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Commits on Jun 3, 2026

• Make the advertised default for `-t, --threshold` match the implementation.

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• Print a warning when `call -m` is used w/o -v

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Commits on Jun 1, 2026

• Convert ambiguous IUPAC bases according to the VCF specification. Resolves #2551

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• Fixed calculation of MAC and MAF in `-i/-e` filtering expressions

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Commits on May 22, 2026

• Add a new -G, --greedy option

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Commits on May 21, 2026

• [Minor] fix typos, add comments

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Commits on May 20, 2026

• Stage text output through canonical VCF consequences

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• Make kput_vcsq() a read-only formatter

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• Add forgotten test file

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Commits on May 19, 2026

• Fix sex handling and report non-error trio states

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Commits on May 18, 2026

• Fix a start_lost issue in haplotype mode

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Commits on May 14, 2026

• Add a CONTRIBUTING file

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• Fix warning about discarding const in init_index2()

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Commits on May 7, 2026

• Add Github actions builds for Linux and Mac OS (needs htslib#2000)

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• Add GSL_LIBS to W32_PLUGIN_LIBS

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• Remove usage of sprintf()

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Commits on Apr 7, 2026

• Fix erroneous INFO/END recalculation; New --no-realign option

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Commits on Apr 3, 2026

• Extend per-population filtering

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Commits on Apr 2, 2026

• Revert a bug introduced by PR #2533

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Commits on Mar 31, 2026

• Fix 10 assorted medium-severity bugs across multiple files

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• Check for faidx_fetch failure, picked from #2536

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• Replace assert() with proper error handling for user-triggerable conditions

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• Fix two bugs in regidx.c: OOB array access and double-free

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• Fix two bugs in tabix.c: dead code and missing NULL check

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• Fix memset bugs in bam2bcf_iaux.c and bam2bcf.c

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• Fix three bugs in bam2bcf indel calling

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• Fix type mismatch in ccall.c and division by zero in mcall.c

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• Minor code tightening

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• Fix three bugs in vcfconvert.c

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• Add test for #2526

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• Allow annotation of Number=A,R INFO tags from tab-delimited files when alleles are split across multiple records

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Commits on Mar 30, 2026

• Update test

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• Update test

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• Add part #1 of #2524, adding a test and fixing the introduced bug

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• Fix wrong array used for float missing-value in split_format_numeric

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