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Commits on Oct 21, 2024

• Replace AppVeyor for GitHub Actions workflow for Windows builds

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• Improve cirrus-CI for shared htslib/bcftools PRs.

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Commits on Oct 3, 2024

• Fix cut and paste errors in writing the get_data.sh script.

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Commits on Sep 11, 2024

• Work around an incompatibility between Perl and clang warnings.

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Commits on Sep 6, 2024

• Fix a regression with -Ou format being the same as -Ob.

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Commits on Aug 14, 2024

• Increase maximum indel size of mpileup --indel-cns to 8192 from 1024

  

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• Fix inserted consensus defaults for --indels-cns mode.

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Commits on Aug 13, 2024

• Improve documentation of mpileup adjust-MQ.

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Commits on Jul 18, 2024

• Fix a trivial undefined behaviour sanitizer issue.

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Commits on May 4, 2024

• Work around ubuntu's latest clang compiler missing address sanitizer

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• Add mpileup_bench/run_multi.sh for multi-sample evaluations

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Commits on Mar 28, 2024

• Fix csq error message for now fasta file.

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

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• Add documentation on the optional =FMT bit of --write-index.

  

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• Fix a bug in expression parsing for type=INDEL with missing quotes.

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• Fix +scatter -n so it honours --write-index

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• Make bcftools isec --write-index=FMT apply to isec directory output too

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

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Commits on Mar 21, 2024

• Fix REF indel calls for multi-sample calling.

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Commits on Mar 14, 2024

• Tweak the condition for calling a 2nd consensus sequence in a deletion.

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• Don't change indel qual when indelQ == 0.

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Commits on Feb 23, 2024

• Fix a trivial memory leak in the mpileup usage (etc) code

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Commits on Feb 9, 2024

• Add some scripts for evaluation bcftools mpileup.

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• Fix a clang16 warning on bit-field overflow.

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• - Rename mpileup --edlib to --indels-cns

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• Fix the indelQ assignment for multi-allelic indel sites.

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• Recompute IDV and IMF if mpileup -a AD is set.

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• - Enable the "edlib mode" for the more recent mpileup -X profiles.

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• Add an mpileup --poly-mqual option for the "edlib" mode.

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• Add a new indel caller.

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Commits on Apr 6, 2023

• Add error checking to gvcf_write_block

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Commits on Mar 7, 2023

• Add --write-index to bcftools view

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Commits on Nov 17, 2021

• Improve merge_vcf() error reporting, following review.

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Commits on Nov 5, 2021

• Further speed up vcf merge.

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• A minor speed up to bcftools merge.

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