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Pull requests list

Add documentation for all VariantHeader related classes
#1394 opened Mar 10, 2026 by TimD1 Loading…
Extract shared PileupColumn validity check
#1392 opened Mar 2, 2026 by nh13 • Draft
1 task
Consolidate aux tag value decoding in get_tag and get_tags
#1391 opened Mar 2, 2026 by nh13 • Draft
1 task
Extract shared helpers for reference_name and next_reference_name
#1390 opened Mar 2, 2026 by nh13 • Draft
1 task
Use bam_set_qname in query_name setter
#1389 opened Mar 2, 2026 by nh13 • Draft
1 task
Use bam_cigar2qlen for query length calculation
#1388 opened Mar 2, 2026 by nh13 • Draft
1 task
Accumulate insertion count during CIGAR loop in build_alignment_sequence
#1387 opened Mar 2, 2026 by nh13 • Draft
1 task
Cache complement translation table in get_forward_sequence
#1386 opened Mar 2, 2026 by nh13 • Draft
1 task
Remove redundant copy in getSequenceInRange
#1385 opened Mar 2, 2026 by nh13 • Draft
1 task
Disable Cython profiling hooks in production builds
#1384 opened Mar 2, 2026 by nh13 • Draft
1 task
Remove unused variables in AlignedSegment compare method
#1383 opened Mar 2, 2026 by nh13 • Draft
1 task
Simplify update_bin by collapsing duplicate branches
#1382 opened Mar 2, 2026 by nh13 • Draft
1 task
Fix TypeError in modified_bases_forward when query_sequence is None
#1381 opened Mar 2, 2026 by nh13 • Draft
1 task
Add missing NULL guard in PileupColumn.get_query_qualities
#1380 opened Mar 2, 2026 by nh13 • Draft
1 task
3
Fix silent truncation in IteratorRowAllRefs on I/O errors
#1379 opened Feb 12, 2026 by gileshall Loading…
Adding option to ignore non-existing references.
#1374 opened Jan 19, 2026 by blaiseli Loading…
1
Fix type hints for get_aligned_pairs
#1371 opened Dec 17, 2025 by gshiba Loading…
2
AlignedSegment.set_tag(): validate Hex values for tag type 'H'
#1366 opened Nov 8, 2025 by bentyeh Loading…
Support value_type of 'B' in get_tag_typecode()
#1365 opened Nov 8, 2025 by bentyeh Loading…
optimize performance of array_to_qualitystring
#1363 opened Oct 2, 2025 by jchorl Loading…
3
Added VariantContig and VariantMetadata documentation.
#1361 opened Sep 18, 2025 by TimD1 Loading…
Add documentation for all VariantRecord related classes
#1359 opened Sep 11, 2025 by TimD1 Loading…
1
Add VariantRecordSample documentation
#1358 opened Sep 10, 2025 by TimD1 Loading…
2
8
feat: add class to generate pileup over AlignedSegments
#1353 opened Jul 4, 2025 by nh13 Loading…
1
6
Add bespoke classes for accessing SEQ and QUAL
#1347 opened Jun 10, 2025 by jmarshall • Draft
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