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Commits on Jun 23, 2021

• Summer 2021 release copyright updates.

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Commits on Jan 19, 2021

• Add explicit --group-samples-tag option. Resolves samtools#1370

  pd3

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Commits on Dec 7, 2020

• [NEWS] Revamp of bcftools call -G

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Commits on Feb 20, 2020

• Use #include <assert.h> in source files that use assert()

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Commits on Sep 9, 2019

• Prepare for 64-bit positions

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Commits on May 30, 2019

• Fix possible out of bounds write in mcall_constrain_alleles()

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Commits on May 8, 2019

• Keep compiler happy, get rid of the harmless "igrp may be used uninitialized" warning

  pd3

  committed
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Commits on May 6, 2019

• Add new bcftools call -G, --group-samples option

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Commits on Nov 17, 2018

• More informative error message to help resolve issues like samtools#915

  pd3

  committed
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• call -C allels -i should not skip sites. Fixes samtools#913

  pd3

  committed
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Commits on Sep 24, 2018

• Make FORMAT/AD work with call -C alleles

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Commits on Apr 28, 2017

• Fix samtools#535

  pd3

  committed
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Commits on Apr 5, 2017

• Tidy upsfor C99 / _XOPEN_SOURCE=700 compliance.

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Commits on Feb 23, 2017

• cleanup clang compiler warnings

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Commits on Jan 19, 2017

• Fix the QUAL calculation at REF-only sites and the use of AFs obtained from QS in haploid calling

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Commits on Jan 3, 2017

• Allow PLs>=256 in call -m

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  committed
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Commits on Jul 22, 2016

• call: improve QUAL calculation (samtools#449)

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  mcshane

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Commits on May 3, 2016

• call: new -F, --prior-freqs option

  

  pd3

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  mcshane

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• mcall: trim all Number=R tags

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Commits on Dec 7, 2015

• call -mC alleles fix: Do not take X as last in ALT list for granted

  

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Commits on Nov 18, 2015

• Prevent empty PL fields on BCF output with "call -C alleles"

  

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  mcshane

  committed
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Commits on Oct 15, 2015

• genaralise mcall_trim_numberR beyond DPR to any Number=R/Type=Integer tag

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Commits on Sep 30, 2015

• Bringing "call --gvcf" from experimental to main repo.

  

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  mcshane

  committed
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Commits on Sep 25, 2015

• Fixed bug in trio calling introduced by bcc7b26

  

  pd3

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  mcshane

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Commits on Aug 5, 2015

• call -m fix: skip sites with too many alleles (>32) instead of silently overwriting internal data structures..

  

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  mcshane

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Commits on Dec 5, 2014

• call: Trim FORMAT/DPR for REF-only sites as well

  pd3

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Commits on Nov 7, 2014

• Calling improvements:

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  pd3

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Commits on Nov 5, 2014

• call: -A must not include records discarded by -v with -m

  pd3

  committed
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Commits on Oct 21, 2014

• Do not use 0x80 & co for missing alleles

  pd3

  committed
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Commits on Oct 8, 2014

• DPR trimmed with call -c

  pd3

  committed
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Commits on Aug 14, 2014

• Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT

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  jmarshall

  committed
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• Merge copyright notice and licensing boilerplate corrections

  jmarshall

  committed
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Commits on Aug 13, 2014

• mcall: Prevent -0 in QUAL output; clean old unused lk2 stuff

  pd3

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• Reformat license text

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  jmarshall

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Commits on Aug 11, 2014

• Update copyright years to reflect when changes were made

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