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Pull requests: samtools/bcftools

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Pull requests list

Fix 10 assorted medium-severity bugs across multiple files
#2537 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
1
Fix missing header finalization and unchecked faidx return
#2536 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 3 tasks
Replace assert() with proper error handling for user-triggerable conditions
#2535 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Fix vcfstats per-sample statistics using wrong FORMAT column index
#2534 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
1
Fix regidx out-of-bounds array access and double free
#2533 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Fix tabix NULL deref on open failure and dead detect=0 code
#2532 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Fix bam2bcf indel calling: memset destroying consensus, uninit variable, wrong sizes
#2531 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Fix ccall type-punning and mcall division by zero
#2530 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Fix vcfcnv OOB read with control sample and AA skip mismatch
#2529 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Fix vcfconvert ALT parsing, null deref, and sample compression
#2528 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 3 tasks
Fix csq consequence prediction: sref offset, OOB codon, stop codon, splice
#2527 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 3 tasks
1
Fix literal string matching for external annotation filter values
#2526 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
1
Fix vcfannotate type mismatch, null deref, and stale buffer
#2524 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Fix filter engine: OOB write, undefined shift, wrong fallbacks, debug output
#2523 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
1
Fix vcfnorm writing float missing values to wrong buffer
#2522 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Fix merge -m none incorrectly merging records with different allele sets
#2521 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
1
Fix vcfmerge format field handling for Number=G, INT8 PL, and dst buffer
#2520 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Fix off-by-one in HMM forward-backward posterior indexing
#2519 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Fix wrong loop variable in family trio sample remapping
#2518 opened Mar 26, 2026 by sirus20x6 Loading…
1 of 2 tasks
Make the mpileup BAM_CREF_SKIP filter optional.
#2282 opened Sep 17, 2024 by jkbonfield Loading…
1
Remove the mpileup BAM_CREF_SKIP filter.
#2281 opened Sep 17, 2024 by jkbonfield Loading…
1
2
Check fclose(stdout) at the end of main() [and miscellanea]
#2046 opened Nov 27, 2023 by jmarshall • Draft
average(FORMAT/GQ) for vcfstats
#1941 opened Jun 9, 2023 by lindenb Loading…
1
Support for telomere (POS=0) coordinate
#1875 opened Mar 1, 2023 by pd3 Loading…
New mpileup2 draft (intended for discussions, not ready to merge!)
#1842 opened Jan 3, 2023 by pd3 Loading…
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