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Commits on Oct 8, 2018

• Fix a bug in duplicates removal.

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Commits on Oct 4, 2018

• New +gvcfz plugin

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Commits on Oct 3, 2018

• Add tentative support for symbolic insertions. Do not limit the number of sequences to 256, this should fix samtools#895

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• Make consensus work with insertions immediately following deletions

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• A single dot is a valid Number=G,Type=String field - missing value

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Commits on Oct 1, 2018

• Prevent int overflow with +100k genotypes by casting to double. Fixes samtools#894

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Commits on Sep 30, 2018

• Let N_PASS,F_PASS also set samples, not just sites.

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• Add +trio-stats -P, --pfm option

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Commits on Sep 29, 2018

• Allow empty FORMAT strings, skip them instead of exiting via assert. Fixes samtools#303 (comment)

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Commits on Sep 24, 2018

• Minor fix: add missing test file; add missing long options. Fixes samtools#890

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• Make FORMAT/AD work with call -C alleles

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Commits on Sep 19, 2018

• Make fill-tags work with large number of alleles. Fixes samtools#621

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Commits on Sep 18, 2018

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

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• Make the sample mapping work again with annotate. Fixes samtools#123

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Commits on Sep 14, 2018

• Merge pull request samtools#876 from Genomicsplc/develop

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• Merge pull request samtools#883 from jmarshall/reheader-warnings

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• New plugin +trio-dnm

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Commits on Sep 13, 2018

• Silence warnings [minor]

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Commits on Sep 12, 2018

• Add test for reserved INT values, samtools#874

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Commits on Sep 6, 2018

• Update variantkey with the new header-only version

  

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• Merge upstream variantkey optimizations

  

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• Merge pull request samtools#2 from samtools/develop

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Commits on Aug 29, 2018

• Add test for samtools#871. Make F_MISSING and F_PASS aware of the necessacity to keep the FORMAT fields.

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• Do not mix doubles and floats in comparisons. See samtools#871

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• Update doc: pointer to the tutorial about && vs & and || vs | difference

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Commits on Aug 27, 2018

• Support for replacing FMT/GT by a custom tag.

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Commits on Aug 24, 2018

• New reheader -f,--fai option. Resolves samtools#860

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Commits on Aug 23, 2018

• Update documentation to reflect changes in mpileup -d behaviour

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Commits on Aug 22, 2018

• Add sanity checks to catch more user errors in filtering expressions.

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Commits on Aug 21, 2018

• New consensus -p option. Resolves samtools#864

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• Division in Python3 is floating point by default, make plot-vcfstats compatible

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• Make long overlapping deletions work again after 8ee2a03

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• Choose the right output stream for summary counts

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• Fix for transcripts within N_REF_PAD from chromosome ends. Resolves samtools#869

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• More informative error message

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