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Commits on Jan 1, 2025

• Fix Number in the header definition of transferred FILTER and ID tags

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Commits on Oct 31, 2024

• Complain if Number=R,A assumptions not met

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Commits on Oct 22, 2024

• Update documentation

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• Add support for matching VCF lines by ID

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Commits on Jun 3, 2024

• Percent-encode characters with special meaning

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Commits on Apr 19, 2024

• Support dynamic variables read from a tab-delimited annotation file

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Commits on Apr 12, 2024

• Revert "Support dynamic variables read from a tab-delimited annotation file"

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Commits on Apr 11, 2024

• Support dynamic variables read from a tab-delimited annotation file

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Commits on Mar 28, 2024

• Add short option -W for --write-index.

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• Make --write-index have an optional =FMT option.

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Commits on Nov 30, 2023

• Remove forgotten debugging output

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• Replace semicolons with commas

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Commits on Nov 29, 2023

• Add flexibility to FILTER column transfers

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Commits on Sep 5, 2023

• Fix bcftools annotate --mark-sites

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Commits on Jul 12, 2023

• Fix a bug when update of INFO/END results in assertion error

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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 24, 2023

• The -m function did not respect the --min-overlap option

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• The -m, --mark-sites option can be used to mark all sites

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Commits on Nov 2, 2022

• Restore functionality of the --pair-logic option. Fixes #1808

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Commits on Sep 1, 2022

• Support sample reordering of annotation file. Resolves #1785

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Commits on Aug 12, 2022

• When complaining about missing tags, be explicit if it is FORMAT or INFO. Resolves #1770

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Commits on Jun 13, 2022

• Fix a bug introduced in 1.14

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Commits on Apr 6, 2022

• Strip column type prefix to avoid confusion. Resolves #1695

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Commits on Mar 11, 2022

• New -H, --header-line option

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Commits on Feb 17, 2022

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

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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 Nov 2, 2021

• Renaming annotations from the command line

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Commits on Sep 16, 2021

• Use --output-type to override the default compression level

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Commits on Sep 7, 2021

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

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Commits on Aug 26, 2021

• Don't bail on symbolic ALTs

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Commits on Aug 23, 2021

• Allow to change positions using -c CHROM,POS,~POS. Resolves #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 14, 2021

• Exit gracefully instead of segfaulting

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