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Commits on Sep 7, 2021

• Finer control of --regions vs --targets overlap

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Commits on Sep 1, 2021

• Add new --indel-size option

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Commits on Aug 28, 2021

• New --ligate-force and --ligate-warn options

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Commits on Aug 23, 2021

• Allow to change positions using -c CHROM,POS,~POS. Resolves samtools#1545

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• Add new -c ~INFO/END feature to match also by INFO/END tag

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Commits on Aug 21, 2021

• Add a new annotation mode to carry over missing values

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Commits on Aug 10, 2021

• Update documentation to prevent confusion, see samtools#1538

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Commits on Jul 7, 2021

• Release 1.13

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• Correct mpileup --ambig-reads documentation.

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• Add new --ar, --ambig-reads option

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Commits on Jun 14, 2021

• Remove an inaccessible branch, remove optional getopt_long option as it is not supported by all platforms.

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• Parametrize brief-predictions parameter (-b) of bcftools csq

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Commits on May 27, 2021

• Update documentation

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Commits on May 25, 2021

• Add a --seed option to mpileup.

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Commits on May 19, 2021

• Fix a typo. Thanks to Rick Wertenbroek, PR samtools#1485

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• Replace "concat --rm-dup none" with "--rm-dup exact". Resolves samtools#1089 (comment)

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Commits on May 10, 2021

• Update tests and documentation

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Commits on Apr 23, 2021

• Make partial-BAQ the default in mpileup.

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• Add mpileup -U option for old MWU scale.

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• Adjust min/max qual for SNP caller.

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• Add an indel-bias argument to mpileup.

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• Improve mpileup speed by delaying BAQ calculation.

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Commits on Apr 16, 2021

• Support for matching annotation line also by ID,

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• Fix and update documentation, PBINOM should be uppercase

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Commits on Mar 30, 2021

• Support for VCFs with more than 4 ALTs

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Commits on Mar 17, 2021

• Release 1.12

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Commits on Mar 10, 2021

• The csq --ncsq option was handled incorrectly,

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Commits on Mar 9, 2021

• Update documentation to mention GT="mis" as well. See also samtools#1435

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Commits on Feb 25, 2021

• Update man page and INSTALL instructions

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• Prevent invalid memory access

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• Merge pull request samtools#1432 from pd3/atomize

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• Add new --atomize and --old-rec-tag options

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Commits on Feb 24, 2021

• Fix a typo, thanks to @tbenavi1. Resolves samtools#1424

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• Support for FORMAT/VAF,VAF1 annotations. Resolves samtools#1422

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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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