
      - 0
      - ``u``
-     - 
+     -
    * - 4
      - 4
      - 2
      - 0
      - ``u``
-     - 
+     -
    * - 5
      - 4
      - 2
      - 0
      - ``-``
-     - 
+     -
    * - 6
      - 4
      - 3
      - 0
      - ``-``
-     - 
+     -
    * - 7
      - 3
      - 1
      - 0
      - ``-``
-     - 
+     -
    * - 31
      - 1
      - 3
      - 0
      - ``-``
-     - 
+     -
    * - 32
      - 1
      - 1
      - 0
-     - 
+     -
      - ``p.1``
    * - 33
      - 1
      - 2
      - 0
-     - 
+     -
      - ``p.1``
    * - 42
      - 2
      - 3
      - 0
-     - 
+     -
      - ``p.2``
    * - 43
      - 1
      - 1
      - 0
      - ``*``
-     - 
+     -
    * - 44
      - 1
      - 1
      - 1
      - ``*``
-     - 
+     -
    * - 79
      - 2
      - 2
      - 0
      - ``d``
-     - 
-
+     -
 
 
 See section :doc:`api/crossmap` for a detailed description.
@@ -471,7 +470,7 @@ The ``Coding`` class makes use of a number of basic classes described in this
 section.
 
 The ``Locus`` class
-^^^^^^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~~~~~~
 
 The ``Locus`` class is used to deal with offsets with respect to a single
 locus.

From 9bb4501e04a1c5025f2fdba6e4e59cca7746be8d Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Mar 2026 15:56:55 +0100
Subject: [PATCH 088/127] Add backticks

---
 docs/library.rst | 278 ++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 217 insertions(+), 61 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 032b5c8..67bbc75 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -14,9 +14,9 @@ Genomic Position Model
 ~~~~~~~~~~~~~~~~~~~~~~~
 
 Genomic positions follow the HGVS genomic coordinate system.
-They are represented as 1-key dictionaries. Below is an example of `g.1` in HGVS.
+They are represented as 1-key dictionaries. Below is an example of ``g.1`` in HGVS.
 
-.. code-block:: json
+.. code-block:: python
 
     {'position':1}
 
@@ -58,7 +58,7 @@ NonCoding Position Model
 Noncoding positions follow the HGVS ``n`` coordinate system. They are represented
 as 3-key dictionaries. Below is an example of ``n.14+1`` in HGVS.
 
-.. code-block:: json
+.. code-block:: python
 
     {
         'position': 14,
@@ -86,8 +86,8 @@ NonCoding Position Conversion
 Now the functions ``coordinate_to_noncoding()`` and ``noncoding_to_coordinate()``
 can be used.
 
-In our example, the HGVS position "g.36" (coordinate ``35``) is equivalent to
-position "n.14+1". We can convert between these two as follows.
+In our example, the HGVS position ``g.36`` (coordinate `35`) is equivalent to
+position ``n.14+1``. We can convert between these two as follows.
 
 .. code:: python
 
@@ -96,7 +96,7 @@ position "n.14+1". We can convert between these two as follows.
     >>> crossmap.noncoding_to_coordinate({'position':14, 'offset':1, 'region':''})
     {'position':14, 'offset':1, 'region':''}
 
-When the coordinate is upstream or downstream of the transcript,  we use ``'u`` to
+When the coordinate is upstream or downstream of the transcript,  we use ``'u'`` to
 present upstream and ``'d'`` to present downstream.
 
 .. code:: python
@@ -112,8 +112,8 @@ present upstream and ``'d'`` to present downstream.
 
 
 For transcripts that reside on the reverse complement strand, the ``inverted``
-parameter should be set to ``True``. In our example, HGVS position "g.36"
-(coordinate ``35``) is now equivalent to position "n.9-1".
+parameter should be set to ``True``. In our example, HGVS position ``g.36``
+(coordinate `35`) is now equivalent to position ``n.9-1``.
 
 .. code:: python
 
@@ -124,18 +124,56 @@ parameter should be set to ``True``. In our example, HGVS position "g.36"
     35
 
 In the following table, we show a number of annotated examples.
-.. csv-table::
-   :class: table-scroll
-   :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
-
-   "0", "5", "0", `u`, `n.u5`
-   "4", "1", "0", `u`, `n.u1`
-   "5", "1", "0", `""`, `n.1`
-   "24", "9", "5", `""`, `n.9+5`
-   "25", "10", "-5", `""`, `n.10-5`
-   "71", "22", "0", `""`, `n.22`
-   "72", "1", "0", `d`, `n.d1`
-   "79", "8", "0", `d`, `n.d8`
+
+.. _table_noncoding:
+.. list-table:: Coordinates to Noncoding Positions mapping.
+   :header-rows: 1
+
+   * - coordinate
+     - position
+     - offset
+     - region
+     - HGVS
+   * - 0
+     - 5
+     - 0
+     - ``u``
+     - ``n.u5``
+   * - 4
+     - 1
+     - 0
+     - ``u``
+     - ``n.u1``
+   * - 5
+     - 1
+     - 0
+     -
+     - ``n.1``
+   * - 24
+     - 9
+     - 5
+     -
+     - ``n.9+5``
+   * - 25
+     - 10
+     - -5
+     -
+     - ``n.10-5``
+   * - 71
+     - 22
+     - 0
+     -
+     - ``n.22``
+   * - 72
+     - 1
+     - 0
+     - ``d``
+     - ``n.d1``
+   * - 79
+     - 8
+     - 0
+     - ``d``
+     - ``n.d8``
 
 See section :doc:`api/crossmap` for a detailed description.
 
@@ -151,7 +189,7 @@ Coding Position Model
 Coding positions follow the HGVS ``c`` coordinate system. They are
 represented as 3-key dictionaries. Here is an example of ``c.*1+3``.
 
-.. code-block:: json
+.. code-block:: python
 
     {
         'position': 1,
@@ -180,8 +218,8 @@ On top of the functionality provided by the ``NonCoding`` class, the functions
 ``coordinate_to_coding()`` and ``coding_to_coordinate()`` can be used. These
 functions use a 3-key dictionary to represent a coding position.
 
-In our example, the HGVS position "g.32" (coordinate ``31``) is equivalent to
-position "c.-1". We can convert between these two as follows.
+In our example, the HGVS position ``g.32`` (coordinate `31`) is equivalent to
+position ``c.-1``. We can convert between these two as follows.
 
 .. code:: python
 
@@ -203,22 +241,75 @@ longer described using the ``'u'`` or ``'d'`` notation.
 
 In the following table, we show a number of annotated examples.
 
-.. csv-table::
-   :class:
-   :header: "Coordinate", "Position", "Offset", "Region", "HGVS"
-
-   "0", "5", "0", `u`, `c.u5`
-   "4", "1", "0", `u`, `c.u1`
-   "5", "11", "0", `-`, `c.-11`
-   "24", "3", "5", `-`, `c.-3+5`
-   "31", "1", "0", `-`, `c.-1`
-   "32", "1", "0", `""`, `c.1`
-   "37", "3", "3", `""`, `c.3+3`
-   "38", "4", "-2", `""`, `c.4-2`
-   "43", "1", "0", `*`, `c.*1`
-   "61", "4", "-9", `*`, `c.*4+9`
-   "71", "5", "0", `*`, `c.*5`
-   "79", "8", "0", `d`, `c.d8`
+.. _table_coding:
+.. list-table:: Coordinates to Coding Positions mapping
+   :header-rows: 1
+
+   * - coordinate
+     - position
+     - offset
+     - region
+     - HGVS
+   * - 0
+     - 5
+     - 0
+     - ``u``
+     - ``c.u5``
+   * - 4
+     - 1
+     - 0
+     - ``u``
+     - ``c.u1``
+   * - 5
+     - 11
+     - 0
+     - ``-``
+     - ``c.-11``
+   * - 24
+     - 3
+     - 5
+     - ``-``
+     - ``c.-3+5``
+   * - 31
+     - 1
+     - 0
+     - ``-``
+     - ``c.-1``
+   * - 32
+     - 1
+     - 0
+     -
+     - ``c.1``
+   * - 37
+     - 3
+     - 3
+     -
+     - ``c.3+3``
+   * - 38
+     - 4
+     - -2
+     -
+     - ``c.4-2``
+   * - 43
+     - 1
+     - 0
+     - ``*``
+     - ``c.*1``
+   * - 61
+     - 4
+     - -9
+     - ``*``
+     - ``c.*4+9``
+   * - 71
+     - 5
+     - 0
+     - ``*``
+     - ``c.*5``
+   * - 79
+     - 8
+     - 0
+     - ``d``
+     - ``c.d8``
 
 
 Protein
@@ -228,7 +319,7 @@ Additionally, the functions ``coordinate_to_protein()`` and
 ``protein_to_coordinate()`` can be used. These functions use a 4-key dictionary
 to represent a protein position. Here is an example of ``p.1`` in HGVS.
 
-.. code-block:: json
+.. code-block:: python
 
     {
         'position': 1,
@@ -245,37 +336,102 @@ Where:
 - **region**: a string describing the region type (``''`` for standard positions)
 
 
-In our example the HGVS position "g.42" (coordinate ``41``) corresponds with
-position "p.2". We can convert between these to as follows.
+In our example the HGVS position ``g.42`` (coordinate `41`) corresponds with
+position ``p.2``. We can convert between these to as follows.
 
 .. code:: python
 
     >>> crossmap.coordinate_to_protein(41)
     {'position':2, 'position_in_codon':2, 'offset':0, 'region':''}
-    >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon':2, offset':0, 'region':''})
+    >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon':2, 'offset':0, 'region':''})
     41
 
 Note that the protein position only corresponds with the HGVS "p." notation
 when the offset equals ``0`` and the region equals ``1``. In the following
 table, we show a number of annotated examples.
 
-.. csv-table::
-   :class: table-scroll
-   :header: "Coordinate", "Position", "position_in_codon", "Offset", "Region", "HGVS"
-
-   "0", "4", "2", "0", `u`, ``
-   "4", "4", "2", "0", `u`, ``
-   "5", "4", "2", "0", `-`, ``
-   "6", "4", "3", "0", `-`, ``
-   "7", "3", "1", "0", `-`, ``
-   "31", "1", "3", "0", `-`, ``
-   "32", "1", "1", "0", ``, `p.1`
-   "33", "1", "2", "0", ``, `p.1`
-   "42", "2", "3", "0", ``, `p.2`
-   "43", "1", "1", "0", `*`, ``
-   "44", "1", "1", "1", `*`, ``
-   "79", "2", "2", "0", `d`, ``
-
+.. _table_protein:
+.. list-table:: Coordinates to Protein Positions mapping
+   :header-rows: 1
+
+   * - coordinate
+     - position
+     - position_in_codon
+     - offset
+     - region
+     - HGVS
+   * - 0
+     - 4
+     - 2
+     - 0
+     - ``u``
+     -
+   * - 4
+     - 4
+     - 2
+     - 0
+     - ``u``
+     -
+   * - 5
+     - 4
+     - 2
+     - 0
+     - ``-``
+     -
+   * - 6
+     - 4
+     - 3
+     - 0
+     - ``-``
+     -
+   * - 7
+     - 3
+     - 1
+     - 0
+     - ``-``
+     -
+   * - 31
+     - 1
+     - 3
+     - 0
+     - ``-``
+     -
+   * - 32
+     - 1
+     - 1
+     - 0
+     -
+     - ``p.1``
+   * - 33
+     - 1
+     - 2
+     - 0
+     -
+     - ``p.1``
+   * - 42
+     - 2
+     - 3
+     - 0
+     -
+     - ``p.2``
+   * - 43
+     - 1
+     - 1
+     - 0
+     - ``*``
+     -
+   * - 44
+     - 1
+     - 1
+     - 1
+     - ``*``
+     -
+   * - 79
+     - 2
+     - 2
+     - 0
+     - ``d``
+     -
 
 
 See section :doc:`api/crossmap` for a detailed description.
@@ -314,7 +470,7 @@ The ``Coding`` class makes use of a number of basic classes described in this
 section.
 
 The ``Locus`` class
-^^^^^^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~~~~~~
 
 The ``Locus`` class is used to deal with offsets with respect to a single
 locus.

From 691ec354aaad6e7b0ee8d63a826ead3bdf9bbe6d Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Mar 2026 17:01:30 +0100
Subject: [PATCH 089/127] Cleanup

---
 docs/library.rst | 66 +++++++++++++++++++++++++++++-------------------
 1 file changed, 40 insertions(+), 26 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 67bbc75..a1c236e 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -8,7 +8,7 @@ The ``Genomic`` class
 ---------------------
 
 The ``Genomic`` class provides an interface to conversions between genomic
-(``g.``, ``m``, ``n``) positions and coordinates.
+(``g.``, ``m.``, ``n.``) positions and coordinates.
 
 Genomic Position Model
 ~~~~~~~~~~~~~~~~~~~~~~~
@@ -22,7 +22,7 @@ They are represented as 1-key dictionaries. Below is an example of ``g.1`` in HG
 
 Where:
 
-- **position**: a positive integer(>0)
+- **position**: a positive integer repersenting a base position(>0)
 
 Genomic Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -55,7 +55,7 @@ systems should be done via a coordinate.
 NonCoding Position Model
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-Noncoding positions follow the HGVS ``n`` coordinate system. They are represented
+Noncoding positions follow the HGVS ``n.`` coordinate system. They are represented
 as 3-key dictionaries. Below is an example of ``n.14+1`` in HGVS.
 
 .. code-block:: python
@@ -200,9 +200,10 @@ represented as 3-key dictionaries. Here is an example of ``c.*1+3``.
 Where:
 
 - **position**: an interger representing a transcript position (>0)
-- **offset**: an integer indicating the offset relative to the position
-- **region**: a string describing the region type (`''` for standard coding positions,
-  `'-'` for 5' UTR, `'*'` for 3' UTR, `'u'` for upstream and ``'d'`` for downstream)
+- **offset**: an integer indicating the offset relative to the position (negative for upstream,
+  positive for downstream)
+- **region**: a string describing the region type (``''`` for standard coding positions,
+  ``'-'`` for 5' UTR, ``'*'`` for 3' UTR, ``'u'`` for upstream and ``'d'`` for downstream)
 
 Coding Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -230,7 +231,8 @@ position ``c.-1``. We can convert between these two as follows.
 
 The ``coordinate_to_coding()`` function accepts an optional ``degenerate``
 argument. When set to ``True``, positions outside of the transcript are no
-longer described using the ``'u'`` or ``'d'`` notation.
+longer described using the ``'u'`` or ``'d'`` notation, ``'-'`` and ``'*'``
+are used instead.
 
 .. code:: python
 
@@ -299,7 +301,7 @@ In the following table, we show a number of annotated examples.
      - 4
      - -9
      - ``*``
-     - ``c.*4+9``
+     - ``c.*4-9``
    * - 71
      - 5
      - 0
@@ -365,37 +367,37 @@ table, we show a number of annotated examples.
      - 2
      - 0
      - ``u``
-     -
+     - invalid
    * - 4
      - 4
      - 2
      - 0
      - ``u``
-     -
+     - invalid
    * - 5
      - 4
      - 2
      - 0
      - ``-``
-     -
-   * - 6
-     - 4
+     - invalid
+   * - 7
      - 3
+     - 1
      - 0
      - ``-``
-     -
-   * - 7
+     - invalid
+   * - 8
      - 3
      - 1
-     - 0
+     - 1
      - ``-``
-     -
+     - invalid
    * - 31
      - 1
      - 3
      - 0
      - ``-``
-     -
+     - invalid
    * - 32
      - 1
      - 1
@@ -419,19 +421,19 @@ table, we show a number of annotated examples.
      - 1
      - 0
      - ``*``
-     -
+     - invalid
    * - 44
      - 1
      - 1
      - 1
      - ``*``
-     -
+     - invalid
    * - 79
      - 2
      - 2
      - 0
      - ``d``
-     -
+     - invalid
 
 
 See section :doc:`api/crossmap` for a detailed description.
@@ -474,6 +476,9 @@ The ``Locus`` class
 
 The ``Locus`` class is used to deal with offsets with respect to a single
 locus.
+**Note:** the ``position`` values in the position dictionaries are **0-based**,
+so the first base of the locus corresponds to ``{'position': 0, 'offset': 0}``.
+This differs from HGVS numbering, which is **1-based**.
 
 .. code:: python
 
@@ -488,7 +493,9 @@ for the semantics.
 .. code:: python
 
     >>> locus.to_position(9)
-    {'position':1, 'offset':-1}
+    {'position':0, 'offset':-1}
+    >>> locus.to_coordinate({'position':0, 'offset':-1})
+    {'position':0, 'offset':-1}
 
 For loci that reside on the reverse complement strand, the optional
 ``inverted`` constructor parameter should be set to ``True``.
@@ -499,20 +506,27 @@ The ``MultiLocus`` class
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 The ``MultiLocus`` class is used to deal with offsets with respect to multiple
-loci.
+loci. Its positions is
 
 .. code:: python
 
     >>> from mutalyzer_crossmapper import MultiLocus
     >>> multilocus = MultiLocus([(10, 20), (40, 50)])
 
-The interface to this class is similar to that of the ``Locus`` class.
+The interface to this class is similar to that of the ``Locus`` class. Functions
+``to_position()`` and ``to_coordinate()`` work with a 3-key dictionary.
+
+**Note:** again, the ``position`` values in the position dictionaries are **0-based**.
 
 .. code:: python
 
     >>> multilocus.to_position(22)
-    {'position':10, 'offset':3, 'region':''}
+    {'position':9, 'offset':3, 'region':''}
+    >>> multilocus.to_coordinate({'position':9, 'offset':3, 'region':''})
+    22
     >>> multilocus.to_position(38)
-    {'position':11, 'offset':-2, 'region':''}
+    {'position':10, 'offset':-2, 'region':''}
+    >>> multilocus.to_coordinate({'position':10, 'offset':-2, 'region':''}
+    38
 
 See section :doc:`api/multi_locus` for a detailed description.

From bcf7bd21fe0a0a2a98f123db351417f9ffb48aed Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Mar 2026 17:09:01 +0100
Subject: [PATCH 090/127] Cleanup, use '' in dictionary

---
 mutalyzer_crossmapper/crossmapper.py |   4 +-
 mutalyzer_crossmapper/locus.py       |  16 +-
 mutalyzer_crossmapper/multi_locus.py |  28 +--
 tests/helper.py                      |  19 +-
 tests/test_crossmapper.py            | 276 +++++++++++++--------------
 tests/test_locus.py                  |  32 ++--
 tests/test_multi_locus.py            |  84 ++++----
 7 files changed, 224 insertions(+), 235 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 3994271..e68bbbd 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -130,7 +130,7 @@ def _coordinate_to_coding(self, coordinate):
         """
         noncoding_pos_m = self._noncoding.to_position(coordinate)
 
-        if noncoding_pos_m['region'] in ['u', 'd']:
+        if noncoding_pos_m['region'] in ('u', 'd'):
             return noncoding_pos_m
 
         location = noncoding_pos_m['position']
@@ -178,7 +178,7 @@ def _coding_to_coordinate(self, pos_m):
         position = pos_m['position']
         region = pos_m['region']
 
-        if region in ['u', 'd']:
+        if region in ('u', 'd'):
             return self._noncoding.to_coordinate(pos_m)
 
         noncoding_pos_m = {'offset': pos_m['offset'], 'region': ''}
diff --git a/mutalyzer_crossmapper/locus.py b/mutalyzer_crossmapper/locus.py
index 738e87c..eb23efd 100644
--- a/mutalyzer_crossmapper/locus.py
+++ b/mutalyzer_crossmapper/locus.py
@@ -19,16 +19,16 @@ def to_position(self, coordinate):
         """
         if self._inverted:
             if coordinate > self.boundary[1]:
-                return {"position": 0, "offset": self.boundary[1] - coordinate}
+                return {'position': 0, 'offset': self.boundary[1] - coordinate}
             if coordinate < self.boundary[0]:
-                return {"position": self._end, "offset": self.boundary[0] - coordinate}
-            return {"position": self.boundary[1] - coordinate, "offset": 0}
+                return {'position': self._end, 'offset': self.boundary[0] - coordinate}
+            return {'position': self.boundary[1] - coordinate, 'offset': 0}
 
         if coordinate < self.boundary[0]:
-            return {"position": 0, "offset": coordinate - self.boundary[0]}
+            return {'position': 0, 'offset': coordinate - self.boundary[0]}
         if coordinate > self.boundary[1]:
-            return {"position": self._end, "offset": coordinate - self.boundary[1]}
-        return {"position": coordinate - self.boundary[0], "offset": 0}
+            return {'position': self._end, 'offset': coordinate - self.boundary[1]}
+        return {'position': coordinate - self.boundary[0], 'offset': 0}
 
     def to_coordinate(self, pos_m):
         """Convert a position model to a coordinate.
@@ -38,5 +38,5 @@ def to_coordinate(self, pos_m):
         :returns int: Coordinate.
         """
         if self._inverted:
-            return self.boundary[1] - pos_m["position"] - pos_m["offset"]
-        return self.boundary[0] + pos_m["position"] + pos_m["offset"]
+            return self.boundary[1] - pos_m['position'] - pos_m['offset']
+        return self.boundary[0] + pos_m['position'] + pos_m['offset']
diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 861e5cd..c76a39b 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -58,20 +58,20 @@ def to_position(self, coordinate:int):
         """
         index = nearest_location(self._locations, coordinate, self._inverted)
         outside = self._orientation * self.outside(coordinate)
-        region = "u" if outside < 0 else "d" if outside > 0 else ""
+        region = 'u' if outside < 0 else 'd' if outside > 0 else ''
         location = self._loci[index].to_position(coordinate)
 
         if outside:
             return {
-                "position": abs(location["offset"]),
-                "offset": 0,
-                "region": region
+                'position': abs(location['offset']),
+                'offset': 0,
+                'region': region
             }
 
         return {
-            "position": location["position"] + self._offsets[self._direction(index)],
-            "offset": location["offset"],
-            "region": region
+            'position': location['position'] + self._offsets[self._direction(index)],
+            'offset': location['offset'],
+            'region': region
         }
 
     def to_coordinate(self, pos_m:dict):
@@ -81,19 +81,19 @@ def to_coordinate(self, pos_m:dict):
 
         :returns int: Coordinate.
         """
-        region = pos_m["region"]
+        region = pos_m['region']
 
-        if pos_m["region"] in ("u", "d"):
-            is_upstream = region == "u"
+        if pos_m['region'] in ('u', 'd'):
+            is_upstream = region == 'u'
             if self._inverted:
                 is_upstream = not is_upstream
             if is_upstream:
-                return self._locations[0][0] - abs(pos_m["position"]) + pos_m["offset"]
-            return abs(pos_m["position"]) + self._locations[-1][1] + pos_m["offset"] - 1
+                return self._locations[0][0] - abs(pos_m['position']) + pos_m['offset']
+            return abs(pos_m['position']) + self._locations[-1][1] + pos_m['offset'] - 1
 
         index = min(
             len(self._offsets),
-            max(0, bisect_right(self._offsets, pos_m["position"]) - 1)
+            max(0, bisect_right(self._offsets, pos_m['position']) - 1)
         )
-        locus_pos_m = {**pos_m, "position": pos_m["position"] - self._offsets[index]}
+        locus_pos_m = {**pos_m, 'position': pos_m['position'] - self._offsets[index]}
         return self._loci[self._direction(index)].to_coordinate(locus_pos_m)
diff --git a/tests/helper.py b/tests/helper.py
index 9e51367..b3ca042 100644
--- a/tests/helper.py
+++ b/tests/helper.py
@@ -2,19 +2,8 @@ def invariant(f, x, f_i, y):
     assert f(x) == y
     assert f_i(y) == x
 
-def degenerate_equal(f, coordinate, locations):
-    results = [f(loc) for loc in locations]
-
-    # First condition: first maps correctly
-    assert results[0] == coordinate, (
-        f"\nFirst location: {locations[0]}"
-        f"\nExpected:       {coordinate}"
-        f"\nGot:            {results[0]}"
-    )
 
-    # Second condition: all map to same coordinate
-    assert len(set(results)) == 1, (
-        f"\nLocations: {locations}"
-        f"\nResults:   {results}"
-        f"\nExpected all to map to the same coordinate"
-    )
\ No newline at end of file
+def degenerate_equal(f, coordinate, locations):
+    assert f(locations[0]) == coordinate
+    assert len(
+        set(map(f, locations))) == 1
\ No newline at end of file
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index a3bc5f7..97c6262 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -14,13 +14,13 @@ def test_Genomic():
         crossmap.coordinate_to_genomic,
         0,
         crossmap.genomic_to_coordinate,
-        {"position": 1},
+        {'position': 1},
     )
     invariant(
         crossmap.coordinate_to_genomic,
         98,
         crossmap.genomic_to_coordinate,
-        {"position": 99},
+        {'position': 99},
     )
 
 
@@ -33,19 +33,19 @@ def test_NonCoding():
         crossmap.coordinate_to_noncoding,
         3,
         crossmap.noncoding_to_coordinate,
-        {"position": 2, "offset": 0, "region": "u"},
+        {'position': 2, 'offset': 0, 'region': 'u'},
     )
     invariant(
         crossmap.coordinate_to_noncoding,
         4,
         crossmap.noncoding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "u"},
+        {'position': 1, 'offset': 0, 'region': 'u'},
     )
     invariant(
         crossmap.coordinate_to_noncoding,
         5,
         crossmap.noncoding_to_coordinate,
-        {"position": 1, "offset": 0, "region": ""},
+        {'position': 1, 'offset': 0, 'region': ''},
     )
 
     # Boundary between downstream and transcript.
@@ -53,13 +53,13 @@ def test_NonCoding():
         crossmap.coordinate_to_noncoding,
         71,
         crossmap.noncoding_to_coordinate,
-        {"position": 22, "offset": 0, "region": ""},
+        {'position': 22, 'offset': 0, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_noncoding,
         72,
         crossmap.noncoding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "d"},
+        {'position': 1, 'offset': 0, 'region': 'd'},
     )
 
 
@@ -72,13 +72,13 @@ def test_NonCoding_inverted():
         crossmap.coordinate_to_noncoding,
         72,
         crossmap.noncoding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "u"},
+        {'position': 1, 'offset': 0, 'region': 'u'},
     )
     invariant(
         crossmap.coordinate_to_noncoding,
         71,
         crossmap.noncoding_to_coordinate,
-        {"position": 1, "offset": 0, "region": ""},
+        {'position': 1, 'offset': 0, 'region': ''},
     )
 
     # Boundary between downstream and transcript.
@@ -86,13 +86,13 @@ def test_NonCoding_inverted():
         crossmap.coordinate_to_noncoding,
         5,
         crossmap.noncoding_to_coordinate,
-        {"position": 22, "offset": 0, "region": ""},
+        {'position': 22, 'offset': 0, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_noncoding,
         4,
         crossmap.noncoding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "d"},
+        {'position': 1, 'offset': 0, 'region': 'd'},
     )
 
 
@@ -105,8 +105,8 @@ def test_NonCoding_degenerate():
         crossmap.noncoding_to_coordinate,
         4,
         [
-            {"position": 1, "offset": -1, "region": ""},
-            {"position": 1, "offset": 0, "region": "u"},
+            {'position': 1, 'offset': -1, 'region': ''},
+            {'position': 1, 'offset': 0, 'region': 'u'},
         ],
     )
 
@@ -115,9 +115,9 @@ def test_NonCoding_degenerate():
         crossmap.noncoding_to_coordinate,
         72,
         [
-            {"position": 1, "offset": 0, "region": "d"},
-            {"position": 22, "offset": 1, "region": ""},
-            {"position": 23, "offset": 0, "region": ""},
+            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 22, 'offset': 1, 'region': ''},
+            {'position': 23, 'offset': 0, 'region': ''},
         ],
     )
 
@@ -131,8 +131,8 @@ def test_NonCoding_inverted_degenerate():
         crossmap.noncoding_to_coordinate,
         72,
         [
-            {"position": 1, "offset": -1, "region": ""},
-            {"position": 1, "offset": 0, "region": "u"},
+            {'position': 1, 'offset': -1, 'region': ''},
+            {'position': 1, 'offset': 0, 'region': 'u'},
         ],
     )
 
@@ -141,9 +141,9 @@ def test_NonCoding_inverted_degenerate():
         crossmap.noncoding_to_coordinate,
         4,
         [
-            {"position": 1, "offset": 0, "region": "d"},
-            {"position": 23, "offset": 0, "region": ""},
-            {"position": 22, "offset": 1, "region": ""},
+            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 23, 'offset': 0, 'region': ''},
+            {'position': 22, 'offset': 1, 'region': ''},
         ],
     )
 
@@ -157,13 +157,13 @@ def test_Coding():
         crossmap.coordinate_to_coding,
         31,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "-"},
+        {'position': 1, 'offset': 0, 'region': '-'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         32,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": ""},
+        {'position': 1, 'offset': 0, 'region': ''},
     )
 
     # Boundary between CDS and 3'.
@@ -171,13 +171,13 @@ def test_Coding():
         crossmap.coordinate_to_coding,
         42,
         crossmap.coding_to_coordinate,
-        {"position": 6, "offset": 0, "region": ""},
+        {'position': 6, 'offset': 0, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_coding,
         43,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "*"},
+        {'position': 1, 'offset': 0, 'region': '*'},
     )
 
 
@@ -190,13 +190,13 @@ def test_Coding_inverted():
         crossmap.coordinate_to_coding,
         43,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "-"},
+        {'position': 1, 'offset': 0, 'region': '-'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         42,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": ""},
+        {'position': 1, 'offset': 0, 'region': ''},
     )
 
     # Boundary between CDS and 3'.
@@ -204,13 +204,13 @@ def test_Coding_inverted():
         crossmap.coordinate_to_coding,
         32,
         crossmap.coding_to_coordinate,
-        {"position": 6, "offset": 0, "region": ""},
+        {'position': 6, 'offset': 0, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_coding,
         31,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "*"},
+        {'position': 1, 'offset': 0, 'region': '*'},
     )
 
 
@@ -223,13 +223,13 @@ def test_Coding_regions():
         crossmap.coordinate_to_coding,
         25,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 5, "region": "-"},
+        {'position': 1, 'offset': 5, 'region': '-'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         26,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": -4, "region": ""},
+        {'position': 1, 'offset': -4, 'region': ''},
     )
 
     # Downstream odd length intron between two regions.
@@ -237,13 +237,13 @@ def test_Coding_regions():
         crossmap.coordinate_to_coding,
         44,
         crossmap.coding_to_coordinate,
-        {"position": 10, "offset": 5, "region": ""},
+        {'position': 10, 'offset': 5, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_coding,
         45,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": -4, "region": "*"},
+        {'position': 1, 'offset': -4, 'region': '*'},
     )
 
 
@@ -256,13 +256,13 @@ def test_Coding_regions_inverted():
         crossmap.coordinate_to_coding,
         44,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 5, "region": "-"},
+        {'position': 1, 'offset': 5, 'region': '-'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         43,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": -4, "region": ""},
+        {'position': 1, 'offset': -4, 'region': ''},
     )
 
     # Downstream odd length intron between two regions.
@@ -270,13 +270,13 @@ def test_Coding_regions_inverted():
         crossmap.coordinate_to_coding,
         25,
         crossmap.coding_to_coordinate,
-        {"position": 10, "offset": 5, "region": ""},
+        {'position': 10, 'offset': 5, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_coding,
         24,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": -4, "region": "*"},
+        {'position': 1, 'offset': -4, 'region': '*'},
     )
 
 
@@ -289,13 +289,13 @@ def test_Coding_no_utr5():
         crossmap.coordinate_to_coding,
         9,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "u"},
+        {'position': 1, 'offset': 0, 'region': 'u'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         10,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": ""},
+        {'position': 1, 'offset': 0, 'region': ''},
     )
 
 
@@ -308,13 +308,13 @@ def test_Coding_no_utr5_inverted():
         crossmap.coordinate_to_coding,
         20,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "u"},
+        {'position': 1, 'offset': 0, 'region': 'u'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         19,
         crossmap.coding_to_coordinate,
-        {"position": 1 , "offset": 0, "region": ""},
+        {'position': 1 , 'offset': 0, 'region': ''},
     )
 
 
@@ -327,13 +327,13 @@ def test_Coding_no_utr3():
         crossmap.coordinate_to_coding,
         19,
         crossmap.coding_to_coordinate,
-        {"position": 5, "offset": 0, "region": ""},
+        {'position': 5, 'offset': 0, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_coding,
         20,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "d"},
+        {'position': 1, 'offset': 0, 'region': 'd'},
     )
 
 
@@ -346,13 +346,13 @@ def test_Coding_no_utr3_inverted():
         crossmap.coordinate_to_coding,
         10,
         crossmap.coding_to_coordinate,
-        {"position": 5, "offset": 0, "region": ""},
+        {'position': 5, 'offset': 0, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_coding,
         9,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "d"},
+        {'position': 1, 'offset': 0, 'region': 'd'},
     )
 
 
@@ -365,19 +365,19 @@ def test_Coding_small_utr5():
         crossmap.coordinate_to_coding,
         9,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "u"},
+        {'position': 1, 'offset': 0, 'region': 'u'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         10,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "-"},
+        {'position': 1, 'offset': 0, 'region': '-'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         11,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": ""},
+        {'position': 1, 'offset': 0, 'region': ''},
     )
 
 
@@ -390,19 +390,19 @@ def test_Coding_small_utr5_inverted():
         crossmap.coordinate_to_coding,
         20,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "u"},
+        {'position': 1, 'offset': 0, 'region': 'u'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         19,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "-"},
+        {'position': 1, 'offset': 0, 'region': '-'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         18,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": ""},
+        {'position': 1, 'offset': 0, 'region': ''},
     )
 
 
@@ -415,19 +415,19 @@ def test_Coding_small_utr3():
         crossmap.coordinate_to_coding,
         18,
         crossmap.coding_to_coordinate,
-        {"position": 4, "offset": 0, "region": ""},
+        {'position': 4, 'offset': 0, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_coding,
         19,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "*"},
+        {'position': 1, 'offset': 0, 'region': '*'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         20,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "d"},
+        {'position': 1, 'offset': 0, 'region': 'd'},
     )
 
 
@@ -440,19 +440,19 @@ def test_Coding_small_utr3_inverted():
         crossmap.coordinate_to_coding,
         11,
         crossmap.coding_to_coordinate,
-        {"position": 4, "offset": 0, "region": ""},
+        {'position': 4, 'offset': 0, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_coding,
         10,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "*"},
+        {'position': 1, 'offset': 0, 'region': '*'},
     )
     invariant(
         crossmap.coordinate_to_coding,
         9,
         crossmap.coding_to_coordinate,
-        {"position": 1, "offset": 0, "region": "d"},
+        {'position': 1, 'offset': 0, 'region': 'd'},
     )
 
 
@@ -464,25 +464,25 @@ def test_Coding_degenerate():
         crossmap.coding_to_coordinate,
         9,
         [
-            {"position": 1, "offset": 0, "region": "u"},
-            {"position": 2, "offset": 0, "region": "-"},
-            {"position": 1, "offset": -2, "region": ""},
-            {"position": 1, "offset": -10, "region": "*"},
-            {"position": 2, "offset": -11, "region": "*"},
-            {"position": 3, "offset": 1, "region": "-"},
-            {"position": 4, "offset": 2, "region": "-"},
+            {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 2, 'offset': 0, 'region': '-'},
+            {'position': 1, 'offset': -2, 'region': ''},
+            {'position': 1, 'offset': -10, 'region': '*'},
+            {'position': 2, 'offset': -11, 'region': '*'},
+            {'position': 3, 'offset': 1, 'region': '-'},
+            {'position': 4, 'offset': 2, 'region': '-'},
         ],
     )
     degenerate_equal(
         crossmap.coding_to_coordinate,
         20,
         [
-            {"position": 1, "offset": 0, "region": "d"},
-            {"position": 2, "offset": 0, "region": "*"},
-            {"position": 8, "offset": 2, "region": ""},
-            {"position": 1, "offset": 10, "region": "-"},
-            {"position": 2, "offset": 11, "region": "-"},
-            {"position": 7, "offset": 3, "region": ""},
+            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 2, 'offset': 0, 'region': '*'},
+            {'position': 8, 'offset': 2, 'region': ''},
+            {'position': 1, 'offset': 10, 'region': '-'},
+            {'position': 2, 'offset': 11, 'region': '-'},
+            {'position': 7, 'offset': 3, 'region': ''},
         ],
     )
 
@@ -495,24 +495,24 @@ def test_Coding_inverted_degenerate():
         crossmap.coding_to_coordinate,
         20,
         [
-            {"position": 1, "offset": 0, "region": "u"},
-            {"position": 2, "offset": 0, "region": "-"},
-            {"position": 1, "offset": -2, "region": ""},
-            {"position": 1, "offset": -10, "region": "*"},
-            {"position": 1, "offset": -11, "region": "d"},
-            {"position": 2, "offset": -3, "region": ""},
+            {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 2, 'offset': 0, 'region': '-'},
+            {'position': 1, 'offset': -2, 'region': ''},
+            {'position': 1, 'offset': -10, 'region': '*'},
+            {'position': 1, 'offset': -11, 'region': 'd'},
+            {'position': 2, 'offset': -3, 'region': ''},
         ],
     )
     degenerate_equal(
         crossmap.coding_to_coordinate,
         9,
         [
-            {"position": 1, "offset": 0, "region": "d"},
-            {"position": 2, "offset": 0, "region": "*"},
-            {"position": 8, "offset": 2, "region": ""},
-            {"position": 1, "offset": 10, "region": "-"},
-            {"position": 1, "offset": 11, "region": "u"},
-            {"position": 2, "offset": 12, "region": "u"},
+            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 2, 'offset': 0, 'region': '*'},
+            {'position': 8, 'offset': 2, 'region': ''},
+            {'position': 1, 'offset': 10, 'region': '-'},
+            {'position': 1, 'offset': 11, 'region': 'u'},
+            {'position': 2, 'offset': 12, 'region': 'u'},
 
         ],
     )
@@ -523,14 +523,14 @@ def test_Coding_degenerate_return():
     crossmap = Coding([(10, 20)], (11, 19))
 
     assert crossmap.coordinate_to_coding(9, True) == {
-        "position": 2,
-        "offset": 0,
-        "region": "-",
+        'position': 2,
+        'offset': 0,
+        'region': '-',
     }
     assert crossmap.coordinate_to_coding(20, True) == {
-        "position": 2,
-        "offset": 0,
-        "region": "*",
+        'position': 2,
+        'offset': 0,
+        'region': '*',
     }
 
 
@@ -540,14 +540,14 @@ def test_Coding_inverted_degenerate_return():
 
 
     assert crossmap.coordinate_to_coding(20, True) == {
-        "position": 2,
-        "offset": 0,
-        "region": "-",
+        'position': 2,
+        'offset': 0,
+        'region': '-',
     }
     assert crossmap.coordinate_to_coding(9, True) == {
-        "position": 2,
-        "offset": 0,
-        "region": "*",
+        'position': 2,
+        'offset': 0,
+        'region': '*',
     }
 
 
@@ -573,22 +573,22 @@ def test_Coding_no_utr_degenerate():
         crossmap.coding_to_coordinate,
         9,
         [
-            {"position": 1, "offset": 0, "region": "u"},
-            {"position": 1, "offset": 0, "region": "-"},
-            {"position": 1, "offset": -2, "region": "*"},
-            {"position": 1, "offset": -1, "region": ""},
-            {"position": 1, "offset": -2, "region": "d"},
+            {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 1, 'offset': 0, 'region': '-'},
+            {'position': 1, 'offset': -2, 'region': '*'},
+            {'position': 1, 'offset': -1, 'region': ''},
+            {'position': 1, 'offset': -2, 'region': 'd'},
         ],
     )
     degenerate_equal(
         crossmap.coding_to_coordinate,
         11,
         [
-            {"position": 1, "offset": 0, "region": "d"},
-            {"position": 1, "offset": 0, "region": "*"},
-            {"position": 1, "offset": 2, "region": "-"},
-            {"position": 1, "offset": 1, "region": ""},
-            {"position": 1, "offset": 2, "region": "u"},
+            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 1, 'offset': 0, 'region': '*'},
+            {'position': 1, 'offset': 2, 'region': '-'},
+            {'position': 1, 'offset': 1, 'region': ''},
+            {'position': 1, 'offset': 2, 'region': 'u'},
         ],
     )
 
@@ -601,22 +601,22 @@ def test_Coding_inverted_no_utr_degenerate():
         crossmap.coding_to_coordinate,
         11,
         [
-            {"position": 1, "offset": 0, "region": "u"},
-            {"position": 1, "offset": 0, "region": "-"},
-            {"position": 1, "offset": -2, "region": "*"},
-            {"position": 1, "offset": -1, "region": ""},
-            {"position": 1, "offset": -2, "region": "d"},
+            {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 1, 'offset': 0, 'region': '-'},
+            {'position': 1, 'offset': -2, 'region': '*'},
+            {'position': 1, 'offset': -1, 'region': ''},
+            {'position': 1, 'offset': -2, 'region': 'd'},
         ],
     )
     degenerate_equal(
         crossmap.coding_to_coordinate,
         9,
         [
-            {"position": 1, "offset": 0, "region": "d"},
-            {"position": 1, "offset": 0, "region": "*"},
-            {"position": 1, "offset": 2, "region": "-"},
-            {"position": 1, "offset": 1, "region": ""},
-            {"position": 1, "offset": 2, "region": "u"},
+            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 1, 'offset': 0, 'region': '*'},
+            {'position': 1, 'offset': 2, 'region': '-'},
+            {'position': 1, 'offset': 1, 'region': ''},
+            {'position': 1, 'offset': 2, 'region': 'u'},
         ],
     )
 
@@ -626,24 +626,24 @@ def test_Coding_no_utr_degenerate_return():
     crossmap = Coding([(10, 11)], (10, 11))
 
     assert crossmap.coordinate_to_coding(8, True) == {
-        "position": 2,
-        "offset": 0,
-        "region": "-",
+        'position': 2,
+        'offset': 0,
+        'region': '-',
     }
     assert crossmap.coordinate_to_coding(9, True) == {
-        "position": 1,
-        "offset": 0,
-        "region": "-",
+        'position': 1,
+        'offset': 0,
+        'region': '-',
     }
     assert crossmap.coordinate_to_coding(11, True) == {
-        "position": 1,
-        "offset": 0,
-        "region": "*",
+        'position': 1,
+        'offset': 0,
+        'region': '*',
     }
     assert crossmap.coordinate_to_coding(12, True) == {
-        "position": 2,
-        "offset": 0,
-        "region": "*",
+        'position': 2,
+        'offset': 0,
+        'region': '*',
     }
 
 
@@ -652,14 +652,14 @@ def test_Coding_inverted_no_utr_degenerate_return():
     crossmap = Coding([(10, 11)], (10, 11), True)
 
     assert crossmap.coordinate_to_coding(11, True) == {
-        "position": 1,
-        "offset": 0,
-        "region": "-",
+        'position': 1,
+        'offset': 0,
+        'region': '-',
     }
     assert crossmap.coordinate_to_coding(9, True) == {
-        "position": 1,
-        "offset": 0,
-        "region": "*",
+        'position': 1,
+        'offset': 0,
+        'region': '*',
     }
 
 
@@ -672,13 +672,13 @@ def test_Coding_protein():
         crossmap.coordinate_to_protein,
         31,
         crossmap.protein_to_coordinate,
-        {"position": 1, "position_in_codon": 3, "offset": 0, "region": "-"},
+        {'position': 1, 'position_in_codon': 3, 'offset': 0, 'region': '-'},
     )
     invariant(
         crossmap.coordinate_to_protein,
         32,
         crossmap.protein_to_coordinate,
-        {"position": 1, "position_in_codon": 1, "offset": 0, "region": ""},
+        {'position': 1, 'position_in_codon': 1, 'offset': 0, 'region': ''},
     )
 
     # Intron boundary.
@@ -686,13 +686,13 @@ def test_Coding_protein():
         crossmap.coordinate_to_protein,
         34,
         crossmap.protein_to_coordinate,
-        {"position": 1, "position_in_codon": 3, "offset": 0, "region": ""},
+        {'position': 1, 'position_in_codon': 3, 'offset': 0, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_protein,
         35,
         crossmap.protein_to_coordinate,
-        {"position": 1, "position_in_codon": 3, "offset": 1, "region": ""},
+        {'position': 1, 'position_in_codon': 3, 'offset': 1, 'region': ''},
     )
 
     # Boundary between CDS and 3' UTR.
@@ -700,11 +700,11 @@ def test_Coding_protein():
         crossmap.coordinate_to_protein,
         42,
         crossmap.protein_to_coordinate,
-        {"position": 2, "position_in_codon": 3, "offset": 0, "region": ""},
+        {'position': 2, 'position_in_codon': 3, 'offset': 0, 'region': ''},
     )
     invariant(
         crossmap.coordinate_to_protein,
         43,
         crossmap.protein_to_coordinate,
-        {"position": 1, "position_in_codon": 1, "offset": 0, "region": "*"},
+        {'position': 1, 'position_in_codon': 1, 'offset': 0, 'region': '*'},
     )
diff --git a/tests/test_locus.py b/tests/test_locus.py
index b650c1a..535f93d 100644
--- a/tests/test_locus.py
+++ b/tests/test_locus.py
@@ -7,37 +7,37 @@ def test_Locus():
     """Forward orientent Lovus."""
     locus = Locus((30, 35))
 
-    invariant(locus.to_position, 29, locus.to_coordinate, {"position": 0, "offset": -1})
-    invariant(locus.to_position, 30, locus.to_coordinate, {"position": 0, "offset": 0})
-    invariant(locus.to_position, 31, locus.to_coordinate, {"position": 1, "offset": 0})
-    invariant(locus.to_position, 33, locus.to_coordinate, {"position": 3, "offset": 0})
-    invariant(locus.to_position, 34, locus.to_coordinate, {"position": 4, "offset": 0})
-    invariant(locus.to_position, 35, locus.to_coordinate, {"position": 4, "offset": 1})
+    invariant(locus.to_position, 29, locus.to_coordinate, {'position': 0, 'offset': -1})
+    invariant(locus.to_position, 30, locus.to_coordinate, {'position': 0, 'offset': 0})
+    invariant(locus.to_position, 31, locus.to_coordinate, {'position': 1, 'offset': 0})
+    invariant(locus.to_position, 33, locus.to_coordinate, {'position': 3, 'offset': 0})
+    invariant(locus.to_position, 34, locus.to_coordinate, {'position': 4, 'offset': 0})
+    invariant(locus.to_position, 35, locus.to_coordinate, {'position': 4, 'offset': 1})
 
 
 def test_Locus_inverted():
     """Reverse orientent Lovus."""
     locus = Locus((30, 35), True)
 
-    invariant(locus.to_position, 35, locus.to_coordinate, {"position": 0, "offset": -1})
-    invariant(locus.to_position, 34, locus.to_coordinate, {"position": 0, "offset": 0})
-    invariant(locus.to_position, 33, locus.to_coordinate, {"position": 1, "offset": 0})
-    invariant(locus.to_position, 31, locus.to_coordinate, {"position": 3, "offset": 0})
-    invariant(locus.to_position, 30, locus.to_coordinate, {"position": 4, "offset": 0})
-    invariant(locus.to_position, 29, locus.to_coordinate, {"position": 4, "offset": 1})
+    invariant(locus.to_position, 35, locus.to_coordinate, {'position': 0, 'offset': -1})
+    invariant(locus.to_position, 34, locus.to_coordinate, {'position': 0, 'offset': 0})
+    invariant(locus.to_position, 33, locus.to_coordinate, {'position': 1, 'offset': 0})
+    invariant(locus.to_position, 31, locus.to_coordinate, {'position': 3, 'offset': 0})
+    invariant(locus.to_position, 30, locus.to_coordinate, {'position': 4, 'offset': 0})
+    invariant(locus.to_position, 29, locus.to_coordinate, {'position': 4, 'offset': 1})
 
 
 def test_Locus_degenerate():
     """Degenerate positions are silently corrected."""
     locus = Locus((10, 20))
 
-    degenerate_equal(locus.to_coordinate, 9, [{"position": 0, "offset": -1}, {"position": -1, "offset": 0}])
-    degenerate_equal(locus.to_coordinate, 20, [{"position": 9, "offset": 1}, {"position": 10, "offset": 0}])
+    degenerate_equal(locus.to_coordinate, 9, [{'position': 0, 'offset': -1}, {'position': -1, 'offset': 0}])
+    degenerate_equal(locus.to_coordinate, 20, [{'position': 9, 'offset': 1}, {'position': 10, 'offset': 0}])
 
 
 def test_Locus_inverted_degenerate():
     """Degenerate positions are silently corrected."""
     locus = Locus((10, 20), True)
 
-    degenerate_equal(locus.to_coordinate, 20, [{"position": 0, "offset": -1}, {"position": -1, "offset": 0}])
-    degenerate_equal(locus.to_coordinate, 9, [{"position": 9, "offset": 1}, {"position": 10, "offset": 0}])
+    degenerate_equal(locus.to_coordinate, 20, [{'position': 0, 'offset': -1}, {'position': -1, 'offset': 0}])
+    degenerate_equal(locus.to_coordinate, 9, [{'position': 9, 'offset': 1}, {'position': 10, 'offset': 0}])
diff --git a/tests/test_multi_locus.py b/tests/test_multi_locus.py
index 3434a62..ab3b877 100644
--- a/tests/test_multi_locus.py
+++ b/tests/test_multi_locus.py
@@ -35,14 +35,14 @@ def test_MultiLocus():
         multi_locus.to_position,
         4,
         multi_locus.to_coordinate,
-        {"position": 1, "offset": 0, "region": "u"},
+        {'position': 1, 'offset': 0, 'region': 'u'},
     )
 
     invariant(
         multi_locus.to_position,
         5,
         multi_locus.to_coordinate,
-        {"position": 0, "offset": 0, "region": ""},
+        {'position': 0, 'offset': 0, 'region': ''},
     )
 
     # Internal locus.
@@ -50,37 +50,37 @@ def test_MultiLocus():
         multi_locus.to_position,
         29,
         multi_locus.to_coordinate,
-        {"position": 9, "offset": -1, "region": ""},
+        {'position': 9, 'offset': -1, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         30,
         multi_locus.to_coordinate,
-        {"position": 9, "offset": 0, "region": ""},
+        {'position': 9, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         31,
         multi_locus.to_coordinate,
-        {"position": 10, "offset": 0, "region": ""},
+        {'position': 10, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         33,
         multi_locus.to_coordinate,
-        {"position": 12, "offset": 0, "region": ""},
+        {'position': 12, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         34,
         multi_locus.to_coordinate,
-        {"position": 13, "offset": 0, "region": ""},
+        {'position': 13, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         35,
         multi_locus.to_coordinate,
-        {"position": 13, "offset": 1, "region": ""},
+        {'position': 13, 'offset': 1, 'region': ''},
     )
 
     # Boundary between the last locus and downstream.
@@ -88,13 +88,13 @@ def test_MultiLocus():
         multi_locus.to_position,
         71,
         multi_locus.to_coordinate,
-        {"position": 21, "offset": 0, "region": ""},
+        {'position': 21, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         72,
         multi_locus.to_coordinate,
-        {"position": 1, "offset": 0, "region": "d"},
+        {'position': 1, 'offset': 0, 'region': 'd'},
     )
 
 
@@ -107,13 +107,13 @@ def test_MultiLocus_inverted():
         multi_locus.to_position,
         72,
         multi_locus.to_coordinate,
-        {"position": 1, "offset": 0, "region": "u"},
+        {'position': 1, 'offset': 0, 'region': 'u'},
     )
     invariant(
         multi_locus.to_position,
         71,
         multi_locus.to_coordinate,
-        {"position": 0, "offset": 0, "region": ""},
+        {'position': 0, 'offset': 0, 'region': ''},
     )
 
     # Internal locus.
@@ -121,37 +121,37 @@ def test_MultiLocus_inverted():
         multi_locus.to_position,
         35,
         multi_locus.to_coordinate,
-        {"position": 8, "offset": -1, "region": ""},
+        {'position': 8, 'offset': -1, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         34,
         multi_locus.to_coordinate,
-        {"position": 8, "offset": 0, "region": ""},
+        {'position': 8, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         33,
         multi_locus.to_coordinate,
-        {"position": 9, "offset": 0, "region": ""},
+        {'position': 9, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         31,
         multi_locus.to_coordinate,
-        {"position": 11, "offset": 0, "region": ""},
+        {'position': 11, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         30,
         multi_locus.to_coordinate,
-        {"position": 12, "offset": 0, "region": ""},
+        {'position': 12, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         29,
         multi_locus.to_coordinate,
-        {"position": 12, "offset": 1, "region": ""},
+        {'position': 12, 'offset': 1, 'region': ''},
     )
 
     # Boundary between the last locus and downstream.
@@ -159,13 +159,13 @@ def test_MultiLocus_inverted():
         multi_locus.to_position,
         5,
         multi_locus.to_coordinate,
-        {"position": 21, "offset": 0, "region": ""},
+        {'position': 21, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         4,
         multi_locus.to_coordinate,
-        {"position": 1, "offset": 0, "region": "d"},
+        {'position': 1, 'offset': 0, 'region': 'd'},
     )
 
 
@@ -177,13 +177,13 @@ def test_MultiLocus_adjacent_loci():
         multi_locus.to_position,
         2,
         multi_locus.to_coordinate,
-        {"position": 1, "offset": 0, "region": ""},
+        {'position': 1, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         3,
         multi_locus.to_coordinate,
-        {"position": 2, "offset": 0, "region": ""},
+        {'position': 2, 'offset': 0, 'region': ''},
     )
 
 
@@ -195,13 +195,13 @@ def test_MultiLocus_adjacent_loci_inverted():
         multi_locus.to_position,
         3,
         multi_locus.to_coordinate,
-        {"position": 1, "offset": 0, "region": ""},
+        {'position': 1, 'offset': 0, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         2,
         multi_locus.to_coordinate,
-        {"position": 2, "offset": 0, "region": ""},
+        {'position': 2, 'offset': 0, 'region': ''},
     )
 
 
@@ -213,13 +213,13 @@ def test_MultiLocus_offsets_odd():
         multi_locus.to_position,
         4,
         multi_locus.to_coordinate,
-        {"position": 1, "offset": 2, "region": ""},
+        {'position': 1, 'offset': 2, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         5,
         multi_locus.to_coordinate,
-        {"position": 2, "offset": -1, "region": ""},
+        {'position': 2, 'offset': -1, 'region': ''},
     )
 
 
@@ -231,13 +231,13 @@ def test_MultiLocus_offsets_odd_inverted():
         multi_locus.to_position,
         4,
         multi_locus.to_coordinate,
-        {"position": 1, "offset": 2, "region": ""},
+        {'position': 1, 'offset': 2, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         3,
         multi_locus.to_coordinate,
-        {"position": 2, "offset": -1, "region": ""},
+        {'position': 2, 'offset': -1, 'region': ''},
     )
 
 
@@ -249,13 +249,13 @@ def test_MultiLocus_offsets_even():
         multi_locus.to_position,
         4,
         multi_locus.to_coordinate,
-        {"position": 1, "offset": 2, "region": ""},
+        {'position': 1, 'offset': 2, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         5,
         multi_locus.to_coordinate,
-        {"position": 2, "offset": -2, "region": ""},
+        {'position': 2, 'offset': -2, 'region': ''},
     )
 
 
@@ -267,13 +267,13 @@ def test_MultiLocus_offsets_even_inverted():
         multi_locus.to_position,
         5,
         multi_locus.to_coordinate,
-        {"position": 1, "offset": 2, "region": ""},
+        {'position': 1, 'offset': 2, 'region': ''},
     )
     invariant(
         multi_locus.to_position,
         4,
         multi_locus.to_coordinate,
-        {"position": 2, "offset": -2, "region": ""},
+        {'position': 2, 'offset': -2, 'region': ''},
     )
 
 
@@ -285,9 +285,9 @@ def test_MultiLocus_degenerate():
         multi_locus.to_coordinate,
         4,
         [
-            {"position": 0, "offset": -1, "region": "u"},
-            {"position": 1, "offset": 0, "region": "u"},
-            {"position": -1, "offset": 0, "region": "u"},
+            {'position': 0, 'offset': -1, 'region': 'u'},
+            {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': -1, 'offset': 0, 'region': 'u'},
         ],
     )
 
@@ -295,8 +295,8 @@ def test_MultiLocus_degenerate():
         multi_locus.to_coordinate,
         72,
         [
-            {"position": 0, "offset": 1, "region": "d"},
-            {"position": 1, "offset": 0, "region": "d"},
+            {'position': 0, 'offset': 1, 'region': 'd'},
+            {'position': 1, 'offset': 0, 'region': 'd'},
         ],
     )
 
@@ -309,9 +309,9 @@ def test_MultiLocus_inverted_degenerate():
         multi_locus.to_coordinate,
         72,
         [
-            {"position": 0, "offset": 1, "region": "u"},
-            {"position": -1, "offset": 0, "region": "u"},
-            {"position": 1, "offset": 0, "region": "u"},
+            {'position': 0, 'offset': 1, 'region': 'u'},
+            {'position': -1, 'offset': 0, 'region': 'u'},
+            {'position': 1, 'offset': 0, 'region': 'u'},
         ],
     )
 
@@ -319,7 +319,7 @@ def test_MultiLocus_inverted_degenerate():
         multi_locus.to_coordinate,
         4,
         [
-            {"position": 0, "offset": -1, "region": "d"},
-            {"position": 1, "offset": 0, "region": "d"},
+            {'position': 0, 'offset': -1, 'region': 'd'},
+            {'position': 1, 'offset': 0, 'region': 'd'},
         ],
     )

From 2f167e0d7abebbfe90a4e784f11b89af3202df08 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 20 Mar 2026 17:29:27 +0100
Subject: [PATCH 091/127] Cleanup, use typings

---
 mutalyzer_crossmapper/crossmapper.py | 28 ++++++++++++++--------------
 mutalyzer_crossmapper/location.py    |  4 ++--
 mutalyzer_crossmapper/locus.py       |  6 +++---
 mutalyzer_crossmapper/multi_locus.py | 12 ++++++------
 4 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index e68bbbd..42ab6d5 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -3,7 +3,7 @@
 
 class Genomic(object):
     """Genomic crossmap object."""
-    def coordinate_to_genomic(self, coordinate):
+    def coordinate_to_genomic(self, coordinate: int) -> dict:
         """Convert a coordinate to a genomic position (g./m./o.).
 
         :arg int coordinate: Coordinate.
@@ -12,7 +12,7 @@ def coordinate_to_genomic(self, coordinate):
         """
         return {'position': coordinate + 1}
 
-    def genomic_to_coordinate(self, pos_m):
+    def genomic_to_coordinate(self, pos_m: dict) -> int:
         """Convert a genomic position (g./m./o.) to a coordinate.
 
         :arg dict pos_m: Genomic position model.
@@ -24,7 +24,7 @@ def genomic_to_coordinate(self, pos_m):
 
 class NonCoding(Genomic):
     """NonCoding crossmap object."""
-    def __init__(self, locations, inverted=False):
+    def __init__(self, locations: list[tuple[int, int]], inverted: bool = False) -> None:
         """
         :arg list locations: List of locus locations.
         :arg bool inverted: Orientation.
@@ -33,7 +33,7 @@ def __init__(self, locations, inverted=False):
 
         self._noncoding = MultiLocus(locations, inverted)
 
-    def coordinate_to_noncoding(self, coordinate):
+    def coordinate_to_noncoding(self, coordinate: int) -> dict:
         """Convert a coordinate to a noncoding position (n./r.).
 
         :arg int coordinate: Coordinate.
@@ -45,7 +45,7 @@ def coordinate_to_noncoding(self, coordinate):
             pos_m['position'] = pos_m['position'] + 1
         return pos_m
 
-    def noncoding_to_coordinate(self, pos_m):
+    def noncoding_to_coordinate(self, pos_m: dict) -> int:
         """Convert a noncoding position (n./r.) to a coordinate.
 
         :arg dict pos_m: Noncoding position model.
@@ -60,7 +60,7 @@ def noncoding_to_coordinate(self, pos_m):
 
 class Coding(NonCoding):
     """Coding crossmap object."""
-    def __init__(self, locations, cds, inverted=False):
+    def __init__(self, locations: list[tuple[int,int]], cds: tuple[int,int], inverted : bool=False) -> None:
         """
         :arg list locations: List of locus locations.
         :arg tuple cds: Locus location.
@@ -80,7 +80,7 @@ def __init__(self, locations, cds, inverted=False):
             self._coding = (b0['position'] + b0['offset'], b1['position'] + b1['offset'] +1)
             self._exons = (e0['position'], e1['position'])
 
-    def _degenerate_position(self, pos_m):
+    def _degenerate_position(self, pos_m: dict) -> dict:
         """Degenerate a coding position model (c./r.).
 
         :arg dict pos_m: Coding position model.
@@ -106,7 +106,7 @@ def _degenerate_position(self, pos_m):
             degenerated_pos_m['region'] = '*'
         return degenerated_pos_m
 
-    def _normalize_position(self, pos_m):
+    def _normalize_position(self, pos_m: dict) -> dict:
         """Normalize a coding position model (c./r.).
 
         :arg dict pos_m: Coding position model.
@@ -121,7 +121,7 @@ def _normalize_position(self, pos_m):
             coordinate = coordinate + pos_m['offset']
         return self.coordinate_to_coding(coordinate)
 
-    def _coordinate_to_coding(self, coordinate):
+    def _coordinate_to_coding(self, coordinate: int) -> dict:
         """Convert a coordinate to a coding position (c./r.).
 
         :arg int coordinate: Coordinate.
@@ -153,7 +153,7 @@ def _coordinate_to_coding(self, coordinate):
             'region': ''
         }
 
-    def coordinate_to_coding(self, coordinate, degenerate=False):
+    def coordinate_to_coding(self, coordinate: tuple[int, int], degenerate: bool=False) -> dict:
         """Convert a coordinate to a coding position (c./r.).
 
         :arg int coordinate: Coordinate.
@@ -168,7 +168,7 @@ def coordinate_to_coding(self, coordinate, degenerate=False):
 
         return pos_m
 
-    def _coding_to_coordinate(self, pos_m):
+    def _coding_to_coordinate(self, pos_m: dict) -> int:
         """Convert a coding position (c./r.) to a coordinate.
 
         :arg dict pos_m: Coding position model (c./r.).
@@ -191,7 +191,7 @@ def _coding_to_coordinate(self, pos_m):
 
         return self._noncoding.to_coordinate(noncoding_pos_m)
 
-    def coding_to_coordinate(self, pos_m):
+    def coding_to_coordinate(self, pos_m: dict) -> int:
         """Convert a coding position (c./r.) to a coordinate.
 
         :arg dict pos_m: Coding position model (c./r.).
@@ -202,7 +202,7 @@ def coding_to_coordinate(self, pos_m):
 
         return self._coding_to_coordinate(normalized_pos_m)
 
-    def coordinate_to_protein(self, coordinate):
+    def coordinate_to_protein(self, coordinate: int) -> dict:
         """Convert a coordinate to a protein position (p.).
 
         :arg int coordinate: Coordinate.
@@ -227,7 +227,7 @@ def coordinate_to_protein(self, coordinate):
                 'position_in_codon': (position + 2) % 3 + 1,
                 **{k: v for k, v in pos.items() if k != 'position'}}
 
-    def protein_to_coordinate(self, pos_m):
+    def protein_to_coordinate(self, pos_m: dict) -> int:
         """Convert a protein position (p.) to a coordinate.
 
         :arg dict position: Protein position model(p.).
diff --git a/mutalyzer_crossmapper/location.py b/mutalyzer_crossmapper/location.py
index e580672..1bf7a06 100644
--- a/mutalyzer_crossmapper/location.py
+++ b/mutalyzer_crossmapper/location.py
@@ -1,4 +1,4 @@
-def _nearest_boundary(lb, rb, c, p):
+def _nearest_boundary(lb: int, rb: int, c: int, p: int) -> int:
     """Find the boundary nearest to `c`. In case of a draw, the parameter `p`
     decides which one is chosen.
 
@@ -19,7 +19,7 @@ def _nearest_boundary(lb, rb, c, p):
     return p
 
 
-def nearest_location(ls, c, p=0):
+def nearest_location(ls: list[tuple[int,int]], c: int, p: int = 0) -> int:
     """Find the location nearest to `c`. In case of a draw, the parameter `p`
     decides which index is chosen.
 
diff --git a/mutalyzer_crossmapper/locus.py b/mutalyzer_crossmapper/locus.py
index eb23efd..15b15a0 100644
--- a/mutalyzer_crossmapper/locus.py
+++ b/mutalyzer_crossmapper/locus.py
@@ -1,6 +1,6 @@
 class Locus(object):
     """Locus object."""
-    def __init__(self, location, inverted=False):
+    def __init__(self, location: list[tuple[int, int]], inverted=False) -> None:
         """
         :arg tuple location: Locus location.
         :arg bool inverted: Orientation.
@@ -10,7 +10,7 @@ def __init__(self, location, inverted=False):
         self.boundary = location[0], location[1] - 1
         self._end = self.boundary[1] - self.boundary[0]
 
-    def to_position(self, coordinate):
+    def to_position(self, coordinate: int) -> dict:
         """Convert a coordinate to a proper position model.
 
         :arg int coordinate: Coordinate.
@@ -30,7 +30,7 @@ def to_position(self, coordinate):
             return {'position': self._end, 'offset': coordinate - self.boundary[1]}
         return {'position': coordinate - self.boundary[0], 'offset': 0}
 
-    def to_coordinate(self, pos_m):
+    def to_coordinate(self, pos_m: dict) -> int:
         """Convert a position model to a coordinate.
 
         :arg dict position: Position model with 'position' and 'offset' keys.
diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index c76a39b..001ed2c 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -5,7 +5,7 @@
 from .locus import Locus
 
 
-def _offsets(locations, orientation):
+def _offsets(locations: list[tuple[int, int]], orientation: int) -> list[int]:
     """For each location, calculate the length of the preceding locations.
 
     :arg list locations: List of locations.
@@ -19,7 +19,7 @@ def _offsets(locations, orientation):
 
 class MultiLocus(object):
     """MultiLocus object."""
-    def __init__(self, locations:list, inverted=False):
+    def __init__(self, locations: list[tuple[int, int]], inverted=False) -> None:
         """
         :arg list locations: List of locus locations.
         :arg bool inverted: Orientation.
@@ -31,12 +31,12 @@ def __init__(self, locations:list, inverted=False):
         self._orientation = -1 if inverted else 1
         self._offsets = _offsets(locations, self._orientation)
 
-    def _direction(self, index):
+    def _direction(self, index: int) -> int:
         if self._inverted:
             return len(self._offsets) - index - 1
         return index
 
-    def outside(self, coordinate:int):
+    def outside(self, coordinate: int) -> int:
         """Calculate the offset relative to this MultiLocus.
 
         :arg int coordinate: Coordinate.
@@ -49,7 +49,7 @@ def outside(self, coordinate:int):
             return coordinate - self._loci[-1].boundary[1]
         return 0
 
-    def to_position(self, coordinate:int):
+    def to_position(self, coordinate: int) -> dict:
         """Convert a coordinate to a position.
 
         :arg int coordinate: Coordinate.
@@ -74,7 +74,7 @@ def to_position(self, coordinate:int):
             'region': region
         }
 
-    def to_coordinate(self, pos_m:dict):
+    def to_coordinate(self, pos_m: dict) -> int:
         """Convert a position model to a coordinate.
 
         :arg dict pos_m: Position model with 'position','offset' and 'region' keys.

From ac0cd16d0cbfdfb49abcab494f5d52228fe36a7d Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 23 Mar 2026 10:35:49 +0100
Subject: [PATCH 092/127] Cleanup

---
 docs/library.rst | 46 ++++++++++++++++++++++++++--------------------
 1 file changed, 26 insertions(+), 20 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index a1c236e..83bf73a 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -22,7 +22,7 @@ They are represented as 1-key dictionaries. Below is an example of ``g.1`` in HG
 
 Where:
 
-- **position**: a positive integer repersenting a base position(>0)
+- **position**: an integer repersenting a base position (>0)
 
 Genomic Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -32,7 +32,7 @@ Genomic Position Conversion
     >>> from mutalyzer_crossmapper import Genomic
     >>> crossmap = Genomic()
 
-The functions ``coordinate_to_genomic()`` and ``genomic_to_coordinate`` can be
+The functions ``coordinate_to_genomic()`` and ``genomic_to_coordinate()`` can be
 used to convert to and from genomic positions.
 
 .. code:: python
@@ -181,7 +181,7 @@ The ``Coding`` class
 --------------------
 
 The ``Coding`` class provides an interface to all conversions between
-coding (``c.``, ``r.``) rpositioning systems and coordinates. Conversions between
+coding (``c.``, ``r.``) positions and coordinates. Conversions between
 positioning systems should be done via a coordinate.
 
 Coding Position Model
@@ -307,6 +307,11 @@ In the following table, we show a number of annotated examples.
      - 0
      - ``*``
      - ``c.*5``
+   * - 72
+     - 1
+     - 0
+     - ``d``
+     - ``c.d1``
    * - 79
      - 8
      - 0
@@ -348,8 +353,8 @@ position ``p.2``. We can convert between these to as follows.
     >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon':2, 'offset':0, 'region':''})
     41
 
-Note that the protein position only corresponds with the HGVS "p." notation
-when the offset equals ``0`` and the region equals ``1``. In the following
+**Note:** protein position only corresponds with the HGVS "p." notation
+when the offset equals ``0`` and the region equals ``''``. In the following
 table, we show a number of annotated examples.
 
 .. _table_protein:
@@ -380,18 +385,6 @@ table, we show a number of annotated examples.
      - 0
      - ``-``
      - invalid
-   * - 7
-     - 3
-     - 1
-     - 0
-     - ``-``
-     - invalid
-   * - 8
-     - 3
-     - 1
-     - 1
-     - ``-``
-     - invalid
    * - 31
      - 1
      - 3
@@ -410,6 +403,18 @@ table, we show a number of annotated examples.
      - 0
      -
      - ``p.1``
+   * - 34
+     - 1
+     - 3
+     - 0
+     -
+     - ``p.1``
+   * - 35
+     - 1
+     - 3
+     - 1
+     -
+     - ``p.1``
    * - 42
      - 2
      - 3
@@ -476,9 +481,6 @@ The ``Locus`` class
 
 The ``Locus`` class is used to deal with offsets with respect to a single
 locus.
-**Note:** the ``position`` values in the position dictionaries are **0-based**,
-so the first base of the locus corresponds to ``{'position': 0, 'offset': 0}``.
-This differs from HGVS numbering, which is **1-based**.
 
 .. code:: python
 
@@ -490,6 +492,10 @@ converting from a locus position to a coordinate and vice versa. These
 functions work with a 2-key dictionary, see the section about `The NonCoding class`_
 for the semantics.
 
+**Note:** the ``position`` values in the position dictionaries are **0-based**,
+so the first base of the locus corresponds to ``{'position': 0, 'offset': 0}``.
+This differs from HGVS numbering, which is **1-based**.
+
 .. code:: python
 
     >>> locus.to_position(9)

From 2ebf6c95df03a381b3f2cba8b5ebc82fd5266ef0 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 23 Mar 2026 11:08:40 +0100
Subject: [PATCH 093/127] Cleanup

---
 Makefile  | 20 --------------------
 conf.py   | 28 ----------------------------
 index.rst | 17 -----------------
 make.bat  | 35 -----------------------------------
 4 files changed, 100 deletions(-)
 delete mode 100644 Makefile
 delete mode 100644 conf.py
 delete mode 100644 index.rst
 delete mode 100644 make.bat

diff --git a/Makefile b/Makefile
deleted file mode 100644
index d4bb2cb..0000000
--- a/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/conf.py b/conf.py
deleted file mode 100644
index a50b31a..0000000
--- a/conf.py
+++ /dev/null
@@ -1,28 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-
-project = 'crossmapper_dict'
-copyright = '2026, Xiaoyun Liu'
-author = 'Xiaoyun Liu'
-release = '1.0.0'
-
-# -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
-
-extensions = []
-
-templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
-
-
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-html_theme = 'alabaster'
-html_static_path = ['_static']
diff --git a/index.rst b/index.rst
deleted file mode 100644
index 3d88e72..0000000
--- a/index.rst
+++ /dev/null
@@ -1,17 +0,0 @@
-.. crossmapper_dict documentation master file, created by
-   sphinx-quickstart on Fri Mar 20 15:13:36 2026.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-crossmapper_dict documentation
-==============================
-
-Add your content using ``reStructuredText`` syntax. See the
-`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
-documentation for details.
-
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
diff --git a/make.bat b/make.bat
deleted file mode 100644
index 32bb245..0000000
--- a/make.bat
+++ /dev/null
@@ -1,35 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd

From f2e8efa7e49b0706111dc97970d4e190a189f62a Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 23 Mar 2026 11:13:44 +0100
Subject: [PATCH 094/127] Stop trackinhg local file

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 381420f..324acae 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ docs/_build/
 mutalyzer_crossmapper.egg-info/
 mutalyzer_crossmapper/__pycache__/
 tests/__pycache__/
+tmp
\ No newline at end of file

From 4e6443c797c35760367dafb93fcaf3da48c2781e Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 23 Mar 2026 11:16:27 +0100
Subject: [PATCH 095/127] Delete tmp files from branch

---
 tmp/t.t                | 80 ------------------------------------------
 tmp/test_degenerate.py | 51 ---------------------------
 2 files changed, 131 deletions(-)
 delete mode 100644 tmp/t.t
 delete mode 100644 tmp/test_degenerate.py

diff --git a/tmp/t.t b/tmp/t.t
deleted file mode 100644
index b473489..0000000
--- a/tmp/t.t
+++ /dev/null
@@ -1,80 +0,0 @@
-"0", "4", "2", "0", "u"
-"1", "4", "2", "0", "u"
-"2", "4", "2", "0", "u"
-"3", "4", "2", "0", "u"
-"4", "4", "2", "0", "u"
-"5", "4", "2", "0", "-"
-"6", "4", "3", "0", "-"
-"7", "3", "1", "0", "-"
-"8", "3", "1", "1", "-"
-"9", "3", "1", "2", "-"
-"10", "3", "1", "3", "-"
-"11", "3", "2", "-3", "-"
-"12", "3", "2", "-2", "-"
-"13", "3", "2", "-1", "-"
-"14", "3", "2", "0", "-"
-"15", "3", "3", "0", "-"
-"16", "2", "1", "0", "-"
-"17", "2", "2", "0", "-"
-"18", "2", "3", "0", "-"
-"19", "1", "1", "0", "-"
-"20", "1", "1", "1", "-"
-"21", "1", "1", "2", "-"
-"22", "1", "1", "3", "-"
-"23", "1", "1", "4", "-"
-"24", "1", "1", "5", "-"
-"25", "1", "2", "-5", "-"
-"26", "1", "2", "-4", "-"
-"27", "1", "2", "-3", "-"
-"28", "1", "2", "-2", "-"
-"29", "1", "2", "-1", "-"
-"30", "1", "2", "0", "-"
-"31", "1", "3", "0", "-"
-"32", "1", "1", "0", ""
-"33", "1", "2", "0", ""
-"34", "1", "3", "0", ""
-"35", "1", "3", "1", ""
-"36", "1", "3", "2", ""
-"37", "1", "3", "3", ""
-"38", "2", "1", "-2", ""
-"39", "2", "1", "-1", ""
-"40", "2", "1", "0", ""
-"41", "2", "2", "0", ""
-"42", "2", "3", "0", ""
-"43", "1", "1", "0", "*"
-"44", "1", "1", "1", "*"
-"45", "1", "1", "2", "*"
-"46", "1", "1", "3", "*"
-"47", "1", "2", "-3", "*"
-"48", "1", "2", "-2", "*"
-"49", "1", "2", "-1", "*"
-"50", "1", "2", "0", "*"
-"51", "1", "3", "0", "*"
-"52", "1", "3", "1", "*"
-"53", "1", "3", "2", "*"
-"54", "1", "3", "3", "*"
-"55", "1", "3", "4", "*"
-"56", "1", "3", "5", "*"
-"57", "1", "3", "6", "*"
-"58", "1", "3", "7", "*"
-"59", "1", "3", "8", "*"
-"60", "1", "3", "9", "*"
-"61", "2", "1", "-9", "*"
-"62", "2", "1", "-8", "*"
-"63", "2", "1", "-7", "*"
-"64", "2", "1", "-6", "*"
-"65", "2", "1", "-5", "*"
-"66", "2", "1", "-4", "*"
-"67", "2", "1", "-3", "*"
-"68", "2", "1", "-2", "*"
-"69", "2", "1", "-1", "*"
-"70", "2", "1", "0", "*"
-"71", "2", "2", "0", "*"
-"72", "2", "2", "0", "d"
-"73", "2", "2", "0", "d"
-"74", "2", "2", "0", "d"
-"75", "2", "2", "0", "d"
-"76", "2", "2", "0", "d"
-"77", "2", "2", "0", "d"
-"78", "2", "2", "0", "d"
-"79", "2", "2", "0", "d"
diff --git a/tmp/test_degenerate.py b/tmp/test_degenerate.py
deleted file mode 100644
index c513d0e..0000000
--- a/tmp/test_degenerate.py
+++ /dev/null
@@ -1,51 +0,0 @@
-"""a script to check degenerate option"""
-from mutalyzer_crossmapper import Coding, Genomic, NonCoding
-
-
-def serialize(pos_m: dict):
-    if pos_m["offset"] > 0:
-        return f"{pos_m['region']}{pos_m['position']}+{pos_m['offset']}"
-    elif pos_m["offset"] < 0:
-        return f"{pos_m['region']}{pos_m['position']}{pos_m['offset']}"
-    else:
-        return f"{pos_m['region']}{pos_m['position']}"
-
-_exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
-_cds = (32, 43)
-
-
-nc_crossmap = NonCoding(_exons, True)
-c_crossmap = Coding(_exons, _cds)
-test = Coding([(10, 11)], (10, 11))
-
-
-for i in range(0, 80):
-    # nc = nc_crossmap.coordinate_to_noncoding(i)
-    c = c_crossmap.coordinate_to_protein(i)
-
-    # print(i, c, c_crossmap.coding_to_coordinate(c))
-    # c_de = nc_crossmap.coordinate_to_coding(i, True)
-    # nc_de = nc_crossmap.coordinate_to_coding(i, True)
-    print(i, c)
-    # print(f'"{i}", "{c["position"]}", "{c["position_in_codon"]}", "{c["offset"]}", "{c["region"]}"')
-
-
-# crossmap = Coding(_exons, _cds)
-# for i in range(0, 80):
-#     print(i,  crossmap.coordinate_to_coding(i), crossmap.coordinate_to_coding(i, degenerate=True))
-
-# nc_crossmap = NonCoding(_exons)
-# for i in range(0, 80):
-#     print(i, nc_crossmap.coordinate_to_noncoding(i))
-
-
-
-
-
-
-# degereate option
-"""
-With this option, it keeps counting c_pos outside the exons range
-e.g., (-16, 0, -1, -5) means
-c_pos=16, offset_to_c_pos=0, before_CDS, offset_to_exons_range = -5
-"""

From 8deedc15cfc7d1aab64a9d47833cdf54d62ff2ff Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 23 Mar 2026 11:43:08 +0100
Subject: [PATCH 096/127] Cleanup

---
 mutalyzer_crossmapper/crossmapper.py | 19 ++++++++++---------
 mutalyzer_crossmapper/locus.py       |  2 +-
 mutalyzer_crossmapper/multi_locus.py |  5 ++---
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 42ab6d5..6d4f656 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -88,10 +88,11 @@ def _degenerate_position(self, pos_m: dict) -> dict:
         :returns dict: a generate coding position model.
         """
         region = pos_m['region']
-        position = pos_m['position']
+        if region not in ('u', 'd'):
+            return pos_m
 
         degenerated_pos_m = {'offset': pos_m['offset']}
-
+        position = pos_m['position']
         if region == 'u':
             if self._inverted:
                 degenerated_pos_m['position'] = position + self._exons[1] - self._coding[1] + 1
@@ -113,13 +114,13 @@ def _normalize_position(self, pos_m: dict) -> dict:
 
         :returns dict: a normalized coding postion model.
         """
-        initial_pos = {**pos_m, 'offset': 0}
-        coordinate = self._coding_to_coordinate(initial_pos)
+        base_pos = {**pos_m, 'offset': 0}
+        base_coordinate = self._coding_to_coordinate(base_pos)
         if self._inverted:
-            coordinate = coordinate - pos_m['offset']
+            base_coordinate = base_coordinate - pos_m['offset']
         else:
-            coordinate = coordinate + pos_m['offset']
-        return self.coordinate_to_coding(coordinate)
+            base_coordinate = base_coordinate + pos_m['offset']
+        return self.coordinate_to_coding(base_coordinate)
 
     def _coordinate_to_coding(self, coordinate: int) -> dict:
         """Convert a coordinate to a coding position (c./r.).
@@ -163,7 +164,7 @@ def coordinate_to_coding(self, coordinate: tuple[int, int], degenerate: bool=Fal
         """
         pos_m = self._coordinate_to_coding(coordinate)
 
-        if degenerate and pos_m['region'] in ('u', 'd'):
+        if degenerate:
             pos_m = self._degenerate_position(pos_m)
 
         return pos_m
@@ -209,7 +210,7 @@ def coordinate_to_protein(self, coordinate: int) -> dict:
 
         :returns dict: Protein position model(p.).
         """
-        pos = self.coordinate_to_coding(coordinate)
+        pos = self.coordinate_to_coding(coordinate, True)
 
         if pos['region'] == 'u':
             pos = self.coordinate_to_coding(coordinate + pos['position'])
diff --git a/mutalyzer_crossmapper/locus.py b/mutalyzer_crossmapper/locus.py
index 15b15a0..fff0c66 100644
--- a/mutalyzer_crossmapper/locus.py
+++ b/mutalyzer_crossmapper/locus.py
@@ -10,7 +10,7 @@ def __init__(self, location: list[tuple[int, int]], inverted=False) -> None:
         self.boundary = location[0], location[1] - 1
         self._end = self.boundary[1] - self.boundary[0]
 
-    def to_position(self, coordinate: int) -> dict:
+    def to_position(self, coordinate: int) -> dict[str, int]:
         """Convert a coordinate to a proper position model.
 
         :arg int coordinate: Coordinate.
diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 001ed2c..0b1ef52 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -19,7 +19,7 @@ def _offsets(locations: list[tuple[int, int]], orientation: int) -> list[int]:
 
 class MultiLocus(object):
     """MultiLocus object."""
-    def __init__(self, locations: list[tuple[int, int]], inverted=False) -> None:
+    def __init__(self, locations: list[tuple[int, int]], inverted: bool=False) -> None:
         """
         :arg list locations: List of locus locations.
         :arg bool inverted: Orientation.
@@ -49,7 +49,7 @@ def outside(self, coordinate: int) -> int:
             return coordinate - self._loci[-1].boundary[1]
         return 0
 
-    def to_position(self, coordinate: int) -> dict:
+    def to_position(self, coordinate: int) -> dict[str: int | str]:
         """Convert a coordinate to a position.
 
         :arg int coordinate: Coordinate.
@@ -67,7 +67,6 @@ def to_position(self, coordinate: int) -> dict:
                 'offset': 0,
                 'region': region
             }
-
         return {
             'position': location['position'] + self._offsets[self._direction(index)],
             'offset': location['offset'],

From f5f7a51353337a4795b78b96c6aea9fba3a0cb3b Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 23 Mar 2026 16:19:50 +0100
Subject: [PATCH 097/127] Refactor protein conversion

---
 docs/library.rst                     | 13 ++++++++++---
 mutalyzer_crossmapper/crossmapper.py | 13 ++++---------
 tests/test_crossmapper.py            | 28 ++++++++++++++++++++++++++++
 3 files changed, 42 insertions(+), 12 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 83bf73a..118c9e8 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -368,14 +368,14 @@ table, we show a number of annotated examples.
      - region
      - HGVS
    * - 0
-     - 4
+     - 2
      - 2
      - 0
      - ``u``
      - invalid
    * - 4
-     - 4
-     - 2
+     - 1
+     - 3
      - 0
      - ``u``
      - invalid
@@ -433,6 +433,13 @@ table, we show a number of annotated examples.
      - 1
      - ``*``
      - invalid
+   * - 72
+     - 1
+     - 1
+     - 0
+     - ``d``
+     - invalid
+
    * - 79
      - 2
      - 2
diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 6d4f656..4ac0ce4 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -77,7 +77,7 @@ def __init__(self, locations: list[tuple[int,int]], cds: tuple[int,int], inverte
             self._coding = (b1['position'] + b1['offset'], b0['position'] + b0['offset'] + 1)
             self._exons = (e1['position'], e0['position'])
         else:
-            self._coding = (b0['position'] + b0['offset'], b1['position'] + b1['offset'] +1)
+            self._coding = (b0['position'] + b0['offset'], b1['position'] + b1['offset'] + 1)
             self._exons = (e0['position'], e1['position'])
 
     def _degenerate_position(self, pos_m: dict) -> dict:
@@ -210,15 +210,10 @@ def coordinate_to_protein(self, coordinate: int) -> dict:
 
         :returns dict: Protein position model(p.).
         """
-        pos = self.coordinate_to_coding(coordinate, True)
-
-        if pos['region'] == 'u':
-            pos = self.coordinate_to_coding(coordinate + pos['position'])
-        elif pos['region'] == 'd':
-            pos = self.coordinate_to_coding(coordinate - pos['position'])
+        pos = self.coordinate_to_coding(coordinate)
 
         position = pos['position']
-        if pos['region'] == '-':
+        if pos['region'] in ('-', 'u'):
             return {
                 'position': abs(-position // 3),
                 'position_in_codon': -position % 3 + 1,
@@ -235,7 +230,7 @@ def protein_to_coordinate(self, pos_m: dict) -> int:
 
         :returns int: Coordinate.
         """
-        if pos_m['region'] == '-':
+        if pos_m['region'] in ('-', 'u'):
             return self.coding_to_coordinate(
                 {'position': 3 * pos_m['position'] - pos_m['position_in_codon'] + 1,
                  'offset': pos_m['offset'],
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 97c6262..7265507 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -667,6 +667,20 @@ def test_Coding_protein():
     """Protein positions."""
     crossmap = Coding(_exons, _cds)
 
+    # Boundary between upstream and 5' UTR
+    invariant(
+        crossmap.coordinate_to_protein,
+        4,
+        crossmap.protein_to_coordinate,
+        {'position': 1, 'position_in_codon': 3, 'offset': 0, 'region': 'u'}
+    )
+    invariant(
+        crossmap.coordinate_to_protein,
+        5,
+        crossmap.protein_to_coordinate,
+        {'position': 4, 'position_in_codon': 2, 'offset': 0, 'region': '-'}
+    )
+
     # Boundary between 5' UTR and CDS
     invariant(
         crossmap.coordinate_to_protein,
@@ -708,3 +722,17 @@ def test_Coding_protein():
         crossmap.protein_to_coordinate,
         {'position': 1, 'position_in_codon': 1, 'offset': 0, 'region': '*'},
     )
+
+    # Boundary between 3' UTR and downstream
+    invariant(
+        crossmap.coordinate_to_protein,
+        71,
+        crossmap.protein_to_coordinate,
+        {'position': 2, 'position_in_codon': 2, 'offset': 0, 'region': '*'}
+    )
+    invariant(
+        crossmap.coordinate_to_protein,
+        72,
+        crossmap.protein_to_coordinate,
+        {'position': 1, 'position_in_codon': 1, 'offset': 0, 'region': 'd'}
+    )

From 79cbcc0266ea94626c00b08b6f88cdde9e44c99d Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 23 Mar 2026 16:39:00 +0100
Subject: [PATCH 098/127] Add degenerate tests

---
 tests/test_multi_locus.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/tests/test_multi_locus.py b/tests/test_multi_locus.py
index ab3b877..259eafa 100644
--- a/tests/test_multi_locus.py
+++ b/tests/test_multi_locus.py
@@ -285,7 +285,8 @@ def test_MultiLocus_degenerate():
         multi_locus.to_coordinate,
         4,
         [
-            {'position': 0, 'offset': -1, 'region': 'u'},
+            {'position': 0, 'offset': -1, 'region': ''},
+            {'position': -1, 'offset': 0, 'region': ''},
             {'position': 1, 'offset': 0, 'region': 'u'},
             {'position': -1, 'offset': 0, 'region': 'u'},
         ],
@@ -295,6 +296,8 @@ def test_MultiLocus_degenerate():
         multi_locus.to_coordinate,
         72,
         [
+            {'position': 21, 'offset': 1, 'region': ''},
+            {'position': 22, 'offset': 0, 'region': ''},
             {'position': 0, 'offset': 1, 'region': 'd'},
             {'position': 1, 'offset': 0, 'region': 'd'},
         ],
@@ -310,7 +313,8 @@ def test_MultiLocus_inverted_degenerate():
         72,
         [
             {'position': 0, 'offset': 1, 'region': 'u'},
-            {'position': -1, 'offset': 0, 'region': 'u'},
+            {'position': -1, 'offset': 0, 'region': ''},
+            {'position': 0, 'offset': -1, 'region': ''},
             {'position': 1, 'offset': 0, 'region': 'u'},
         ],
     )
@@ -320,6 +324,8 @@ def test_MultiLocus_inverted_degenerate():
         4,
         [
             {'position': 0, 'offset': -1, 'region': 'd'},
+            {'position': 21, 'offset': 1, 'region': ''},
+            {'position': 22, 'offset': 0, 'region': ''},
             {'position': 1, 'offset': 0, 'region': 'd'},
         ],
     )

From 1459451f4f263b80713b01cbc56c5c6731154724 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 23 Mar 2026 16:58:03 +0100
Subject: [PATCH 099/127] Add backticks for region in table

---
 docs/library.rst | 44 ++++++++++++++++++++++----------------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 118c9e8..a069719 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -137,12 +137,12 @@ In the following table, we show a number of annotated examples.
    * - 0
      - 5
      - 0
-     - ``u``
+     - ``'u'``
      - ``n.u5``
    * - 4
      - 1
      - 0
-     - ``u``
+     - ``'u'``
      - ``n.u1``
    * - 5
      - 1
@@ -167,12 +167,12 @@ In the following table, we show a number of annotated examples.
    * - 72
      - 1
      - 0
-     - ``d``
+     - ``'d'``
      - ``n.d1``
    * - 79
      - 8
      - 0
-     - ``d``
+     - ``'d'``
      - ``n.d8``
 
 See section :doc:`api/crossmap` for a detailed description.
@@ -255,27 +255,27 @@ In the following table, we show a number of annotated examples.
    * - 0
      - 5
      - 0
-     - ``u``
+     - ``'u'``
      - ``c.u5``
    * - 4
      - 1
      - 0
-     - ``u``
+     - ``'u'``
      - ``c.u1``
    * - 5
      - 11
      - 0
-     - ``-``
+     - ``'-'``
      - ``c.-11``
    * - 24
      - 3
      - 5
-     - ``-``
+     - ``'-'``
      - ``c.-3+5``
    * - 31
      - 1
      - 0
-     - ``-``
+     - ``'-'``
      - ``c.-1``
    * - 32
      - 1
@@ -295,27 +295,27 @@ In the following table, we show a number of annotated examples.
    * - 43
      - 1
      - 0
-     - ``*``
+     - ``'*'``
      - ``c.*1``
    * - 61
      - 4
      - -9
-     - ``*``
+     - ``'*'``
      - ``c.*4-9``
    * - 71
      - 5
      - 0
-     - ``*``
+     - ``'*'``
      - ``c.*5``
    * - 72
      - 1
      - 0
-     - ``d``
+     - ``'d'``
      - ``c.d1``
    * - 79
      - 8
      - 0
-     - ``d``
+     - ``'d'``
      - ``c.d8``
 
 
@@ -371,25 +371,25 @@ table, we show a number of annotated examples.
      - 2
      - 2
      - 0
-     - ``u``
+     - ``'u'``
      - invalid
    * - 4
      - 1
      - 3
      - 0
-     - ``u``
+     - ``'u'``
      - invalid
    * - 5
      - 4
      - 2
      - 0
-     - ``-``
+     - ``'-'``
      - invalid
    * - 31
      - 1
      - 3
      - 0
-     - ``-``
+     - ``'-'``
      - invalid
    * - 32
      - 1
@@ -425,26 +425,26 @@ table, we show a number of annotated examples.
      - 1
      - 1
      - 0
-     - ``*``
+     - ``'*'``
      - invalid
    * - 44
      - 1
      - 1
      - 1
-     - ``*``
+     - ``'*'``
      - invalid
    * - 72
      - 1
      - 1
      - 0
-     - ``d``
+     - ``'d'``
      - invalid
 
    * - 79
      - 2
      - 2
      - 0
-     - ``d``
+     - ``'d'``
      - invalid
 
 

From e92c78e5276187cc798796720c56c8d09ef4c385 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 23 Mar 2026 17:38:39 +0100
Subject: [PATCH 100/127] Cleanup

---
 mutalyzer_crossmapper/crossmapper.py | 38 ++++++++++++++--------------
 mutalyzer_crossmapper/multi_locus.py |  8 +++---
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 4ac0ce4..4630e7d 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -53,7 +53,7 @@ def noncoding_to_coordinate(self, pos_m: dict) -> int:
         :returns int: Coordinate.
         """
         multilocus_pos_m = {**pos_m}
-        if pos_m['region'] == '':
+        if multilocus_pos_m['region'] == '':
             multilocus_pos_m['position'] = pos_m['position'] - 1
         return self._noncoding.to_coordinate(multilocus_pos_m)
 
@@ -91,21 +91,21 @@ def _degenerate_position(self, pos_m: dict) -> dict:
         if region not in ('u', 'd'):
             return pos_m
 
-        degenerated_pos_m = {'offset': pos_m['offset']}
-        position = pos_m['position']
+        degenerate_pos_m = {'offset': pos_m['offset']}
+        location = pos_m['position']
         if region == 'u':
             if self._inverted:
-                degenerated_pos_m['position'] = position + self._exons[1] - self._coding[1] + 1
+                degenerate_pos_m['position'] = location + self._exons[1] - self._coding[1] + 1
             else:
-                degenerated_pos_m['position'] = position + self._coding[0]
-            degenerated_pos_m['region'] = '-'
+                degenerate_pos_m['position'] = location + self._coding[0]
+            degenerate_pos_m['region'] = '-'
         if region == 'd':
             if self._inverted:
-                degenerated_pos_m['position'] = position + self._coding[0]
+                degenerate_pos_m['position'] = location + self._coding[0]
             else:
-                degenerated_pos_m['position'] = position + self._exons[1]- self._coding[1] + 1
-            degenerated_pos_m['region'] = '*'
-        return degenerated_pos_m
+                degenerate_pos_m['position'] = location + self._exons[1]- self._coding[1] + 1
+            degenerate_pos_m['region'] = '*'
+        return degenerate_pos_m
 
     def _normalize_position(self, pos_m: dict) -> dict:
         """Normalize a coding position model (c./r.).
@@ -176,7 +176,7 @@ def _coding_to_coordinate(self, pos_m: dict) -> int:
 
         :returns int: Coordinate.
         """
-        position = pos_m['position']
+        location = pos_m['position']
         region = pos_m['region']
 
         if region in ('u', 'd'):
@@ -184,11 +184,11 @@ def _coding_to_coordinate(self, pos_m: dict) -> int:
 
         noncoding_pos_m = {'offset': pos_m['offset'], 'region': ''}
         if region == '':
-            noncoding_pos_m['position'] = position + self._coding[0] - 1
+            noncoding_pos_m['position'] = location + self._coding[0] - 1
         elif region == '-':
-            noncoding_pos_m['position'] = self._coding[0] - position
+            noncoding_pos_m['position'] = self._coding[0] - location
         else:
-            noncoding_pos_m['position'] = self._coding[1] + position - 1
+            noncoding_pos_m['position'] = self._coding[1] + location - 1
 
         return self._noncoding.to_coordinate(noncoding_pos_m)
 
@@ -212,15 +212,15 @@ def coordinate_to_protein(self, coordinate: int) -> dict:
         """
         pos = self.coordinate_to_coding(coordinate)
 
-        position = pos['position']
+        location = pos['position']
         if pos['region'] in ('-', 'u'):
             return {
-                'position': abs(-position // 3),
-                'position_in_codon': -position % 3 + 1,
+                'position': abs(-location // 3),
+                'position_in_codon': -location % 3 + 1,
                 **{k: v for k, v in pos.items() if k != 'position'}}
         return {
-                'position': (position + 2) // 3,
-                'position_in_codon': (position + 2) % 3 + 1,
+                'position': (location + 2) // 3,
+                'position_in_codon': (location + 2) % 3 + 1,
                 **{k: v for k, v in pos.items() if k != 'position'}}
 
     def protein_to_coordinate(self, pos_m: dict) -> int:
diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 0b1ef52..2f67777 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -59,17 +59,17 @@ def to_position(self, coordinate: int) -> dict[str: int | str]:
         index = nearest_location(self._locations, coordinate, self._inverted)
         outside = self._orientation * self.outside(coordinate)
         region = 'u' if outside < 0 else 'd' if outside > 0 else ''
-        location = self._loci[index].to_position(coordinate)
+        locus_pos_m = self._loci[index].to_position(coordinate)
 
         if outside:
             return {
-                'position': abs(location['offset']),
+                'position': abs(locus_pos_m['offset']),
                 'offset': 0,
                 'region': region
             }
         return {
-            'position': location['position'] + self._offsets[self._direction(index)],
-            'offset': location['offset'],
+            'position': locus_pos_m['position'] + self._offsets[self._direction(index)],
+            'offset': locus_pos_m['offset'],
             'region': region
         }
 

From f8105676ff7f1f01c296f1887d778644c9d184ce Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 25 Mar 2026 13:54:51 +0100
Subject: [PATCH 101/127] Discard normalize position model

---
 mutalyzer_crossmapper/crossmapper.py | 25 +++++++------------------
 mutalyzer_crossmapper/multi_locus.py | 13 +++++++------
 2 files changed, 14 insertions(+), 24 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 4630e7d..6ad0140 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -45,7 +45,7 @@ def coordinate_to_noncoding(self, coordinate: int) -> dict:
             pos_m['position'] = pos_m['position'] + 1
         return pos_m
 
-    def noncoding_to_coordinate(self, pos_m: dict) -> int:
+    def noncoding_to_coordinate(self, pos_m: dict, degenerate: bool=True) -> int:
         """Convert a noncoding position (n./r.) to a coordinate.
 
         :arg dict pos_m: Noncoding position model.
@@ -53,6 +53,11 @@ def noncoding_to_coordinate(self, pos_m: dict) -> int:
         :returns int: Coordinate.
         """
         multilocus_pos_m = {**pos_m}
+        if degenerate:
+            if multilocus_pos_m["region"] == '-':
+                multilocus_pos_m["region"] = 'u'
+            elif multilocus_pos_m["region"] == '*':
+                multilocus_pos_m['region'] = 'd'
         if multilocus_pos_m['region'] == '':
             multilocus_pos_m['position'] = pos_m['position'] - 1
         return self._noncoding.to_coordinate(multilocus_pos_m)
@@ -107,21 +112,6 @@ def _degenerate_position(self, pos_m: dict) -> dict:
             degenerate_pos_m['region'] = '*'
         return degenerate_pos_m
 
-    def _normalize_position(self, pos_m: dict) -> dict:
-        """Normalize a coding position model (c./r.).
-
-        :arg dict pos_m: Coding position model.
-
-        :returns dict: a normalized coding postion model.
-        """
-        base_pos = {**pos_m, 'offset': 0}
-        base_coordinate = self._coding_to_coordinate(base_pos)
-        if self._inverted:
-            base_coordinate = base_coordinate - pos_m['offset']
-        else:
-            base_coordinate = base_coordinate + pos_m['offset']
-        return self.coordinate_to_coding(base_coordinate)
-
     def _coordinate_to_coding(self, coordinate: int) -> dict:
         """Convert a coordinate to a coding position (c./r.).
 
@@ -199,9 +189,8 @@ def coding_to_coordinate(self, pos_m: dict) -> int:
 
         :returns int: Coordinate.
         """
-        normalized_pos_m = self._normalize_position(pos_m)
 
-        return self._coding_to_coordinate(normalized_pos_m)
+        return self._coding_to_coordinate(pos_m)
 
     def coordinate_to_protein(self, coordinate: int) -> dict:
         """Convert a coordinate to a protein position (p.).
diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 2f67777..a60e6da 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -82,13 +82,14 @@ def to_coordinate(self, pos_m: dict) -> int:
         """
         region = pos_m['region']
 
-        if pos_m['region'] in ('u', 'd'):
-            is_upstream = region == 'u'
+        if region == 'u':
             if self._inverted:
-                is_upstream = not is_upstream
-            if is_upstream:
-                return self._locations[0][0] - abs(pos_m['position']) + pos_m['offset']
-            return abs(pos_m['position']) + self._locations[-1][1] + pos_m['offset'] - 1
+                return self._locations[-1][1] + abs(pos_m['position']) - pos_m['offset'] - 1
+            return self._locations[0][0] - abs(pos_m['position']) + pos_m['offset']
+        elif region == 'd':
+            if self._inverted:
+                return self._locations[0][0] - abs(pos_m['position']) - pos_m['offset']
+            return self._locations[-1][1] + abs(pos_m['position']) + pos_m['offset'] - 1
 
         index = min(
             len(self._offsets),

From c5d773254d8081db3303a16516af28fec599723d Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 25 Mar 2026 17:26:22 +0100
Subject: [PATCH 102/127] Fix test

---
 tests/test_multi_locus.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_multi_locus.py b/tests/test_multi_locus.py
index 259eafa..99c7e50 100644
--- a/tests/test_multi_locus.py
+++ b/tests/test_multi_locus.py
@@ -312,7 +312,7 @@ def test_MultiLocus_inverted_degenerate():
         multi_locus.to_coordinate,
         72,
         [
-            {'position': 0, 'offset': 1, 'region': 'u'},
+            {'position': 0, 'offset': -1, 'region': 'u'},
             {'position': -1, 'offset': 0, 'region': ''},
             {'position': 0, 'offset': -1, 'region': ''},
             {'position': 1, 'offset': 0, 'region': 'u'},
@@ -323,9 +323,9 @@ def test_MultiLocus_inverted_degenerate():
         multi_locus.to_coordinate,
         4,
         [
-            {'position': 0, 'offset': -1, 'region': 'd'},
             {'position': 21, 'offset': 1, 'region': ''},
             {'position': 22, 'offset': 0, 'region': ''},
             {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 0, 'offset': 1, 'region': 'd'},
         ],
     )

From 49ecb5f849b65d2e3403cb9b51646a4364f5cc99 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 26 Mar 2026 12:34:19 +0100
Subject: [PATCH 103/127] Add degenerate for NonCoding

---
 mutalyzer_crossmapper/crossmapper.py | 48 +++++++++++-----------------
 tests/test_crossmapper.py            |  6 ++++
 2 files changed, 24 insertions(+), 30 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 6ad0140..2838da7 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -85,33 +85,6 @@ def __init__(self, locations: list[tuple[int,int]], cds: tuple[int,int], inverte
             self._coding = (b0['position'] + b0['offset'], b1['position'] + b1['offset'] + 1)
             self._exons = (e0['position'], e1['position'])
 
-    def _degenerate_position(self, pos_m: dict) -> dict:
-        """Degenerate a coding position model (c./r.).
-
-        :arg dict pos_m: Coding position model.
-
-        :returns dict: a generate coding position model.
-        """
-        region = pos_m['region']
-        if region not in ('u', 'd'):
-            return pos_m
-
-        degenerate_pos_m = {'offset': pos_m['offset']}
-        location = pos_m['position']
-        if region == 'u':
-            if self._inverted:
-                degenerate_pos_m['position'] = location + self._exons[1] - self._coding[1] + 1
-            else:
-                degenerate_pos_m['position'] = location + self._coding[0]
-            degenerate_pos_m['region'] = '-'
-        if region == 'd':
-            if self._inverted:
-                degenerate_pos_m['position'] = location + self._coding[0]
-            else:
-                degenerate_pos_m['position'] = location + self._exons[1]- self._coding[1] + 1
-            degenerate_pos_m['region'] = '*'
-        return degenerate_pos_m
-
     def _coordinate_to_coding(self, coordinate: int) -> dict:
         """Convert a coordinate to a coding position (c./r.).
 
@@ -154,10 +127,25 @@ def coordinate_to_coding(self, coordinate: tuple[int, int], degenerate: bool=Fal
         """
         pos_m = self._coordinate_to_coding(coordinate)
 
-        if degenerate:
-            pos_m = self._degenerate_position(pos_m)
+        region = pos_m['region']
+        if not degenerate or region =='':
+            return pos_m
 
-        return pos_m
+        degenerate_pos_m = {'offset': pos_m['offset']}
+        location = pos_m['position']
+        if region == 'u':
+            if self._inverted:
+                degenerate_pos_m['position'] = location + self._exons[1] - self._coding[1] + 1
+            else:
+                degenerate_pos_m['position'] = location + self._coding[0]
+            degenerate_pos_m['region'] = '-'
+        if region == 'd':
+            if self._inverted:
+                degenerate_pos_m['position'] = location + self._coding[0]
+            else:
+                degenerate_pos_m['position'] = location + self._exons[1]- self._coding[1] + 1
+            degenerate_pos_m['region'] = '*'
+        return degenerate_pos_m
 
     def _coding_to_coordinate(self, pos_m: dict) -> int:
         """Convert a coding position (c./r.) to a coordinate.
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 7265507..8f40840 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -107,6 +107,8 @@ def test_NonCoding_degenerate():
         [
             {'position': 1, 'offset': -1, 'region': ''},
             {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 1, 'offset': 0, 'region': '-'},
+            {'position': 2, 'offset': 1, 'region': '-'},
         ],
     )
 
@@ -118,6 +120,8 @@ def test_NonCoding_degenerate():
             {'position': 1, 'offset': 0, 'region': 'd'},
             {'position': 22, 'offset': 1, 'region': ''},
             {'position': 23, 'offset': 0, 'region': ''},
+            {'position': 24, 'offset': -1, 'region': ''},
+            {'position': 1, 'offset': 0, 'region': '*'},
         ],
     )
 
@@ -133,6 +137,7 @@ def test_NonCoding_inverted_degenerate():
         [
             {'position': 1, 'offset': -1, 'region': ''},
             {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 1, 'offset': 0, 'region': '-'},
         ],
     )
 
@@ -142,6 +147,7 @@ def test_NonCoding_inverted_degenerate():
         4,
         [
             {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 1, 'offset': 0, 'region': '*'},
             {'position': 23, 'offset': 0, 'region': ''},
             {'position': 22, 'offset': 1, 'region': ''},
         ],

From 78491956aeedafbc359b563b6578eb5bc8e5021e Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 26 Mar 2026 15:46:18 +0100
Subject: [PATCH 104/127] Add tests for degenerate in NonCoding

---
 mutalyzer_crossmapper/crossmapper.py | 26 +++++++++------
 tests/test_crossmapper.py            | 47 +++++++++++++++++++++++++++-
 2 files changed, 63 insertions(+), 10 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 2838da7..2fbe449 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -33,7 +33,7 @@ def __init__(self, locations: list[tuple[int, int]], inverted: bool = False) ->
 
         self._noncoding = MultiLocus(locations, inverted)
 
-    def coordinate_to_noncoding(self, coordinate: int) -> dict:
+    def coordinate_to_noncoding(self, coordinate: int, degenerate: bool=False) -> dict:
         """Convert a coordinate to a noncoding position (n./r.).
 
         :arg int coordinate: Coordinate.
@@ -41,11 +41,19 @@ def coordinate_to_noncoding(self, coordinate: int) -> dict:
         :returns dict: Noncoding position model.
         """
         pos_m = self._noncoding.to_position(coordinate)
-        if pos_m['region'] == '':
+        region = pos_m['region']
+        if region == '':
             pos_m['position'] = pos_m['position'] + 1
+            return pos_m
+
+        if degenerate:
+            if region == 'u':
+                pos_m["region"] = '-'
+            elif region == 'd':
+                pos_m['region'] = '*'
         return pos_m
 
-    def noncoding_to_coordinate(self, pos_m: dict, degenerate: bool=True) -> int:
+    def noncoding_to_coordinate(self, pos_m: dict) -> int:
         """Convert a noncoding position (n./r.) to a coordinate.
 
         :arg dict pos_m: Noncoding position model.
@@ -53,13 +61,13 @@ def noncoding_to_coordinate(self, pos_m: dict, degenerate: bool=True) -> int:
         :returns int: Coordinate.
         """
         multilocus_pos_m = {**pos_m}
-        if degenerate:
-            if multilocus_pos_m["region"] == '-':
-                multilocus_pos_m["region"] = 'u'
-            elif multilocus_pos_m["region"] == '*':
-                multilocus_pos_m['region'] = 'd'
-        if multilocus_pos_m['region'] == '':
+        region = multilocus_pos_m['region']
+        if region == '':
             multilocus_pos_m['position'] = pos_m['position'] - 1
+        elif region == '-':
+            multilocus_pos_m['region'] = 'u'
+        elif region == '*':
+            multilocus_pos_m['region'] = 'd'
         return self._noncoding.to_coordinate(multilocus_pos_m)
 
 
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 8f40840..33aec12 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -154,6 +154,52 @@ def test_NonCoding_inverted_degenerate():
     )
 
 
+def test_NonCoding_degenerate_return():
+    crossmap = NonCoding(_exons)
+
+    assert crossmap.coordinate_to_noncoding(4, True) == {
+        'position': 1,
+        'offset': 0,
+        'region': '-',
+    }
+
+    assert crossmap.coordinate_to_noncoding(72, True) == {
+        'position': 1,
+        'offset': 0,
+        'region': '*',
+    }
+
+
+def test_NonCoding_inverted_degenerate_return():
+    crossmap = NonCoding(_exons, True)
+
+    assert crossmap.coordinate_to_noncoding(72, True) == {
+        'position': 1,
+        'offset': 0,
+        'region': '-',
+    }
+
+    assert crossmap.coordinate_to_noncoding(4, True) == {
+        'position': 1,
+        'offset': 0,
+        'region': '*',
+    }
+
+
+def test_NonCoding_degenerate_no_return():
+    """Degenerate internal positions do not exist."""
+    crossmap = NonCoding(_exons)
+
+    assert crossmap.coordinate_to_noncoding(25) == crossmap.coordinate_to_noncoding(25, True)
+
+
+def test_NonCoding_inverted_degenerate_no_return():
+    """Degenerate internal positions do not exist."""
+    crossmap = NonCoding(_exons, True)
+
+    assert crossmap.coordinate_to_noncoding(25) == crossmap.coordinate_to_noncoding(25, True)
+
+
 def test_Coding():
     """Forward oriented coding transcript."""
     crossmap = Coding(_exons, _cds)
@@ -544,7 +590,6 @@ def test_Coding_inverted_degenerate_return():
     """Degenerate upstream and downstream positions may be returned."""
     crossmap = Coding([(10, 20)], (11, 19), True)
 
-
     assert crossmap.coordinate_to_coding(20, True) == {
         'position': 2,
         'offset': 0,

From 7c3cdde5d1efd9b399fddd6904e9f592f2b847e6 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 26 Mar 2026 15:46:48 +0100
Subject: [PATCH 105/127] Update document

---
 docs/library.rst | 161 +++++++++++++++++++++++++----------------------
 1 file changed, 86 insertions(+), 75 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index a069719..564d9cd 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -18,11 +18,11 @@ They are represented as 1-key dictionaries. Below is an example of ``g.1`` in HG
 
 .. code-block:: python
 
-    {'position':1}
+    {'position': 1}
 
 Where:
 
-- **position**: an integer repersenting a base position (>0)
+- **position**: an integer representing a nucleotide position (>0)
 
 Genomic Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -38,8 +38,8 @@ used to convert to and from genomic positions.
 .. code:: python
 
     >>> crossmap.coordinate_to_genomic(0)
-    1
-    >>> crossmap.genomic_to_coordinate({'position':1})
+    {'position': 1}
+    >>> crossmap.genomic_to_coordinate({'position': 1})
     0
 
 See section :doc:`api/crossmap` for a detailed description.
@@ -68,11 +68,11 @@ as 3-key dictionaries. Below is an example of ``n.14+1`` in HGVS.
 
 Where:
 
-- **position**: an interger representing a transcript position (>0)
+- **position**: an integer representing a transcript position (>0)
 - **offset**: an integer indicating the offset relative to the position (negative for upstream,
   positive for downstream)
-- **region**: a string describing the region type (``''`` for standard, ``'u'`` for upstream,
-  ``'d'`` for downstream)
+- **region**: a string describing the region type (empty for positions within a non-coding transcript, ``u`` for upstream,
+  ``d`` for downstream)
 
 NonCoding Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -92,24 +92,35 @@ position ``n.14+1``. We can convert between these two as follows.
 .. code:: python
 
     >>> crossmap.coordinate_to_noncoding(35)
-    {'position':14, 'offset':1, 'region':''}
-    >>> crossmap.noncoding_to_coordinate({'position':14, 'offset':1, 'region':''})
-    {'position':14, 'offset':1, 'region':''}
+    {'position': 14, 'offset': 1, 'region': ''}
+    >>> crossmap.noncoding_to_coordinate({'position': 14, 'offset': 1, 'region': ''})
+    35
 
-When the coordinate is upstream or downstream of the transcript,  we use ``'u'`` to
-present upstream and ``'d'`` to present downstream.
+When the coordinate is upstream or downstream of the transcript,  we use ``u`` to
+present upstream and ``d`` to present downstream.
 
 .. code:: python
 
     >>> crossmap.coordinate_to_noncoding(2)
-    {'position':3, 'offset':0, 'region':'u'}
-    >>> crossmap.noncoding_to_coordinate({'position':3, 'offset':0, 'region':'u'})
+    {'position': 3, 'offset': 0, 'region': 'u'}
+    >>> crossmap.noncoding_to_coordinate({'position': 3, 'offset': 0, 'region': 'u'})
     2
     >>> crossmap.coordinate_to_noncoding(73)
-    {'position':2, 'offset':0, 'region':'d'}
-    >>> crossmap.noncoding_to_coordinate({'position':2, 'offset':0, 'region':'d'})
+    {'position': 2, 'offset': 0, 'region': 'd'}
+    >>> crossmap.noncoding_to_coordinate({'position': 2, 'offset': 0, 'region': 'd'})
     73
 
+The ``coordinate_to_noncoding()`` function accepts an optional ``degenerate``
+argument. When set to ``True``, positions outside of the transcript are no
+longer described using the ``u`` or ``d`` notation, ``-`` and ``*``are used
+instead.
+
+.. code:: python
+
+    >>> crossmap.coordinate_to_noncoding(2)
+    {'position': 3, 'offset': 0, 'region': 'u'}
+    >>> crossmap.coordinate_to_noncoding(2, True)
+    {'position': 3, 'offset': 0, 'region': '-'}
 
 For transcripts that reside on the reverse complement strand, the ``inverted``
 parameter should be set to ``True``. In our example, HGVS position ``g.36``
@@ -119,8 +130,8 @@ parameter should be set to ``True``. In our example, HGVS position ``g.36``
 
     >>> crossmap = NonCoding(exons, inverted=True)
     >>> crossmap.coordinate_to_noncoding(35)
-    {'position':9, 'offset':-1, 'region':''}
-    >>> crossmap.noncoding_to_coordinate({'position':9, 'offset':-1, 'region':''})
+    {'position': 9, 'offset': -1, 'region': ''}
+    >>> crossmap.noncoding_to_coordinate({'position': 9, 'offset': -1, 'region': ''})
     35
 
 In the following table, we show a number of annotated examples.
@@ -137,12 +148,12 @@ In the following table, we show a number of annotated examples.
    * - 0
      - 5
      - 0
-     - ``'u'``
+     - ``u``
      - ``n.u5``
    * - 4
      - 1
      - 0
-     - ``'u'``
+     - ``u``
      - ``n.u1``
    * - 5
      - 1
@@ -167,12 +178,12 @@ In the following table, we show a number of annotated examples.
    * - 72
      - 1
      - 0
-     - ``'d'``
+     - ``d``
      - ``n.d1``
    * - 79
      - 8
      - 0
-     - ``'d'``
+     - ``d``
      - ``n.d8``
 
 See section :doc:`api/crossmap` for a detailed description.
@@ -186,7 +197,7 @@ positioning systems should be done via a coordinate.
 
 Coding Position Model
 ~~~~~~~~~~~~~~~~~~~~~
-Coding positions follow the HGVS ``c`` coordinate system. They are
+Coding positions follow the HGVS ``c.`` coordinate system. They are
 represented as 3-key dictionaries. Here is an example of ``c.*1+3``.
 
 .. code-block:: python
@@ -199,11 +210,11 @@ represented as 3-key dictionaries. Here is an example of ``c.*1+3``.
 
 Where:
 
-- **position**: an interger representing a transcript position (>0)
+- **position**: an integer representing a transcript position (>0)
 - **offset**: an integer indicating the offset relative to the position (negative for upstream,
   positive for downstream)
-- **region**: a string describing the region type (``''`` for standard coding positions,
-  ``'-'`` for 5' UTR, ``'*'`` for 3' UTR, ``'u'`` for upstream and ``'d'`` for downstream)
+- **region**: a string describing the region type (empty for positions within coding DNA sequence,
+  ``-`` for 5' UTR, ``*`` for 3' UTR, ``u`` for upstream and ``d`` for downstream)
 
 Coding Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -225,21 +236,21 @@ position ``c.-1``. We can convert between these two as follows.
 .. code:: python
 
     >>> crossmap.coordinate_to_coding(31)
-    {'position':1, 'offset':0, 'region':'-'}
-    >>> crossmap.coding_to_coordinate({'position':1, 'offset':0, 'region':'-'})
+    {'position': 1, 'offset': 0, 'region': '-'}
+    >>> crossmap.coding_to_coordinate({'position': 1, 'offset': 0, 'region': '-'})
     31
 
 The ``coordinate_to_coding()`` function accepts an optional ``degenerate``
 argument. When set to ``True``, positions outside of the transcript are no
-longer described using the ``'u'`` or ``'d'`` notation, ``'-'`` and ``'*'``
-are used instead.
+longer described using the ``u`` or ``d`` notation, ``-`` and ``*``are used
+instead. Note that the value of `position` is adjusted accordingly.
 
 .. code:: python
 
     >>> crossmap.coordinate_to_coding(4)
-    {'position':1, 'offset':0, 'region':'u'}
+    {'position': 1, 'offset': 0, 'region': 'u'}
     >>> crossmap.coordinate_to_coding(4, True)
-    {'position':12, 'offset':0, 'region':'-'}
+    {'position': 12, 'offset': 0, 'region': '-'}
 
 In the following table, we show a number of annotated examples.
 
@@ -255,27 +266,27 @@ In the following table, we show a number of annotated examples.
    * - 0
      - 5
      - 0
-     - ``'u'``
+     - ``u``
      - ``c.u5``
    * - 4
      - 1
      - 0
-     - ``'u'``
+     - ``u``
      - ``c.u1``
    * - 5
      - 11
      - 0
-     - ``'-'``
+     - ``-``
      - ``c.-11``
    * - 24
      - 3
      - 5
-     - ``'-'``
+     - ``-``
      - ``c.-3+5``
    * - 31
      - 1
      - 0
-     - ``'-'``
+     - ``-``
      - ``c.-1``
    * - 32
      - 1
@@ -295,27 +306,27 @@ In the following table, we show a number of annotated examples.
    * - 43
      - 1
      - 0
-     - ``'*'``
+     - ``*``
      - ``c.*1``
    * - 61
      - 4
      - -9
-     - ``'*'``
+     - ``*``
      - ``c.*4-9``
    * - 71
      - 5
      - 0
-     - ``'*'``
+     - ``*``
      - ``c.*5``
    * - 72
      - 1
      - 0
-     - ``'d'``
+     - ``d``
      - ``c.d1``
    * - 79
      - 8
      - 0
-     - ``'d'``
+     - ``d``
      - ``c.d8``
 
 
@@ -324,24 +335,24 @@ Protein
 
 Additionally, the functions ``coordinate_to_protein()`` and
 ``protein_to_coordinate()`` can be used. These functions use a 4-key dictionary
-to represent a protein position. Here is an example of ``p.1`` in HGVS.
+to represent a protein position. Here is one example of three posibilities
+for ``p.1`` in HGVS.
 
 .. code-block:: python
 
     {
         'position': 1,
         'position_in_codon': 3,
-        'offset': 3,
+        'offset': 0,
         'region': ''
     }
 
 Where:
 
-- **position**: an interger representing the protein position (>0)
+- **position**: an integer representing an amino acid position (>0)
 - **position_in_codon**: an integer indicating the nucleotide index within the codon (1, 2, or 3)
-- **offset**: an integer indicating offset relative to the codon
-- **region**: a string describing the region type (``''`` for standard positions)
-
+- **offset**: an integer indicating offset relative to the nucleotide specified by `position_in_codon` in the codon
+- **region**: a string describing the region type (empty for vaid amino acid positions)
 
 In our example the HGVS position ``g.42`` (coordinate `41`) corresponds with
 position ``p.2``. We can convert between these to as follows.
@@ -349,12 +360,12 @@ position ``p.2``. We can convert between these to as follows.
 .. code:: python
 
     >>> crossmap.coordinate_to_protein(41)
-    {'position':2, 'position_in_codon':2, 'offset':0, 'region':''}
-    >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon':2, 'offset':0, 'region':''})
+    {'position': 2, 'position_in_codon': 2, 'offset': 0, 'region': ''}
+    >>> crossmap.protein_to_coordinate({'position': 2, 'position_in_codon': 2, 'offset': 0, 'region': ''})
     41
 
 **Note:** protein position only corresponds with the HGVS "p." notation
-when the offset equals ``0`` and the region equals ``''``. In the following
+when the offset equals ``0`` and the region equals empty. In the following
 table, we show a number of annotated examples.
 
 .. _table_protein:
@@ -371,26 +382,26 @@ table, we show a number of annotated examples.
      - 2
      - 2
      - 0
-     - ``'u'``
-     - invalid
+     - ``u``
+     -
    * - 4
      - 1
      - 3
      - 0
-     - ``'u'``
-     - invalid
+     - ``u``
+     -
    * - 5
      - 4
      - 2
      - 0
-     - ``'-'``
-     - invalid
+     - ``-``
+     -
    * - 31
      - 1
      - 3
      - 0
-     - ``'-'``
-     - invalid
+     - ``-``
+     -
    * - 32
      - 1
      - 1
@@ -414,7 +425,7 @@ table, we show a number of annotated examples.
      - 3
      - 1
      -
-     - ``p.1``
+     -
    * - 42
      - 2
      - 3
@@ -425,27 +436,27 @@ table, we show a number of annotated examples.
      - 1
      - 1
      - 0
-     - ``'*'``
-     - invalid
+     - ``*``
+     -
    * - 44
      - 1
      - 1
      - 1
-     - ``'*'``
-     - invalid
+     - ``*``
+     -
    * - 72
      - 1
      - 1
      - 0
-     - ``'d'``
-     - invalid
+     - ``d``
+     -
 
    * - 79
      - 2
      - 2
      - 0
-     - ``'d'``
-     - invalid
+     - ``d``
+     -
 
 
 See section :doc:`api/crossmap` for a detailed description.
@@ -506,9 +517,9 @@ This differs from HGVS numbering, which is **1-based**.
 .. code:: python
 
     >>> locus.to_position(9)
-    {'position':0, 'offset':-1}
-    >>> locus.to_coordinate({'position':0, 'offset':-1})
-    {'position':0, 'offset':-1}
+    {'position': 0, 'offset': -1}
+    >>> locus.to_coordinate({'position': 0, 'offset': -1})
+    9
 
 For loci that reside on the reverse complement strand, the optional
 ``inverted`` constructor parameter should be set to ``True``.
@@ -534,12 +545,12 @@ The interface to this class is similar to that of the ``Locus`` class. Functions
 .. code:: python
 
     >>> multilocus.to_position(22)
-    {'position':9, 'offset':3, 'region':''}
-    >>> multilocus.to_coordinate({'position':9, 'offset':3, 'region':''})
+    {'position': 9, 'offset': 3, 'region': ''}
+    >>> multilocus.to_coordinate({'position': 9, 'offset': 3, 'region': ''})
     22
     >>> multilocus.to_position(38)
-    {'position':10, 'offset':-2, 'region':''}
-    >>> multilocus.to_coordinate({'position':10, 'offset':-2, 'region':''}
+    {'position': 10, 'offset': -2, 'region': ''}
+    >>> multilocus.to_coordinate({'position': 10, 'offset': -2, 'region': ''})
     38
 
 See section :doc:`api/multi_locus` for a detailed description.

From 651d1700881835eed4f6b34a5ae4faf32c957165 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 26 Mar 2026 15:56:28 +0100
Subject: [PATCH 106/127] Formatting

---
 README.rst       | 14 +++++++-------
 docs/library.rst |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/README.rst b/README.rst
index fd0308c..ebd1ed6 100644
--- a/README.rst
+++ b/README.rst
@@ -53,8 +53,8 @@ positions and coordinates.
     >>> from mutalyzer_crossmapper import Genomic
     >>> crossmap = Genomic()
     >>> crossmap.coordinate_to_genomic(0)
-    1
-    >>> crossmap.genomic_to_coordinate({'position':1})
+    {'position': 1}
+    >>> crossmap.genomic_to_coordinate({'position': 1})
     0
 
 On top of the functionality provided by the ``Genomic`` class, the
@@ -67,8 +67,8 @@ positions and coordinates.
     >>> exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
     >>> crossmap = NonCoding(exons)
     >>> crossmap.coordinate_to_noncoding(35)
-    {'position':14, 'offset':1, 'region':''}
-    >>> crossmap.noncoding_to_coordinate({'position':14, 'offset':1, 'region':''})
+    {'position': 14, 'offset': 1, 'region': ''}
+    >>> crossmap.noncoding_to_coordinate({'position': 14, 'offset': 1, 'region': ''})
     35
 
 Add the flag ``inverted=True`` to the constructor when the transcript resides
@@ -84,7 +84,7 @@ coordinates as well as conversions between protein positions and coordinates.
     >>> cds = (32, 43)
     >>> crossmap = Coding(exons, cds)
     >>> crossmap.coordinate_to_coding(31)
-    {'position':1, 'offset':0, 'region':'-'}
+    {'position': 1, 'offset': 0, 'region': '-'}
     >>> crossmap.coding_to_coordinate({'position':1, 'offset':0, 'region':'-'})
     31
 
@@ -96,8 +96,8 @@ Conversions between protein positions and coordinates are done as follows.
 .. code:: python
 
     >>> crossmap.coordinate_to_protein(41)
-    {'position':2, 'position_in_codon': 2, 'offset':0, 'region':''}
-    >>> crossmap.protein_to_coordinate({'position':2, 'position_in_codon':2, 'offset':0, 'region':''})
+    {'position': 2, 'position_in_codon': 2, 'offset': 0, 'region': ''}
+    >>> crossmap.protein_to_coordinate({'position': 2, 'position_in_codon': 2, 'offset': 0, 'region': ''})
     41
 
 
diff --git a/docs/library.rst b/docs/library.rst
index 564d9cd..bc982a0 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -8,7 +8,7 @@ The ``Genomic`` class
 ---------------------
 
 The ``Genomic`` class provides an interface to conversions between genomic
-(``g.``, ``m.``, ``n.``) positions and coordinates.
+(``g.``, ``m.``, ``o.``) positions and coordinates.
 
 Genomic Position Model
 ~~~~~~~~~~~~~~~~~~~~~~~

From 21f84582e8ae16f04706a7f22265f4ed0455c63d Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Thu, 26 Mar 2026 16:08:51 +0100
Subject: [PATCH 107/127] Update library.rst

---
 docs/library.rst | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index bc982a0..4264ff9 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -71,8 +71,8 @@ Where:
 - **position**: an integer representing a transcript position (>0)
 - **offset**: an integer indicating the offset relative to the position (negative for upstream,
   positive for downstream)
-- **region**: a string describing the region type (empty for positions within a non-coding transcript, ``u`` for upstream,
-  ``d`` for downstream)
+- **region**: a string describing the region type (empty for positions within a non-coding 
+  transcript, ``u`` for upstream, ``d`` for downstream)
 
 NonCoding Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -112,7 +112,7 @@ present upstream and ``d`` to present downstream.
 
 The ``coordinate_to_noncoding()`` function accepts an optional ``degenerate``
 argument. When set to ``True``, positions outside of the transcript are no
-longer described using the ``u`` or ``d`` notation, ``-`` and ``*``are used
+longer described using the ``u`` or ``d`` notation, ``-`` and ``*`` are used
 instead.
 
 .. code:: python
@@ -242,7 +242,7 @@ position ``c.-1``. We can convert between these two as follows.
 
 The ``coordinate_to_coding()`` function accepts an optional ``degenerate``
 argument. When set to ``True``, positions outside of the transcript are no
-longer described using the ``u`` or ``d`` notation, ``-`` and ``*``are used
+longer described using the ``u`` or ``d`` notation, ``-`` and ``*`` are used
 instead. Note that the value of `position` is adjusted accordingly.
 
 .. code:: python

From 34d084479060863c305b580edf7d7d9f7e764d8d Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Thu, 26 Mar 2026 16:21:40 +0100
Subject: [PATCH 108/127] Fix typo

---
 docs/library.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 4264ff9..ec1bdc2 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -71,7 +71,7 @@ Where:
 - **position**: an integer representing a transcript position (>0)
 - **offset**: an integer indicating the offset relative to the position (negative for upstream,
   positive for downstream)
-- **region**: a string describing the region type (empty for positions within a non-coding 
+- **region**: a string describing the region type (empty for positions within a non-coding
   transcript, ``u`` for upstream, ``d`` for downstream)
 
 NonCoding Position Conversion
@@ -243,7 +243,7 @@ position ``c.-1``. We can convert between these two as follows.
 The ``coordinate_to_coding()`` function accepts an optional ``degenerate``
 argument. When set to ``True``, positions outside of the transcript are no
 longer described using the ``u`` or ``d`` notation, ``-`` and ``*`` are used
-instead. Note that the value of `position` is adjusted accordingly.
+instead. Note that the value of ``position`` is adjusted accordingly.
 
 .. code:: python
 

From 8873a779365da276273a33c7e24e764f467ba166 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Thu, 26 Mar 2026 16:23:16 +0100
Subject: [PATCH 109/127] Update .gitignore

---
 .gitignore | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 324acae..381420f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,4 +7,3 @@ docs/_build/
 mutalyzer_crossmapper.egg-info/
 mutalyzer_crossmapper/__pycache__/
 tests/__pycache__/
-tmp
\ No newline at end of file

From c9e58c67df7c26e82c73c4d9e3fcf329d3d7ff4f Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 27 Mar 2026 09:44:09 +0100
Subject: [PATCH 110/127] Set upstream and downstream in multilocus as 0 based

---
 mutalyzer_crossmapper/crossmapper.py | 24 +++++++++++++-----------
 mutalyzer_crossmapper/multi_locus.py | 10 +++++-----
 tests/test_multi_locus.py            | 20 ++++++++------------
 3 files changed, 26 insertions(+), 28 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 2fbe449..63cee23 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -42,8 +42,8 @@ def coordinate_to_noncoding(self, coordinate: int, degenerate: bool=False) -> di
         """
         pos_m = self._noncoding.to_position(coordinate)
         region = pos_m['region']
+        pos_m['position'] = pos_m['position'] + 1
         if region == '':
-            pos_m['position'] = pos_m['position'] + 1
             return pos_m
 
         if degenerate:
@@ -62,9 +62,8 @@ def noncoding_to_coordinate(self, pos_m: dict) -> int:
         """
         multilocus_pos_m = {**pos_m}
         region = multilocus_pos_m['region']
-        if region == '':
-            multilocus_pos_m['position'] = pos_m['position'] - 1
-        elif region == '-':
+        multilocus_pos_m['position'] = multilocus_pos_m['position'] - 1
+        if region == '-':
             multilocus_pos_m['region'] = 'u'
         elif region == '*':
             multilocus_pos_m['region'] = 'd'
@@ -103,6 +102,7 @@ def _coordinate_to_coding(self, coordinate: int) -> dict:
         noncoding_pos_m = self._noncoding.to_position(coordinate)
 
         if noncoding_pos_m['region'] in ('u', 'd'):
+            noncoding_pos_m['position'] = noncoding_pos_m['position'] + 1
             return noncoding_pos_m
 
         location = noncoding_pos_m['position']
@@ -136,7 +136,7 @@ def coordinate_to_coding(self, coordinate: tuple[int, int], degenerate: bool=Fal
         pos_m = self._coordinate_to_coding(coordinate)
 
         region = pos_m['region']
-        if not degenerate or region =='':
+        if not degenerate or region == '':
             return pos_m
 
         degenerate_pos_m = {'offset': pos_m['offset']}
@@ -164,19 +164,21 @@ def _coding_to_coordinate(self, pos_m: dict) -> int:
         """
         location = pos_m['position']
         region = pos_m['region']
+        multilocus_pos_m = {**pos_m}
 
         if region in ('u', 'd'):
-            return self._noncoding.to_coordinate(pos_m)
+            multilocus_pos_m['position'] = location - 1
+            return self._noncoding.to_coordinate(multilocus_pos_m)
 
-        noncoding_pos_m = {'offset': pos_m['offset'], 'region': ''}
+        multilocus_pos_m['region'] = ''
         if region == '':
-            noncoding_pos_m['position'] = location + self._coding[0] - 1
+            multilocus_pos_m['position'] = location + self._coding[0] - 1
         elif region == '-':
-            noncoding_pos_m['position'] = self._coding[0] - location
+            multilocus_pos_m['position'] = self._coding[0] - location
         else:
-            noncoding_pos_m['position'] = self._coding[1] + location - 1
+            multilocus_pos_m['position'] = self._coding[1] + location - 1
 
-        return self._noncoding.to_coordinate(noncoding_pos_m)
+        return self._noncoding.to_coordinate(multilocus_pos_m)
 
     def coding_to_coordinate(self, pos_m: dict) -> int:
         """Convert a coding position (c./r.) to a coordinate.
diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index a60e6da..6984c97 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -63,7 +63,7 @@ def to_position(self, coordinate: int) -> dict[str: int | str]:
 
         if outside:
             return {
-                'position': abs(locus_pos_m['offset']),
+                'position': abs(locus_pos_m['offset']) - 1,
                 'offset': 0,
                 'region': region
             }
@@ -84,12 +84,12 @@ def to_coordinate(self, pos_m: dict) -> int:
 
         if region == 'u':
             if self._inverted:
-                return self._locations[-1][1] + abs(pos_m['position']) - pos_m['offset'] - 1
-            return self._locations[0][0] - abs(pos_m['position']) + pos_m['offset']
+                return self._locations[-1][1] + abs(pos_m['position']) - pos_m['offset']
+            return self._locations[0][0] - abs(pos_m['position']) + pos_m['offset'] - 1
         elif region == 'd':
             if self._inverted:
-                return self._locations[0][0] - abs(pos_m['position']) - pos_m['offset']
-            return self._locations[-1][1] + abs(pos_m['position']) + pos_m['offset'] - 1
+                return self._locations[0][0] - abs(pos_m['position']) - pos_m['offset'] - 1
+            return self._locations[-1][1] + abs(pos_m['position']) + pos_m['offset']
 
         index = min(
             len(self._offsets),
diff --git a/tests/test_multi_locus.py b/tests/test_multi_locus.py
index 99c7e50..9725ad7 100644
--- a/tests/test_multi_locus.py
+++ b/tests/test_multi_locus.py
@@ -35,7 +35,7 @@ def test_MultiLocus():
         multi_locus.to_position,
         4,
         multi_locus.to_coordinate,
-        {'position': 1, 'offset': 0, 'region': 'u'},
+        {'position': 0, 'offset': 0, 'region': 'u'},
     )
 
     invariant(
@@ -94,7 +94,7 @@ def test_MultiLocus():
         multi_locus.to_position,
         72,
         multi_locus.to_coordinate,
-        {'position': 1, 'offset': 0, 'region': 'd'},
+        {'position': 0, 'offset': 0, 'region': 'd'},
     )
 
 
@@ -107,7 +107,7 @@ def test_MultiLocus_inverted():
         multi_locus.to_position,
         72,
         multi_locus.to_coordinate,
-        {'position': 1, 'offset': 0, 'region': 'u'},
+        {'position': 0, 'offset': 0, 'region': 'u'},
     )
     invariant(
         multi_locus.to_position,
@@ -165,7 +165,7 @@ def test_MultiLocus_inverted():
         multi_locus.to_position,
         4,
         multi_locus.to_coordinate,
-        {'position': 1, 'offset': 0, 'region': 'd'},
+        {'position': 0, 'offset': 0, 'region': 'd'},
     )
 
 
@@ -287,8 +287,7 @@ def test_MultiLocus_degenerate():
         [
             {'position': 0, 'offset': -1, 'region': ''},
             {'position': -1, 'offset': 0, 'region': ''},
-            {'position': 1, 'offset': 0, 'region': 'u'},
-            {'position': -1, 'offset': 0, 'region': 'u'},
+            {'position': 0, 'offset': 0, 'region': 'u'},
         ],
     )
 
@@ -298,8 +297,7 @@ def test_MultiLocus_degenerate():
         [
             {'position': 21, 'offset': 1, 'region': ''},
             {'position': 22, 'offset': 0, 'region': ''},
-            {'position': 0, 'offset': 1, 'region': 'd'},
-            {'position': 1, 'offset': 0, 'region': 'd'},
+            {'position': 0, 'offset': 0, 'region': 'd'},
         ],
     )
 
@@ -312,10 +310,9 @@ def test_MultiLocus_inverted_degenerate():
         multi_locus.to_coordinate,
         72,
         [
-            {'position': 0, 'offset': -1, 'region': 'u'},
             {'position': -1, 'offset': 0, 'region': ''},
             {'position': 0, 'offset': -1, 'region': ''},
-            {'position': 1, 'offset': 0, 'region': 'u'},
+            {'position': 0, 'offset': 0, 'region': 'u'},
         ],
     )
 
@@ -325,7 +322,6 @@ def test_MultiLocus_inverted_degenerate():
         [
             {'position': 21, 'offset': 1, 'region': ''},
             {'position': 22, 'offset': 0, 'region': ''},
-            {'position': 1, 'offset': 0, 'region': 'd'},
-            {'position': 0, 'offset': 1, 'region': 'd'},
+            {'position': 0, 'offset': 0, 'region': 'd'},
         ],
     )

From 783223d90ef46422bc14d4e016ad2e06c2ea53a7 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Fri, 27 Mar 2026 11:09:03 +0100
Subject: [PATCH 111/127] Fix typing mistake

---
 mutalyzer_crossmapper/crossmapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 63cee23..6c5a7be 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -125,7 +125,7 @@ def _coordinate_to_coding(self, coordinate: int) -> dict:
             'region': ''
         }
 
-    def coordinate_to_coding(self, coordinate: tuple[int, int], degenerate: bool=False) -> dict:
+    def coordinate_to_coding(self, coordinate: int, degenerate: bool=False) -> dict:
         """Convert a coordinate to a coding position (c./r.).
 
         :arg int coordinate: Coordinate.

From a7196f4a6fb7bbfff0e412a937b8e1428b19a563 Mon Sep 17 00:00:00 2001
From: "X.Liu" <34545147+XLIU-hub@users.noreply.github.com>
Date: Fri, 27 Mar 2026 17:57:10 +0100
Subject: [PATCH 112/127] Use importlib instead of pkg_resources

---
 mutalyzer_crossmapper/__init__.py | 31 ++++++++-----------------------
 1 file changed, 8 insertions(+), 23 deletions(-)

diff --git a/mutalyzer_crossmapper/__init__.py b/mutalyzer_crossmapper/__init__.py
index 284f6c8..7d1abc0 100644
--- a/mutalyzer_crossmapper/__init__.py
+++ b/mutalyzer_crossmapper/__init__.py
@@ -1,18 +1,4 @@
-"""Crossmapper position conversion library.
-
-Definitions:
-
-- Coordinates are zero based, non-negative integers.
-- Locations are zero based right-open non-negative integer intervals,
-  consistent with Python's range() and sequence slicing functions.
-- Loci and exons are locations.
-- An exon list is a list of locations that, when flattened, is an increasing
-  sequence.
-- A position is a 2-tuple of which the first element is a one based non-zero
-  integer relative to an element in a location and the second element is an
-  integer offset relative to the first element.
-"""
-from pkg_resources import get_distribution
+from importlib.metadata import metadata
 
 from .crossmapper import Coding, Genomic, NonCoding
 from .location import nearest_location
@@ -20,14 +6,13 @@
 from .multi_locus import MultiLocus
 
 
-def _get_metadata(name):
-    pkg = get_distribution('mutalyzer_crossmapper')
-
-    for line in pkg.get_metadata_lines(pkg.PKG_INFO):
-        if line.startswith('{}: '.format(name)):
-            return line.split(': ')[1]
-
-    return ''
+def _get_metadata(name: str) -> str:
+    """Get metadata from the package using importlib.metadata"""
+    try:
+        meta = metadata('mutalyzer_crossmapper')
+        return meta.get(name, '')
+    except Exception:
+        return ''
 
 
 _copyright_notice = 'Copyright (c) {} <{}>'.format(

From 88ce74f5bcc0f66d4f074e84fbe43752d7ddab64 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 30 Mar 2026 11:40:58 +0200
Subject: [PATCH 113/127] Fix typing and single quote

---
 mutalyzer_crossmapper/crossmapper.py | 31 +++++++++++++++-------------
 mutalyzer_crossmapper/locus.py       |  4 ++--
 mutalyzer_crossmapper/multi_locus.py |  4 ++--
 3 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 6c5a7be..ac4ef65 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -24,7 +24,7 @@ def genomic_to_coordinate(self, pos_m: dict) -> int:
 
 class NonCoding(Genomic):
     """NonCoding crossmap object."""
-    def __init__(self, locations: list[tuple[int, int]], inverted: bool = False) -> None:
+    def __init__(self, locations: list[tuple[int, int]], inverted: bool=False) -> None:
         """
         :arg list locations: List of locus locations.
         :arg bool inverted: Orientation.
@@ -48,31 +48,34 @@ def coordinate_to_noncoding(self, coordinate: int, degenerate: bool=False) -> di
 
         if degenerate:
             if region == 'u':
-                pos_m["region"] = '-'
+                pos_m['region'] = '-'
             elif region == 'd':
                 pos_m['region'] = '*'
         return pos_m
 
-    def noncoding_to_coordinate(self, pos_m: dict) -> int:
+    def noncoding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a noncoding position (n./r.) to a coordinate.
 
         :arg dict pos_m: Noncoding position model.
 
         :returns int: Coordinate.
         """
-        multilocus_pos_m = {**pos_m}
-        region = multilocus_pos_m['region']
-        multilocus_pos_m['position'] = multilocus_pos_m['position'] - 1
-        if region == '-':
+        multilocus_pos_m = {**pos_m, 'position': pos_m['position'] - 1}
+        if multilocus_pos_m['region'] == '-':
             multilocus_pos_m['region'] = 'u'
-        elif region == '*':
+        elif multilocus_pos_m['region'] == '*':
             multilocus_pos_m['region'] = 'd'
         return self._noncoding.to_coordinate(multilocus_pos_m)
 
 
 class Coding(NonCoding):
     """Coding crossmap object."""
-    def __init__(self, locations: list[tuple[int,int]], cds: tuple[int,int], inverted : bool=False) -> None:
+    def __init__(
+            self,
+            locations: list[tuple[int,int]],
+            cds: tuple[int,int],
+            inverted : bool=False
+    ) -> None:
         """
         :arg list locations: List of locus locations.
         :arg tuple cds: Locus location.
@@ -92,7 +95,7 @@ def __init__(self, locations: list[tuple[int,int]], cds: tuple[int,int], inverte
             self._coding = (b0['position'] + b0['offset'], b1['position'] + b1['offset'] + 1)
             self._exons = (e0['position'], e1['position'])
 
-    def _coordinate_to_coding(self, coordinate: int) -> dict:
+    def _coordinate_to_coding(self, coordinate: int) -> dict[str, int | str]:
         """Convert a coordinate to a coding position (c./r.).
 
         :arg int coordinate: Coordinate.
@@ -155,7 +158,7 @@ def coordinate_to_coding(self, coordinate: int, degenerate: bool=False) -> dict:
             degenerate_pos_m['region'] = '*'
         return degenerate_pos_m
 
-    def _coding_to_coordinate(self, pos_m: dict) -> int:
+    def _coding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a coding position (c./r.) to a coordinate.
 
         :arg dict pos_m: Coding position model (c./r.).
@@ -180,7 +183,7 @@ def _coding_to_coordinate(self, pos_m: dict) -> int:
 
         return self._noncoding.to_coordinate(multilocus_pos_m)
 
-    def coding_to_coordinate(self, pos_m: dict) -> int:
+    def coding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a coding position (c./r.) to a coordinate.
 
         :arg dict pos_m: Coding position model (c./r.).
@@ -190,7 +193,7 @@ def coding_to_coordinate(self, pos_m: dict) -> int:
 
         return self._coding_to_coordinate(pos_m)
 
-    def coordinate_to_protein(self, coordinate: int) -> dict:
+    def coordinate_to_protein(self, coordinate: int) -> dict[str, int | str]:
         """Convert a coordinate to a protein position (p.).
 
         :arg int coordinate: Coordinate.
@@ -210,7 +213,7 @@ def coordinate_to_protein(self, coordinate: int) -> dict:
                 'position_in_codon': (location + 2) % 3 + 1,
                 **{k: v for k, v in pos.items() if k != 'position'}}
 
-    def protein_to_coordinate(self, pos_m: dict) -> int:
+    def protein_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a protein position (p.) to a coordinate.
 
         :arg dict position: Protein position model(p.).
diff --git a/mutalyzer_crossmapper/locus.py b/mutalyzer_crossmapper/locus.py
index fff0c66..d62144d 100644
--- a/mutalyzer_crossmapper/locus.py
+++ b/mutalyzer_crossmapper/locus.py
@@ -1,6 +1,6 @@
 class Locus(object):
     """Locus object."""
-    def __init__(self, location: list[tuple[int, int]], inverted=False) -> None:
+    def __init__(self, location: tuple[int, int], inverted: bool=False) -> None:
         """
         :arg tuple location: Locus location.
         :arg bool inverted: Orientation.
@@ -30,7 +30,7 @@ def to_position(self, coordinate: int) -> dict[str, int]:
             return {'position': self._end, 'offset': coordinate - self.boundary[1]}
         return {'position': coordinate - self.boundary[0], 'offset': 0}
 
-    def to_coordinate(self, pos_m: dict) -> int:
+    def to_coordinate(self, pos_m: dict[str, int]) -> int:
         """Convert a position model to a coordinate.
 
         :arg dict position: Position model with 'position' and 'offset' keys.
diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 6984c97..5f1cee0 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -49,7 +49,7 @@ def outside(self, coordinate: int) -> int:
             return coordinate - self._loci[-1].boundary[1]
         return 0
 
-    def to_position(self, coordinate: int) -> dict[str: int | str]:
+    def to_position(self, coordinate: int) -> dict[str, int | str]:
         """Convert a coordinate to a position.
 
         :arg int coordinate: Coordinate.
@@ -73,7 +73,7 @@ def to_position(self, coordinate: int) -> dict[str: int | str]:
             'region': region
         }
 
-    def to_coordinate(self, pos_m: dict) -> int:
+    def to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a position model to a coordinate.
 
         :arg dict pos_m: Position model with 'position','offset' and 'region' keys.

From 6d5e2827e0d4da6b127892c2ab2c272f6da7bb6a Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 30 Mar 2026 11:55:45 +0200
Subject: [PATCH 114/127] Fix doc string

---
 docs/library.rst                     | 2 +-
 mutalyzer_crossmapper/crossmapper.py | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index ec1bdc2..6b358f9 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -530,7 +530,7 @@ The ``MultiLocus`` class
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 The ``MultiLocus`` class is used to deal with offsets with respect to multiple
-loci. Its positions is
+loci.
 
 .. code:: python
 
diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index ac4ef65..dd0a774 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -3,7 +3,7 @@
 
 class Genomic(object):
     """Genomic crossmap object."""
-    def coordinate_to_genomic(self, coordinate: int) -> dict:
+    def coordinate_to_genomic(self, coordinate: int) -> dict[str, int]:
         """Convert a coordinate to a genomic position (g./m./o.).
 
         :arg int coordinate: Coordinate.
@@ -12,7 +12,7 @@ def coordinate_to_genomic(self, coordinate: int) -> dict:
         """
         return {'position': coordinate + 1}
 
-    def genomic_to_coordinate(self, pos_m: dict) -> int:
+    def genomic_to_coordinate(self, pos_m: dict[str, int]) -> int:
         """Convert a genomic position (g./m./o.) to a coordinate.
 
         :arg dict pos_m: Genomic position model.
@@ -216,7 +216,7 @@ def coordinate_to_protein(self, coordinate: int) -> dict[str, int | str]:
     def protein_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a protein position (p.) to a coordinate.
 
-        :arg dict position: Protein position model(p.).
+        :arg dict pos_m: Protein position model(p.).
 
         :returns int: Coordinate.
         """

From 8fba978d4755cdcfabf6f6f174b453eb5f104d08 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 30 Mar 2026 12:10:20 +0200
Subject: [PATCH 115/127] Update python version in setup

---
 setup.cfg | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.cfg b/setup.cfg
index ca7be54..c58c160 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -17,6 +17,7 @@ classifiers =
 
 [options]
 packages = find:
+python_requires = >=3.10
 
 [options.extras_require]
 tests =

From 2867ea8d5febc79bd86d57f1c8ca18b158a2a345 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 30 Mar 2026 14:28:54 +0200
Subject: [PATCH 116/127] Rename multilocus positon model

---
 mutalyzer_crossmapper/crossmapper.py | 45 ++++++++++++++--------------
 1 file changed, 23 insertions(+), 22 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index dd0a774..8ece035 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -40,18 +40,18 @@ def coordinate_to_noncoding(self, coordinate: int, degenerate: bool=False) -> di
 
         :returns dict: Noncoding position model.
         """
-        pos_m = self._noncoding.to_position(coordinate)
-        region = pos_m['region']
-        pos_m['position'] = pos_m['position'] + 1
+        multilocus_pos_m = self._noncoding.to_position(coordinate)
+        noncoding_pos_m = {**multilocus_pos_m, 'position': multilocus_pos_m['position'] + 1}
+        region = noncoding_pos_m['region']
         if region == '':
-            return pos_m
+            return noncoding_pos_m
 
         if degenerate:
             if region == 'u':
-                pos_m['region'] = '-'
+                noncoding_pos_m['region'] = '-'
             elif region == 'd':
-                pos_m['region'] = '*'
-        return pos_m
+                noncoding_pos_m['region'] = '*'
+        return noncoding_pos_m
 
     def noncoding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a noncoding position (n./r.) to a coordinate.
@@ -84,16 +84,16 @@ def __init__(
         NonCoding.__init__(self, locations, inverted)
 
         b0 = self._noncoding.to_position(cds[0])
-        b1 = self._noncoding.to_position(cds[1]-1)
+        b1 = self._noncoding.to_position(cds[1] - 1)
         e0 = self._noncoding.to_position(locations[0][0])
-        e1 = self._noncoding.to_position(locations[-1][1]-1)
+        e1 = self._noncoding.to_position(locations[-1][1] - 1)
 
         if self._inverted:
             self._coding = (b1['position'] + b1['offset'], b0['position'] + b0['offset'] + 1)
-            self._exons = (e1['position'], e0['position'])
+            self._exons = (e1['position'], e0['position'] + 1)
         else:
             self._coding = (b0['position'] + b0['offset'], b1['position'] + b1['offset'] + 1)
-            self._exons = (e0['position'], e1['position'])
+            self._exons = (e0['position'], e1['position'] + 1)
 
     def _coordinate_to_coding(self, coordinate: int) -> dict[str, int | str]:
         """Convert a coordinate to a coding position (c./r.).
@@ -102,14 +102,13 @@ def _coordinate_to_coding(self, coordinate: int) -> dict[str, int | str]:
 
         :returns dict: Coding position model (c./r.).
         """
-        noncoding_pos_m = self._noncoding.to_position(coordinate)
+        multilocus_pos_m = self._noncoding.to_position(coordinate)
 
-        if noncoding_pos_m['region'] in ('u', 'd'):
-            noncoding_pos_m['position'] = noncoding_pos_m['position'] + 1
-            return noncoding_pos_m
+        if multilocus_pos_m['region'] in ('u', 'd'):
+            return {**multilocus_pos_m, 'position': multilocus_pos_m['position'] + 1}
 
-        location = noncoding_pos_m['position']
-        offset = noncoding_pos_m['offset']
+        location = multilocus_pos_m['position']
+        offset = multilocus_pos_m['offset']
         if location < self._coding[0]:
             return {
                 'position': self._coding[0] - location,
@@ -142,11 +141,11 @@ def coordinate_to_coding(self, coordinate: int, degenerate: bool=False) -> dict:
         if not degenerate or region == '':
             return pos_m
 
-        degenerate_pos_m = {'offset': pos_m['offset']}
+        degenerate_pos_m = {**pos_m, 'offset': pos_m['offset']}
         location = pos_m['position']
         if region == 'u':
             if self._inverted:
-                degenerate_pos_m['position'] = location + self._exons[1] - self._coding[1] + 1
+                degenerate_pos_m['position'] = location + self._exons[1] - self._coding[1]
             else:
                 degenerate_pos_m['position'] = location + self._coding[0]
             degenerate_pos_m['region'] = '-'
@@ -154,7 +153,7 @@ def coordinate_to_coding(self, coordinate: int, degenerate: bool=False) -> dict:
             if self._inverted:
                 degenerate_pos_m['position'] = location + self._coding[0]
             else:
-                degenerate_pos_m['position'] = location + self._exons[1]- self._coding[1] + 1
+                degenerate_pos_m['position'] = location + self._exons[1] - self._coding[1]
             degenerate_pos_m['region'] = '*'
         return degenerate_pos_m
 
@@ -207,11 +206,13 @@ def coordinate_to_protein(self, coordinate: int) -> dict[str, int | str]:
             return {
                 'position': abs(-location // 3),
                 'position_in_codon': -location % 3 + 1,
-                **{k: v for k, v in pos.items() if k != 'position'}}
+                'region': pos['region'],
+                'offset': pos['offset']}
         return {
                 'position': (location + 2) // 3,
                 'position_in_codon': (location + 2) % 3 + 1,
-                **{k: v for k, v in pos.items() if k != 'position'}}
+                'region': pos['region'],
+                'offset': pos['offset']}
 
     def protein_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a protein position (p.) to a coordinate.

From 12229cd508988f85a3cca102005778cb5e76886f Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 30 Mar 2026 14:30:12 +0200
Subject: [PATCH 117/127] Remove unneccessary elif

---
 mutalyzer_crossmapper/multi_locus.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 5f1cee0..627a31b 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -86,7 +86,7 @@ def to_coordinate(self, pos_m: dict[str, int | str]) -> int:
             if self._inverted:
                 return self._locations[-1][1] + abs(pos_m['position']) - pos_m['offset']
             return self._locations[0][0] - abs(pos_m['position']) + pos_m['offset'] - 1
-        elif region == 'd':
+        if region == 'd':
             if self._inverted:
                 return self._locations[0][0] - abs(pos_m['position']) - pos_m['offset'] - 1
             return self._locations[-1][1] + abs(pos_m['position']) + pos_m['offset']

From c6455e907f25ffe9c0aa74906af80912bb733558 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 30 Mar 2026 15:04:05 +0200
Subject: [PATCH 118/127] Fix flake8 whitespace issues

---
 mutalyzer_crossmapper/crossmapper.py | 12 ++++++------
 mutalyzer_crossmapper/location.py    |  2 +-
 mutalyzer_crossmapper/locus.py       |  2 +-
 mutalyzer_crossmapper/multi_locus.py |  2 +-
 tests/test_crossmapper.py            |  9 +++++++++
 5 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 8ece035..7a38392 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -24,7 +24,7 @@ def genomic_to_coordinate(self, pos_m: dict[str, int]) -> int:
 
 class NonCoding(Genomic):
     """NonCoding crossmap object."""
-    def __init__(self, locations: list[tuple[int, int]], inverted: bool=False) -> None:
+    def __init__(self, locations: list[tuple[int, int]], inverted: bool = False) -> None:
         """
         :arg list locations: List of locus locations.
         :arg bool inverted: Orientation.
@@ -33,7 +33,7 @@ def __init__(self, locations: list[tuple[int, int]], inverted: bool=False) -> No
 
         self._noncoding = MultiLocus(locations, inverted)
 
-    def coordinate_to_noncoding(self, coordinate: int, degenerate: bool=False) -> dict:
+    def coordinate_to_noncoding(self, coordinate: int, degenerate: bool = False) -> dict:
         """Convert a coordinate to a noncoding position (n./r.).
 
         :arg int coordinate: Coordinate.
@@ -72,9 +72,9 @@ class Coding(NonCoding):
     """Coding crossmap object."""
     def __init__(
             self,
-            locations: list[tuple[int,int]],
-            cds: tuple[int,int],
-            inverted : bool=False
+            locations: list[tuple[int, int]],
+            cds: tuple[int, int],
+            inverted: bool = False
     ) -> None:
         """
         :arg list locations: List of locus locations.
@@ -127,7 +127,7 @@ def _coordinate_to_coding(self, coordinate: int) -> dict[str, int | str]:
             'region': ''
         }
 
-    def coordinate_to_coding(self, coordinate: int, degenerate: bool=False) -> dict:
+    def coordinate_to_coding(self, coordinate: int, degenerate: bool = False) -> dict:
         """Convert a coordinate to a coding position (c./r.).
 
         :arg int coordinate: Coordinate.
diff --git a/mutalyzer_crossmapper/location.py b/mutalyzer_crossmapper/location.py
index 1bf7a06..9b534e4 100644
--- a/mutalyzer_crossmapper/location.py
+++ b/mutalyzer_crossmapper/location.py
@@ -19,7 +19,7 @@ def _nearest_boundary(lb: int, rb: int, c: int, p: int) -> int:
     return p
 
 
-def nearest_location(ls: list[tuple[int,int]], c: int, p: int = 0) -> int:
+def nearest_location(ls: list[tuple[int, int]], c: int, p: int = 0) -> int:
     """Find the location nearest to `c`. In case of a draw, the parameter `p`
     decides which index is chosen.
 
diff --git a/mutalyzer_crossmapper/locus.py b/mutalyzer_crossmapper/locus.py
index d62144d..7fbb7b3 100644
--- a/mutalyzer_crossmapper/locus.py
+++ b/mutalyzer_crossmapper/locus.py
@@ -1,6 +1,6 @@
 class Locus(object):
     """Locus object."""
-    def __init__(self, location: tuple[int, int], inverted: bool=False) -> None:
+    def __init__(self, location: tuple[int, int], inverted: bool = False) -> None:
         """
         :arg tuple location: Locus location.
         :arg bool inverted: Orientation.
diff --git a/mutalyzer_crossmapper/multi_locus.py b/mutalyzer_crossmapper/multi_locus.py
index 627a31b..d2c5662 100644
--- a/mutalyzer_crossmapper/multi_locus.py
+++ b/mutalyzer_crossmapper/multi_locus.py
@@ -19,7 +19,7 @@ def _offsets(locations: list[tuple[int, int]], orientation: int) -> list[int]:
 
 class MultiLocus(object):
     """MultiLocus object."""
-    def __init__(self, locations: list[tuple[int, int]], inverted: bool=False) -> None:
+    def __init__(self, locations: list[tuple[int, int]], inverted: bool = False) -> None:
         """
         :arg list locations: List of locus locations.
         :arg bool inverted: Orientation.
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 33aec12..f69ee05 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -112,6 +112,15 @@ def test_NonCoding_degenerate():
         ],
     )
 
+    # # Boundary between exon and intron
+    # degenerate_equal(
+    #     crossmap.noncoding_to_coordinate,
+    #     29,
+    #     [
+
+    #     ]
+    # )
+
     # Boundary between downstream and transcript.
     degenerate_equal(
         crossmap.noncoding_to_coordinate,

From 12e8e1f67c47d9f87c9f3c8b0ab17c7208a457c9 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 30 Mar 2026 15:40:33 +0200
Subject: [PATCH 119/127] Fix whitespaces

---
 tests/test_crossmapper.py | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index f69ee05..0ed4c47 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -112,15 +112,6 @@ def test_NonCoding_degenerate():
         ],
     )
 
-    # # Boundary between exon and intron
-    # degenerate_equal(
-    #     crossmap.noncoding_to_coordinate,
-    #     29,
-    #     [
-
-    #     ]
-    # )
-
     # Boundary between downstream and transcript.
     degenerate_equal(
         crossmap.noncoding_to_coordinate,
@@ -375,7 +366,7 @@ def test_Coding_no_utr5_inverted():
         crossmap.coordinate_to_coding,
         19,
         crossmap.coding_to_coordinate,
-        {'position': 1 , 'offset': 0, 'region': ''},
+        {'position': 1, 'offset': 0, 'region': ''},
     )
 
 
@@ -521,6 +512,7 @@ def test_Coding_degenerate():
     """Degenerate upstream and downstream positions are silently corrected."""
     crossmap = Coding([(10, 20)], (11, 19))
 
+    # Degenerate position in upstream.
     degenerate_equal(
         crossmap.coding_to_coordinate,
         9,

From e2f2a43184023a36b38f6758bb1837fdb36b970a Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Mon, 30 Mar 2026 16:18:24 +0200
Subject: [PATCH 120/127] Add tests for protein positions from the reverse
 strand

---
 tests/test_crossmapper.py | 97 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 97 insertions(+)

diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 0ed4c47..87b5ea7 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -351,6 +351,28 @@ def test_Coding_no_utr5():
     )
 
 
+def test_Coding_no_intron():
+    crossmap = Coding([(10, 20), (20, 30)], (15, 25))
+
+    invariant(
+        crossmap.coordinate_to_coding,
+        20,
+        crossmap.coding_to_coordinate,
+        {'position': 6, 'offset': 0, 'region': ''},
+    )
+
+
+def test_Coding_no_intron_inverted():
+    crossmap = Coding([(10, 20), (20, 30)], (15, 25), True)
+
+    invariant(
+        crossmap.coordinate_to_coding,
+        20,
+        crossmap.coding_to_coordinate,
+        {'position': 5, 'offset': 0, 'region': ''},
+    )
+
+
 def test_Coding_no_utr5_inverted():
     """A 5' UTR may be missing."""
     crossmap = Coding([(10, 20)], (15, 20), True)
@@ -788,3 +810,78 @@ def test_Coding_protein():
         crossmap.protein_to_coordinate,
         {'position': 1, 'position_in_codon': 1, 'offset': 0, 'region': 'd'}
     )
+
+
+def test_Coding_inverted_protein():
+    """Protein positions."""
+    crossmap = Coding(_exons, _cds, True)
+
+    # Boundary between upstream and 5' UTR
+    invariant(
+        crossmap.coordinate_to_protein,
+        4,
+        crossmap.protein_to_coordinate,
+        {'position': 1, 'position_in_codon': 1, 'offset': 0, 'region': 'd'}
+    )
+    invariant(
+        crossmap.coordinate_to_protein,
+        5,
+        crossmap.protein_to_coordinate,
+        {'position': 4, 'position_in_codon': 2, 'offset': 0, 'region': '*'}
+    )
+
+    # Boundary between 5' UTR and CDS
+    invariant(
+        crossmap.coordinate_to_protein,
+        31,
+        crossmap.protein_to_coordinate,
+        {'position': 1, 'position_in_codon': 1, 'offset': 0, 'region': '*'},
+    )
+    invariant(
+        crossmap.coordinate_to_protein,
+        32,
+        crossmap.protein_to_coordinate,
+        {'position': 2, 'position_in_codon': 3, 'offset': 0, 'region': ''},
+    )
+
+    # Intron boundary.
+    invariant(
+        crossmap.coordinate_to_protein,
+        34,
+        crossmap.protein_to_coordinate,
+        {'position': 2, 'position_in_codon': 1, 'offset': 0, 'region': ''},
+    )
+    invariant(
+        crossmap.coordinate_to_protein,
+        35,
+        crossmap.protein_to_coordinate,
+        {'position': 2, 'position_in_codon': 1, 'offset': -1, 'region': ''},
+    )
+
+    # Boundary between CDS and 3' UTR.
+    invariant(
+        crossmap.coordinate_to_protein,
+        42,
+        crossmap.protein_to_coordinate,
+        {'position': 1, 'position_in_codon': 1, 'offset': 0, 'region': ''},
+    )
+    invariant(
+        crossmap.coordinate_to_protein,
+        43,
+        crossmap.protein_to_coordinate,
+        {'position': 1, 'position_in_codon': 3, 'offset': 0, 'region': '-'},
+    )
+
+    # Boundary between 3' UTR and downstream
+    invariant(
+        crossmap.coordinate_to_protein,
+        71,
+        crossmap.protein_to_coordinate,
+        {'position': 2, 'position_in_codon': 2, 'offset': 0, 'region': '-'}
+    )
+    invariant(
+        crossmap.coordinate_to_protein,
+        72,
+        crossmap.protein_to_coordinate,
+        {'position': 1, 'position_in_codon': 3, 'offset': 0, 'region': 'u'}
+    )

From 50d50b57798c90396f5792c5ccf5692914d3551d Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 31 Mar 2026 13:37:16 +0200
Subject: [PATCH 121/127] Rename external (input/output) variable to pos_m and
 add test for a one base intron in coding

---
 mutalyzer_crossmapper/crossmapper.py | 66 ++++++++++++++++------------
 tests/test_crossmapper.py            | 22 ++++++++++
 2 files changed, 59 insertions(+), 29 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 7a38392..d10ec14 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -33,7 +33,11 @@ def __init__(self, locations: list[tuple[int, int]], inverted: bool = False) ->
 
         self._noncoding = MultiLocus(locations, inverted)
 
-    def coordinate_to_noncoding(self, coordinate: int, degenerate: bool = False) -> dict:
+    def coordinate_to_noncoding(
+                self,
+                coordinate: int,
+                degenerate: bool = False
+            ) -> dict[str, int | str]:
         """Convert a coordinate to a noncoding position (n./r.).
 
         :arg int coordinate: Coordinate.
@@ -41,17 +45,14 @@ def coordinate_to_noncoding(self, coordinate: int, degenerate: bool = False) ->
         :returns dict: Noncoding position model.
         """
         multilocus_pos_m = self._noncoding.to_position(coordinate)
-        noncoding_pos_m = {**multilocus_pos_m, 'position': multilocus_pos_m['position'] + 1}
-        region = noncoding_pos_m['region']
-        if region == '':
-            return noncoding_pos_m
-
+        pos_m = {**multilocus_pos_m, 'position': multilocus_pos_m['position'] + 1}
+        region = pos_m['region']
         if degenerate:
             if region == 'u':
-                noncoding_pos_m['region'] = '-'
+                pos_m['region'] = '-'
             elif region == 'd':
-                noncoding_pos_m['region'] = '*'
-        return noncoding_pos_m
+                pos_m['region'] = '*'
+        return pos_m
 
     def noncoding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a noncoding position (n./r.) to a coordinate.
@@ -61,9 +62,9 @@ def noncoding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         :returns int: Coordinate.
         """
         multilocus_pos_m = {**pos_m, 'position': pos_m['position'] - 1}
-        if multilocus_pos_m['region'] == '-':
+        if pos_m['region'] == '-':
             multilocus_pos_m['region'] = 'u'
-        elif multilocus_pos_m['region'] == '*':
+        elif pos_m['region'] == '*':
             multilocus_pos_m['region'] = 'd'
         return self._noncoding.to_coordinate(multilocus_pos_m)
 
@@ -83,17 +84,25 @@ def __init__(
         """
         NonCoding.__init__(self, locations, inverted)
 
-        b0 = self._noncoding.to_position(cds[0])
-        b1 = self._noncoding.to_position(cds[1] - 1)
-        e0 = self._noncoding.to_position(locations[0][0])
-        e1 = self._noncoding.to_position(locations[-1][1] - 1)
+        cds_start = self._noncoding.to_position(cds[0])
+        cds_end = self._noncoding.to_position(cds[1] - 1)
+        exons_start = self._noncoding.to_position(locations[0][0])
+        exons_end = self._noncoding.to_position(locations[-1][1] - 1)
 
         if self._inverted:
-            self._coding = (b1['position'] + b1['offset'], b0['position'] + b0['offset'] + 1)
-            self._exons = (e1['position'], e0['position'] + 1)
+            self._coding = (
+                cds_end['position'] + cds_end['offset'],
+                cds_start['position'] + cds_start['offset'] + 1
+            )
+            # Used in degenerate option
+            self._exons_len = exons_start['position'] + 1
         else:
-            self._coding = (b0['position'] + b0['offset'], b1['position'] + b1['offset'] + 1)
-            self._exons = (e0['position'], e1['position'] + 1)
+            self._coding = (
+                cds_start['position'] + cds_start['offset'],
+                cds_end['position'] + cds_end['offset'] + 1
+            )
+            # Used in degenerate option
+            self._exons_len = exons_end['position'] + 1
 
     def _coordinate_to_coding(self, coordinate: int) -> dict[str, int | str]:
         """Convert a coordinate to a coding position (c./r.).
@@ -145,7 +154,7 @@ def coordinate_to_coding(self, coordinate: int, degenerate: bool = False) -> dic
         location = pos_m['position']
         if region == 'u':
             if self._inverted:
-                degenerate_pos_m['position'] = location + self._exons[1] - self._coding[1]
+                degenerate_pos_m['position'] = location + self._exons_len - self._coding[1]
             else:
                 degenerate_pos_m['position'] = location + self._coding[0]
             degenerate_pos_m['region'] = '-'
@@ -153,7 +162,7 @@ def coordinate_to_coding(self, coordinate: int, degenerate: bool = False) -> dic
             if self._inverted:
                 degenerate_pos_m['position'] = location + self._coding[0]
             else:
-                degenerate_pos_m['position'] = location + self._exons[1] - self._coding[1]
+                degenerate_pos_m['position'] = location + self._exons_len - self._coding[1]
             degenerate_pos_m['region'] = '*'
         return degenerate_pos_m
 
@@ -179,7 +188,6 @@ def _coding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
             multilocus_pos_m['position'] = self._coding[0] - location
         else:
             multilocus_pos_m['position'] = self._coding[1] + location - 1
-
         return self._noncoding.to_coordinate(multilocus_pos_m)
 
     def coding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
@@ -199,20 +207,20 @@ def coordinate_to_protein(self, coordinate: int) -> dict[str, int | str]:
 
         :returns dict: Protein position model(p.).
         """
-        pos = self.coordinate_to_coding(coordinate)
+        pos_m = self.coordinate_to_coding(coordinate)
 
-        location = pos['position']
-        if pos['region'] in ('-', 'u'):
+        location = pos_m['position']
+        if pos_m['region'] in ('-', 'u'):
             return {
                 'position': abs(-location // 3),
                 'position_in_codon': -location % 3 + 1,
-                'region': pos['region'],
-                'offset': pos['offset']}
+                'region': pos_m['region'],
+                'offset': pos_m['offset']}
         return {
                 'position': (location + 2) // 3,
                 'position_in_codon': (location + 2) % 3 + 1,
-                'region': pos['region'],
-                'offset': pos['offset']}
+                'region': pos_m['region'],
+                'offset': pos_m['offset']}
 
     def protein_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a protein position (p.) to a coordinate.
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 87b5ea7..098508b 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -373,6 +373,28 @@ def test_Coding_no_intron_inverted():
     )
 
 
+def test_Coding_one_base_intron():
+    crossmap = Coding([(10, 19), (20, 30)], (15, 25))
+
+    invariant(
+        crossmap.coordinate_to_coding,
+        19,
+        crossmap.coding_to_coordinate,
+        {'position': 4, 'offset': 1, 'region': ''},
+    )
+
+
+def test_Coding_one_base_intron_inverted():
+    crossmap = Coding([(10, 19), (20, 30)], (15, 25), True)
+
+    invariant(
+        crossmap.coordinate_to_coding,
+        19,
+        crossmap.coding_to_coordinate,
+        {'position': 5, 'offset': 1, 'region': ''},
+    )
+
+
 def test_Coding_no_utr5_inverted():
     """A 5' UTR may be missing."""
     crossmap = Coding([(10, 20)], (15, 20), True)

From 73e2965be5899da0e1f02d0e18df49e42e9645cc Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Tue, 31 Mar 2026 14:29:57 +0200
Subject: [PATCH 122/127] Fix typo and font

---
 docs/library.rst | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 6b358f9..7720088 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -22,7 +22,7 @@ They are represented as 1-key dictionaries. Below is an example of ``g.1`` in HG
 
 Where:
 
-- **position**: an integer representing a nucleotide position (>0)
+- **position**: an integer representing a nucleotide position (> 0)
 
 Genomic Position Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -68,7 +68,7 @@ as 3-key dictionaries. Below is an example of ``n.14+1`` in HGVS.
 
 Where:
 
-- **position**: an integer representing a transcript position (>0)
+- **position**: an integer representing a nucleotide position (> 0)
 - **offset**: an integer indicating the offset relative to the position (negative for upstream,
   positive for downstream)
 - **region**: a string describing the region type (empty for positions within a non-coding
@@ -86,7 +86,7 @@ NonCoding Position Conversion
 Now the functions ``coordinate_to_noncoding()`` and ``noncoding_to_coordinate()``
 can be used.
 
-In our example, the HGVS position ``g.36`` (coordinate `35`) is equivalent to
+In our example, the HGVS position ``g.36`` (coordinate *35*) is equivalent to
 position ``n.14+1``. We can convert between these two as follows.
 
 .. code:: python
@@ -96,8 +96,8 @@ position ``n.14+1``. We can convert between these two as follows.
     >>> crossmap.noncoding_to_coordinate({'position': 14, 'offset': 1, 'region': ''})
     35
 
-When the coordinate is upstream or downstream of the transcript,  we use ``u`` to
-present upstream and ``d`` to present downstream.
+When the coordinate is upstream or downstream of the transcript, we use ``u`` to
+denote upstream and ``d`` to denote downstream.
 
 .. code:: python
 
@@ -124,7 +124,7 @@ instead.
 
 For transcripts that reside on the reverse complement strand, the ``inverted``
 parameter should be set to ``True``. In our example, HGVS position ``g.36``
-(coordinate `35`) is now equivalent to position ``n.9-1``.
+(coordinate *35*) is now equivalent to position ``n.9-1``.
 
 .. code:: python
 
@@ -210,7 +210,7 @@ represented as 3-key dictionaries. Here is an example of ``c.*1+3``.
 
 Where:
 
-- **position**: an integer representing a transcript position (>0)
+- **position**: an integer representing a transcript position (> 0)
 - **offset**: an integer indicating the offset relative to the position (negative for upstream,
   positive for downstream)
 - **region**: a string describing the region type (empty for positions within coding DNA sequence,
@@ -230,7 +230,7 @@ On top of the functionality provided by the ``NonCoding`` class, the functions
 ``coordinate_to_coding()`` and ``coding_to_coordinate()`` can be used. These
 functions use a 3-key dictionary to represent a coding position.
 
-In our example, the HGVS position ``g.32`` (coordinate `31`) is equivalent to
+In our example, the HGVS position ``g.32`` (coordinate *31*) is equivalent to
 position ``c.-1``. We can convert between these two as follows.
 
 .. code:: python
@@ -335,7 +335,7 @@ Protein
 
 Additionally, the functions ``coordinate_to_protein()`` and
 ``protein_to_coordinate()`` can be used. These functions use a 4-key dictionary
-to represent a protein position. Here is one example of three posibilities
+to represent a protein position. Here is one example of three possibilities
 for ``p.1`` in HGVS.
 
 .. code-block:: python
@@ -349,13 +349,13 @@ for ``p.1`` in HGVS.
 
 Where:
 
-- **position**: an integer representing an amino acid position (>0)
-- **position_in_codon**: an integer indicating the nucleotide index within the codon (1, 2, or 3)
+- **position**: an integer representing an amino acid position (> 0)
+- **position_in_codon**: an integer indexing the position in a codon (1, 2, or 3)
 - **offset**: an integer indicating offset relative to the nucleotide specified by `position_in_codon` in the codon
-- **region**: a string describing the region type (empty for vaid amino acid positions)
+- **region**: a string describing the region type (empty for valid amino acid positions)
 
-In our example the HGVS position ``g.42`` (coordinate `41`) corresponds with
-position ``p.2``. We can convert between these to as follows.
+In our example, the HGVS position ``g.42`` (coordinate *41*) corresponds with
+position ``p.2``. We can convert between these two as follows.
 
 .. code:: python
 

From 3ec8ab476a021a2a8369067c4b8791b5ba628f00 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 1 Apr 2026 11:37:08 +0200
Subject: [PATCH 123/127] Update degenerate for noncoding and tests

---
 mutalyzer_crossmapper/crossmapper.py | 16 ++++++++++++++--
 tests/test_crossmapper.py            | 21 ++++++++++-----------
 2 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index d10ec14..2e948bd 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -32,6 +32,10 @@ def __init__(self, locations: list[tuple[int, int]], inverted: bool = False) ->
         self._inverted = inverted
 
         self._noncoding = MultiLocus(locations, inverted)
+        if self._inverted:
+            self._exons_len = self._noncoding.to_position(locations[0][0])['position'] + 1
+        else:
+            self._exons_len = self._noncoding.to_position(locations[-1][1] - 1)['position'] + 1
 
     def coordinate_to_noncoding(
                 self,
@@ -50,8 +54,12 @@ def coordinate_to_noncoding(
         if degenerate:
             if region == 'u':
                 pos_m['region'] = '-'
+                pos_m['offset'] = -pos_m['position']
+                pos_m['position'] = 1
             elif region == 'd':
                 pos_m['region'] = '*'
+                pos_m['offset'] = pos_m['position']
+                pos_m['position'] = self._exons_len
         return pos_m
 
     def noncoding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
@@ -62,10 +70,14 @@ def noncoding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         :returns int: Coordinate.
         """
         multilocus_pos_m = {**pos_m, 'position': pos_m['position'] - 1}
-        if pos_m['region'] == '-':
+        if pos_m['region'] == '-': # degenerate results
             multilocus_pos_m['region'] = 'u'
-        elif pos_m['region'] == '*':
+            multilocus_pos_m['position'] = abs(pos_m['offset']) -1
+            multilocus_pos_m['offset'] = 0
+        if pos_m['region'] == '*': # degenerate results
             multilocus_pos_m['region'] = 'd'
+            multilocus_pos_m['position'] = abs(pos_m['offset']) -1
+            multilocus_pos_m['offset'] = 0
         return self._noncoding.to_coordinate(multilocus_pos_m)
 
 
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index 098508b..bc33282 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -107,8 +107,7 @@ def test_NonCoding_degenerate():
         [
             {'position': 1, 'offset': -1, 'region': ''},
             {'position': 1, 'offset': 0, 'region': 'u'},
-            {'position': 1, 'offset': 0, 'region': '-'},
-            {'position': 2, 'offset': 1, 'region': '-'},
+            {'position': 1, 'offset': -1, 'region': '-'},
         ],
     )
 
@@ -121,7 +120,7 @@ def test_NonCoding_degenerate():
             {'position': 22, 'offset': 1, 'region': ''},
             {'position': 23, 'offset': 0, 'region': ''},
             {'position': 24, 'offset': -1, 'region': ''},
-            {'position': 1, 'offset': 0, 'region': '*'},
+            {'position': 22, 'offset': 1, 'region': '*'}, # standard degenerate result
         ],
     )
 
@@ -137,7 +136,7 @@ def test_NonCoding_inverted_degenerate():
         [
             {'position': 1, 'offset': -1, 'region': ''},
             {'position': 1, 'offset': 0, 'region': 'u'},
-            {'position': 1, 'offset': 0, 'region': '-'},
+            {'position': 1, 'offset': -1, 'region': '-'},
         ],
     )
 
@@ -147,7 +146,7 @@ def test_NonCoding_inverted_degenerate():
         4,
         [
             {'position': 1, 'offset': 0, 'region': 'd'},
-            {'position': 1, 'offset': 0, 'region': '*'},
+            {'position': 22, 'offset': 1, 'region': '*'},
             {'position': 23, 'offset': 0, 'region': ''},
             {'position': 22, 'offset': 1, 'region': ''},
         ],
@@ -159,13 +158,13 @@ def test_NonCoding_degenerate_return():
 
     assert crossmap.coordinate_to_noncoding(4, True) == {
         'position': 1,
-        'offset': 0,
+        'offset': -1,
         'region': '-',
     }
 
     assert crossmap.coordinate_to_noncoding(72, True) == {
-        'position': 1,
-        'offset': 0,
+        'position': 22,
+        'offset': 1,
         'region': '*',
     }
 
@@ -175,13 +174,13 @@ def test_NonCoding_inverted_degenerate_return():
 
     assert crossmap.coordinate_to_noncoding(72, True) == {
         'position': 1,
-        'offset': 0,
+        'offset': -1,
         'region': '-',
     }
 
     assert crossmap.coordinate_to_noncoding(4, True) == {
-        'position': 1,
-        'offset': 0,
+        'position': 22,
+        'offset': 1,
         'region': '*',
     }
 

From ba091d536a4f323db490174d4e6421aee75795b1 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 1 Apr 2026 12:04:53 +0200
Subject: [PATCH 124/127] Update degenerate for noncoding example in
 documentation

---
 docs/library.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/library.rst b/docs/library.rst
index 7720088..64aa788 100644
--- a/docs/library.rst
+++ b/docs/library.rst
@@ -113,14 +113,14 @@ denote upstream and ``d`` to denote downstream.
 The ``coordinate_to_noncoding()`` function accepts an optional ``degenerate``
 argument. When set to ``True``, positions outside of the transcript are no
 longer described using the ``u`` or ``d`` notation, ``-`` and ``*`` are used
-instead.
+instead. The values in ``position`` and ``offset`` will change accordingly.
 
 .. code:: python
 
     >>> crossmap.coordinate_to_noncoding(2)
     {'position': 3, 'offset': 0, 'region': 'u'}
     >>> crossmap.coordinate_to_noncoding(2, True)
-    {'position': 3, 'offset': 0, 'region': '-'}
+    {'position': 1, 'offset': -3, 'region': '-'}
 
 For transcripts that reside on the reverse complement strand, the ``inverted``
 parameter should be set to ``True``. In our example, HGVS position ``g.36``

From 39d1d6b5fe5a09e112f61b310da6cb6a751327b4 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 1 Apr 2026 15:02:02 +0200
Subject: [PATCH 125/127] Discard unneccessary functions for coding

---
 mutalyzer_crossmapper/crossmapper.py | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 2e948bd..117a62e 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -178,7 +178,7 @@ def coordinate_to_coding(self, coordinate: int, degenerate: bool = False) -> dic
             degenerate_pos_m['region'] = '*'
         return degenerate_pos_m
 
-    def _coding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
+    def coding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         """Convert a coding position (c./r.) to a coordinate.
 
         :arg dict pos_m: Coding position model (c./r.).
@@ -202,16 +202,6 @@ def _coding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
             multilocus_pos_m['position'] = self._coding[1] + location - 1
         return self._noncoding.to_coordinate(multilocus_pos_m)
 
-    def coding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
-        """Convert a coding position (c./r.) to a coordinate.
-
-        :arg dict pos_m: Coding position model (c./r.).
-
-        :returns int: Coordinate.
-        """
-
-        return self._coding_to_coordinate(pos_m)
-
     def coordinate_to_protein(self, coordinate: int) -> dict[str, int | str]:
         """Convert a coordinate to a protein position (p.).
 

From 915e8453a90bdf470b60d2c11dee11462598e84c Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 1 Apr 2026 15:15:43 +0200
Subject: [PATCH 126/127] Cleanup

---
 mutalyzer_crossmapper/crossmapper.py | 8 ++++----
 tests/test_crossmapper.py            | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 117a62e..0687b2b 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -70,13 +70,13 @@ def noncoding_to_coordinate(self, pos_m: dict[str, int | str]) -> int:
         :returns int: Coordinate.
         """
         multilocus_pos_m = {**pos_m, 'position': pos_m['position'] - 1}
-        if pos_m['region'] == '-': # degenerate results
+        if pos_m['region'] == '-':  # degenerate results
             multilocus_pos_m['region'] = 'u'
-            multilocus_pos_m['position'] = abs(pos_m['offset']) -1
+            multilocus_pos_m['position'] = abs(pos_m['offset']) - 1
             multilocus_pos_m['offset'] = 0
-        if pos_m['region'] == '*': # degenerate results
+        if pos_m['region'] == '*':  # degenerate results
             multilocus_pos_m['region'] = 'd'
-            multilocus_pos_m['position'] = abs(pos_m['offset']) -1
+            multilocus_pos_m['position'] = abs(pos_m['offset']) - 1
             multilocus_pos_m['offset'] = 0
         return self._noncoding.to_coordinate(multilocus_pos_m)
 
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index bc33282..a186937 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -120,7 +120,7 @@ def test_NonCoding_degenerate():
             {'position': 22, 'offset': 1, 'region': ''},
             {'position': 23, 'offset': 0, 'region': ''},
             {'position': 24, 'offset': -1, 'region': ''},
-            {'position': 22, 'offset': 1, 'region': '*'}, # standard degenerate result
+            {'position': 22, 'offset': 1, 'region': '*'},  # standard degenerate result
         ],
     )
 

From 69eb98589a7851f6f2dbec3a480eca92ad25e895 Mon Sep 17 00:00:00 2001
From: Xiaoyun Liu <x.liu@lumc.nl>
Date: Wed, 1 Apr 2026 16:04:40 +0200
Subject: [PATCH 127/127] Fix error for inverted coding

---
 mutalyzer_crossmapper/crossmapper.py | 10 ++--------
 tests/test_crossmapper.py            | 30 ++++++++++++++++++++++++++++
 2 files changed, 32 insertions(+), 8 deletions(-)

diff --git a/mutalyzer_crossmapper/crossmapper.py b/mutalyzer_crossmapper/crossmapper.py
index 0687b2b..88cba2e 100644
--- a/mutalyzer_crossmapper/crossmapper.py
+++ b/mutalyzer_crossmapper/crossmapper.py
@@ -165,16 +165,10 @@ def coordinate_to_coding(self, coordinate: int, degenerate: bool = False) -> dic
         degenerate_pos_m = {**pos_m, 'offset': pos_m['offset']}
         location = pos_m['position']
         if region == 'u':
-            if self._inverted:
-                degenerate_pos_m['position'] = location + self._exons_len - self._coding[1]
-            else:
-                degenerate_pos_m['position'] = location + self._coding[0]
+            degenerate_pos_m['position'] = location + self._coding[0]
             degenerate_pos_m['region'] = '-'
         if region == 'd':
-            if self._inverted:
-                degenerate_pos_m['position'] = location + self._coding[0]
-            else:
-                degenerate_pos_m['position'] = location + self._exons_len - self._coding[1]
+            degenerate_pos_m['position'] = location + self._exons_len - self._coding[1]
             degenerate_pos_m['region'] = '*'
         return degenerate_pos_m
 
diff --git a/tests/test_crossmapper.py b/tests/test_crossmapper.py
index a186937..dcdb718 100644
--- a/tests/test_crossmapper.py
+++ b/tests/test_crossmapper.py
@@ -639,6 +639,11 @@ def test_Coding_inverted_degenerate_return():
         'offset': 0,
         'region': '-',
     }
+    assert crossmap.coordinate_to_coding(25, True) == {
+        'position': 7,
+        'offset': 0,
+        'region': '-',
+    }
     assert crossmap.coordinate_to_coding(9, True) == {
         'position': 2,
         'offset': 0,
@@ -646,6 +651,31 @@ def test_Coding_inverted_degenerate_return():
     }
 
 
+def test_Coding_two_exons_inverted_degenerate_return():
+    """Degenerate upstream and downstream positions may be returned."""
+    crossmap = Coding([(10, 20), (30, 40)], (18, 37), True)
+
+    assert crossmap.coordinate_to_coding(5, True) == {
+        'position': 13,
+        'offset': 0,
+        'region': '*',
+    }
+    assert crossmap.coordinate_to_coding(25, True) == {
+        'position': 7,
+        'offset': 5,
+        'region': '',
+    }
+    assert crossmap.coordinate_to_coding(35, True) == {
+        'position': 2,
+        'offset': 0,
+        'region': '',
+    }
+    assert crossmap.coordinate_to_coding(38, True) == {
+        'position': 2,
+        'offset': 0,
+        'region': '-',
+    }
+
 def test_Coding_degenerate_no_return():
     """Degenerate internal positions do not exist."""
     crossmap = Coding([(10, 20), (30, 40)], (10, 40))