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Commits on Aug 6, 2024

• Keep only one implementation of calc_binom()

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• Fix a severe bug in merging of FORMAT fields

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• Fix the error message which reports the wrong sample when non-existent sample is given.

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Commits on Aug 5, 2024

• Fix a bug in --atomize

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Commits on Jul 25, 2024

• Update --gvcf documentation

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Commits on Jul 18, 2024

• Fix a trivial undefined behaviour sanitizer issue.

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Commits on Jul 16, 2024

• Read SVLEN as four bytes of int32_t rather than just one byte

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  jmarshall

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Commits on Jul 15, 2024

• Make explicit conversions, such as --LAD-to-AD, work

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Commits on Jun 28, 2024

• Fix bug in the new -m 'min(QUAL)' code

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• Allow to apply a reference allele which overlaps a previous deletion

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Commits on Jun 27, 2024

• Merge branch 'develop' of github.com:samtools/bcftools into develop

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• Fix a hopefully rare bug

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Commits on Jun 26, 2024

• Merge branch 'develop' of github.com:samtools/bcftools into develop

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Commits on Jun 25, 2024

• Fix segfault, wrong index used

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• Remove unused variable, previously intended for debugging

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  298b366

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• Fix a misplaced if statement I/O check

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  e214be3

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• Fix a few bugs introduced by aa3bf89

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  27980a8

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• Revamp the program to allow greater flexibility

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Commits on Jun 20, 2024

• Update a non-functional link in the commented source code

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Commits on Jun 7, 2024

• Fix error in DCv2 output

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Commits on Jun 5, 2024

• Merge branch 'develop' of github.com:samtools/bcftools into develop

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• Add ngood_alt stats

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• Make test use the correct BCFTOOLS_PLUGINS directory

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Commits on Jun 3, 2024

• Percent-encode characters with special meaning

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Commits on May 31, 2024

• Update documentation on -A, --count-orphans option

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• Add the -i/-e filtering options to select records for normalization.

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Commits on May 29, 2024

• Fix typos

  

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• Remove an overly strict sanity check

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Commits on May 27, 2024

• Support multiple semicolon-separated strings when filtering by ID

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Commits on May 24, 2024

• Update test for 379e1b6

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• Add -S, --sort switch to optionally sort output records by allele

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• Extend file format description

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• Add FORMAT/AD annotation by default, disable with -a -AD

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• Propagate bam_mplp_auto() error code, throw an error on truncated bam/cram files

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Commits on May 21, 2024

• [MINOR] Print correct index in the header

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