From 460c9c4f7380be1779651363da110a80d8abaee4 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 27 Feb 2026 06:57:02 +0000
Subject: [PATCH 1/2] Initial plan


From 283d2012ebd0b7f582b7dd5b52da7869f7db7a41 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 27 Feb 2026 06:59:29 +0000
Subject: [PATCH 2/2] fix: guard against mismatched array lengths in
 extractFieldsFromRecord

Co-authored-by: holmeso <7066552+holmeso@users.noreply.github.com>
---
 .../au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java  | 2 +-
 .../edu/qimr/qannotate/nanno/AnnotationSourceTSVTest.java | 8 ++++++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java b/qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java
index 41e20e907..8d91add62 100644
--- a/qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java
+++ b/qannotate/src/au/edu/qimr/qannotate/nanno/AnnotationSourceTSV.java
@@ -112,7 +112,7 @@ public static String extractFieldsFromRecord(String[] record, String[] fieldName
 		StringBuilder dataToReturn = new StringBuilder();
 		int recordLength = null != record ? record.length : 0;
 		if (recordLength > 0 && null != fieldNames && null != fieldPositions) {
-			for (int i = 0; i < fieldNames.length; i++) {
+			for (int i = 0; i < Math.min(fieldNames.length, fieldPositions.length); i++) {
 				int pos = fieldPositions[i];
 				if (recordLength > pos) {
 					dataToReturn.append((!dataToReturn.isEmpty()) ? FIELD_DELIMITER_TAB : "")
diff --git a/qannotate/test/au/edu/qimr/qannotate/nanno/AnnotationSourceTSVTest.java b/qannotate/test/au/edu/qimr/qannotate/nanno/AnnotationSourceTSVTest.java
index 0754e6865..b45dc0562 100644
--- a/qannotate/test/au/edu/qimr/qannotate/nanno/AnnotationSourceTSVTest.java
+++ b/qannotate/test/au/edu/qimr/qannotate/nanno/AnnotationSourceTSVTest.java
@@ -37,6 +37,14 @@ public void extractFieldsFromRecord() {
 		fieldPositions = new int[]{100, 11};
 		assertEquals("", AnnotationSourceTSV.extractFieldsFromRecord(new String[]{"slightly_longer","record","","","","","","","","","bar"}, fieldNames,  fieldPositions));
 		
+		// mismatched array lengths - fieldNames longer than fieldPositions
+		fieldNames = new String[]{"foo", "foo2", "foo3"};
+		fieldPositions = new int[]{10};
+		assertEquals("foo=bar", AnnotationSourceTSV.extractFieldsFromRecord(new String[]{"slightly_longer", "record", "", "", "", "", "", "", "", "", "bar"}, fieldNames, fieldPositions));
+		// mismatched array lengths - fieldPositions longer than fieldNames
+		fieldNames = new String[]{"foo"};
+		fieldPositions = new int[]{10, 1, 0};
+		assertEquals("foo=bar", AnnotationSourceTSV.extractFieldsFromRecord(new String[]{"slightly_longer", "record", "", "", "", "", "", "", "", "", "bar"}, fieldNames, fieldPositions));
 	}
 	
 	@Test