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Commits on Dec 13, 2022

• Refer to the correct option --samples, rather than --sample

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Commits on Dec 12, 2022

• Change the behavior of the -I, --iupac-codes option

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Commits on Apr 26, 2022

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

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• Add pointer to extended consensus documentation

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Commits on Apr 11, 2022

• Prevent segfault, fix samtools#1700

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Commits on Nov 24, 2021

• Symbolic allele strings cannot be trimmed

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Commits on Oct 22, 2021

• Apply mask even if the VCF has no notion about the chromosome

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Commits on Feb 25, 2021

• Fix a signed comparison as pointed by samtools#1400 (comment)

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Commits on Feb 11, 2021

• Make consensus -I and -H I work with arbitrary ploidy. Resolves samtools#1400

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Commits on Feb 2, 2021

• Support for IUPAC codes in insertions and MNVs, plus a new -H I option. Resolves samtools#1241,samtools#1393

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• Throw an error if -i/-e expression is given multiple times. Prevents errors samtools#1388

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Commits on Jan 27, 2021

• Add a new consensus --mask-with option. Resolves samtools#1382

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Commits on Jan 25, 2021

• Add forgotten \0 string termination

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Commits on Jan 22, 2021

• Add new --mark-del, --mark-ins, and --mark-snv options. Resolves samtools#1381 and samtools#1170

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Commits on Nov 19, 2020

• Make an assumption about <DEL> start when strlen(REF)!=1. Resolves samtools#1319

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Commits on Oct 27, 2020

• When first base of the reference genome is deleted,

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Commits on Sep 3, 2020

• Extend dc26549, handle cases where a SNP is immediately followed by a <DEL>. See also samtools#1295

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Commits on Sep 2, 2020

• Prevent buffer overrun on symbolic <DEL> alleles, driven by INFO/END. Replaces samtools#1295

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Commits on Aug 17, 2020

• Prevent segfault on REF-only positions with ALT="." and -I. Fixes samtools#1273

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Commits on Jun 17, 2020

• Prevent segfault on first block. Fixes samtools#1245

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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 Feb 19, 2020

• Determine the case of the fasta sequence locally,

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Commits on Feb 18, 2020

• Overlapping deletions must not be forgotten in subsequent records with -a N.

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Commits on Feb 6, 2020

• Fix samtools#1149

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Commits on Dec 28, 2019

• Add new -a, --absent option.

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Commits on Sep 9, 2019

• Prepare for 64-bit positions

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Commits on Jun 6, 2019

• Add new -H 1pIu/2pIu feature to consensus. Resolves samtools#1027

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Commits on Apr 15, 2019

• Improve error messages. Resolves samtools#951 and samtools#925

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Commits on Dec 27, 2018

• Improve the recent consensus fixes.

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Commits on Dec 21, 2018

• Make consensus skip duplicate insertions. Fixes samtools#888

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Commits on Oct 3, 2018

• Make consensus work with insertions immediately following deletions

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Commits on Aug 21, 2018

• New consensus -p option. Resolves samtools#864

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Commits on Jul 17, 2018

• Fix tautological compare warnings from clang

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Commits on Jul 12, 2018

• Fix a harmless warning

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Commits on Jun 27, 2018

• Use bgzf_open() to read FASTA file

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