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Commits on Jun 21, 2023

• Clarify the XXXXXX template convention of mkdtemp

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Commits on Jun 2, 2023

• Add stats for the number of sites matched in the GT-vs-GT, GT-vs-PL, etc modes.

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Commits on May 30, 2023

• Update documentation

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Commits on May 9, 2023

• Support for conversion from tab-delimited files (CHROM,POS,REF,ALT) to sites-only VCFs

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Commits on Apr 25, 2023

• Improvements in GFF parsing code

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Commits on Apr 7, 2023

• Allow --mark-ins and --mark-snv with a character, similarly to --mark-del

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Commits on Mar 28, 2023

• Support higher-ploidy genotypes with -H, --haplotype

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Commits on Mar 22, 2023

• Give control over creation of vectors with mixed known and missing values

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Commits on Mar 10, 2023

• Support auto indexing during writing BCF and VCF.gz via new --write-index option

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Commits on Feb 20, 2023

• Clarify -R/-T format to prevent confusion such as samtools#1862

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Commits on Jan 24, 2023

• Arrays in Number=R tags can be now subscripted by alleles found in FORMAT/GT

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Commits on Jan 19, 2023

• Update man page to prevent future confusion as in samtools#1851

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Commits on Jan 3, 2023

• Add error checks to prevent incorrect use of vector arithmetics in -i/-e.

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Commits on Dec 12, 2022

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

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Commits on Nov 23, 2022

• Update documentation and NEWS

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Commits on Nov 1, 2022

• New +mendelian2 plugin, deprecates the original +mendelian

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Commits on Oct 12, 2022

• New norm --multi-overlaps option. Resolves samtools#1802 and samtools#1764

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Commits on Sep 8, 2022

• Document explicitly output format of roh

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Commits on Aug 15, 2022

• Merge pull request samtools#1772 from jmarshall/index-stats-all

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Commits on Aug 12, 2022

• Fix a documentation typo

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Commits on Aug 11, 2022

• New -m snp-ins-del switch to merge SNVs, insertions and deletions separately

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Commits on Aug 6, 2022

• Print unknown stats as '.' rather than 0

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• Add bcftools index --stats --all option to display all contigs

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Commits on Jul 6, 2022

• Add modulo operator to filtering expressions. Resolves samtools#1744

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Commits on May 31, 2022

• Add support for querying multiple filters

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Commits on Apr 26, 2022

• Add pointer to extended consensus documentation

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Commits on Apr 6, 2022

• New plugin +variant-distance

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Commits on Mar 3, 2022

• Document supported consequence types. Resolves samtools#1671

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Commits on Feb 17, 2022

• Add --regions/--targets-overlap pos|record|variant mnemonic options

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Commits on Feb 9, 2022

• Document missing option

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Commits on Jan 31, 2022

• Support for transfering ALT from VCF

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Commits on Jan 28, 2022

• Add new option --min-overlap to bcftools annotate

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Commits on Jan 17, 2022

• New --mask, --mask-file and --mask-overlap options

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• Merge develop

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• More flexible read filtering

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