[Feature]: Add BAM format support #20
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AdityaPandeyCN wants to merge 2 commits intocompiler-research:developfrom
Open
[Feature]: Add BAM format support #20AdityaPandeyCN wants to merge 2 commits intocompiler-research:developfrom
AdityaPandeyCN wants to merge 2 commits intocompiler-research:developfrom
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Codecov Report❌ Patch coverage is ❌ Your patch status has failed because the patch coverage (81.49%) is below the target coverage (85.00%). You can increase the patch coverage or adjust the target coverage. Additional details and impacted files@@ Coverage Diff @@
## develop #20 +/- ##
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+ Coverage 64.78% 68.04% +3.25%
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Files 16 19 +3
Lines 1525 1887 +362
Branches 632 760 +128
===========================================
+ Hits 988 1284 +296
- Misses 462 508 +46
- Partials 75 95 +20
Flags with carried forward coverage won't be shown. Click here to find out more.
... and 1 file with indirect coverage changes
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Can you rebase? |
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| bam_aux_append(rec, "XS", 'S', sizeof(val_S), static_cast<const uint8_t *>(static_cast<const void *>(&val_S))); | ||
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| int32_t val_i = -100000; | ||
| bam_aux_append(rec, "Xi", 'i', sizeof(val_i), static_cast<const uint8_t *>(static_cast<const void *>(&val_i))); |
There was a problem hiding this comment.
warning: do not cast 'int32_t *' (aka 'int *') to 'const uint8_t *' (aka 'const unsigned char *') through 'const void *' [bugprone-casting-through-void]
bam_aux_append(rec, "Xi", 'i', sizeof(val_i), static_cast<const uint8_t *>(static_cast<const void *>(&val_i)));
^| bam_aux_append(rec, "Xi", 'i', sizeof(val_i), static_cast<const uint8_t *>(static_cast<const void *>(&val_i))); | ||
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| uint32_t val_I = 3000000; | ||
| bam_aux_append(rec, "XI", 'I', sizeof(val_I), static_cast<const uint8_t *>(static_cast<const void *>(&val_I))); |
There was a problem hiding this comment.
warning: do not cast 'uint32_t *' (aka 'unsigned int *') to 'const uint8_t *' (aka 'const unsigned char *') through 'const void *' [bugprone-casting-through-void]
bam_aux_append(rec, "XI", 'I', sizeof(val_I), static_cast<const uint8_t *>(static_cast<const void *>(&val_I)));
^| bam_aux_append(rec, "XI", 'I', sizeof(val_I), static_cast<const uint8_t *>(static_cast<const void *>(&val_I))); | ||
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| float val_f = 3.14F; | ||
| bam_aux_append(rec, "Xf", 'f', sizeof(val_f), static_cast<const uint8_t *>(static_cast<const void *>(&val_f))); |
There was a problem hiding this comment.
warning: do not cast 'float *' to 'const uint8_t *' (aka 'const unsigned char *') through 'const void *' [bugprone-casting-through-void]
bam_aux_append(rec, "Xf", 'f', sizeof(val_f), static_cast<const uint8_t *>(static_cast<const void *>(&val_f)));
^|
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| const char *val_Z = "hello"; | ||
| bam_aux_append(rec, "XZ", 'Z', static_cast<int>(strlen(val_Z) + 1), | ||
| static_cast<const uint8_t *>(static_cast<const void *>(val_Z))); |
There was a problem hiding this comment.
warning: do not cast 'const char *' to 'const uint8_t *' (aka 'const unsigned char *') through 'const void *' [bugprone-casting-through-void]
static_cast<const uint8_t *>(static_cast<const void *>(val_Z)));
^|
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| const char *val_H = "1AE301"; | ||
| bam_aux_append(rec, "XH", 'H', static_cast<int>(strlen(val_H) + 1), | ||
| static_cast<const uint8_t *>(static_cast<const void *>(val_H))); |
There was a problem hiding this comment.
warning: do not cast 'const char *' to 'const uint8_t *' (aka 'const unsigned char *') through 'const void *' [bugprone-casting-through-void]
static_cast<const uint8_t *>(static_cast<const void *>(val_H)));
^| if (arg == "-noindex") | ||
| do_index = false; | ||
| else if (arg == "-illumina") | ||
| quality_mode = RAMNTupleRecord::kIlluminaBinning; |
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warning: repeated branch body in conditional chain [bugprone-branch-clone]
quality_mode = RAMNTupleRecord::kIlluminaBinning;
^Additional context
tools/bamtoramntuple.cxx:30: end of the original
quality_mode = RAMNTupleRecord::kIlluminaBinning;
^tools/bamtoramntuple.cxx:32: clone 1 starts here
quality_mode = RAMNTupleRecord::kDrop;
^
Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>
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@vgvassilev Please take a look |
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This PR adds BAM support, through this we can convert BAM file directly to RNTuple format files without going through the SAM pipeline.