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Commits on Feb 9, 2024

• Fix the indelQ assignment for multi-allelic indel sites.

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  jkbonfield

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• Recompute IDV and IMF if mpileup -a AD is set.

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  jkbonfield

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• - Enable the "edlib mode" for the more recent mpileup -X profiles.

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• Add an mpileup --poly-mqual option for the "edlib" mode.

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• Add a new indel caller.

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Commits on Feb 8, 2024

• Fix bcftools norm -m +indels

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Commits on Jan 31, 2024

• Complain if both --write-index and --naive options are given

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Commits on Jan 29, 2024

• Fix the "Requested allele outside valid range" error.

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• Change of default order of -m,-a operations and fix a few bugs

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Commits on Jan 23, 2024

• [minor] Make fname const char*, as it should be

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

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• Change automatic type parsing of VEP fields DNA_position, CDS_position, and Protein_position

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Commits on Jan 18, 2024

• Happy New Year

  

  daviesrob

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Commits on Jan 16, 2024

• ifndef

  

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• ifndef

  

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• GSL_LIBS

  

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Commits on Jan 10, 2024

• Transcript selection by MANE, PICK, and user-defined transcripts

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Commits on Jan 9, 2024

• Automatically select INFO/BCSQ when INFO/CSQ is not present.

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Commits on Jan 8, 2024

• Exit nicely when non-existent field name requested

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• Clarify that no annotation is added in intergenic regions

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Commits on Jan 4, 2024

• Apply Rob's suggestions from code review

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• vcfplugin.c: improve init functions description.

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• plugins/*.c: improve init functions description.

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• variantkey.h: small description improvement.

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• doc/bcftools.txt: improve "allows one to" wording.

  

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• doc/bcftools.html: improve "allows one to" wording.

  

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• doc/bcftools.1: improve "allows one to" wording.

  

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• NEWS: improve "allows one to" wording.

  

  emollier

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• address multiple typos

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Commits on Jan 2, 2024

• Portability improvements

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  daviesrob

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Commits on Dec 30, 2023

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

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• Support for custom genotypes based on the allele with higher depth

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Commits on Dec 27, 2023

• Improve docs on --soft-filter argument.

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  SpikyClip

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Commits on Dec 18, 2023

• Extend --strictly-novel

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Commits on Dec 12, 2023

• Merge version number bump and NEWS file from master

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