{"push_id":1132059095,"size":3,"distinct_size":3,"ref":"refs/heads/feature/mpileup","head":"e5bcf7a446d149971ad31e6fa319b8e63f761ef2","before":"ed62797de1c11b85a7eb4601a25afaf3d317c4ce","commits":[{"sha":"16b35ed6298b074fc201bfef20b5862a1f09c7c3","author":{"name":"Shane McCarthy","email":"da39a3ee5e6b4b0d3255bfef95601890afd80709"},"message":"remove deprecated options\n\n* remove deprecated `-g`, `-v`, `-u`, `-D`, `-V`, `-S`\n* remove `-R` short option to make way for `--regions-file` option later","distinct":true,"url":"https://api.github.com/repos/samtools/bcftools/commits/16b35ed6298b074fc201bfef20b5862a1f09c7c3"},{"sha":"ec2dca5dc5c773e404f57f520848fa0d888ecc9a","author":{"name":"Shane McCarthy","email":"da39a3ee5e6b4b0d3255bfef95601890afd80709"},"message":"mpileup: add `--gvcf` output mode\n\nThis commit brings over the `--gvcf` functionality from @pd3's branch,\nconsisting of relevant bits from pd3/bcftools@cf3219c3237dbd447bfa31be967f1605f531bfd6\nand pd3/bcftools@ee8210d2f81af007c6b2ad47d699527c50d0a58e\n\nReference only blocks will be merged into gVCF blocks when the\nminimum per-sample depth falls in the intervals defined by the\nargument to the `-gvcf` option. Documentaion added to explain\nthe merging and a test added.","distinct":true,"url":"https://api.github.com/repos/samtools/bcftools/commits/ec2dca5dc5c773e404f57f520848fa0d888ecc9a"},{"sha":"e5bcf7a446d149971ad31e6fa319b8e63f761ef2","author":{"name":"Shane McCarthy","email":"da39a3ee5e6b4b0d3255bfef95601890afd80709"},"message":"mpileup: new `-s` and `-S` options to include only selected samples\n\npulling over of pd3/bcftools@cf5c354859cf7af542ba4cb936233a5ef8d2eb88\nadding in `-S,--samples-file` option and exiting if no samples are\nread from the file or list\n\nTODO: add exclude logic with `^` prefix as in other bcftools commands\n\nremoved `config.h` from `sample.c` as leftover this is in samtools,\nbut not bcftools at the moment","distinct":true,"url":"https://api.github.com/repos/samtools/bcftools/commits/e5bcf7a446d149971ad31e6fa319b8e63f761ef2"}]}
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