{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":11368595,"defaultBranch":"develop","name":"bcftools","ownerLogin":"samtools","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2013-07-12T12:55:22.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/1518450?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1713535356.0","currentOid":""},"activityList":{"items":[{"before":"f313599887a647df4b35b0799cb154c050c722c4","after":"3dd8429a6d50edd0563a80fbd4401b9697fc25be","ref":"refs/heads/develop","pushedAt":"2024-06-05T15:14:48.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Merge branch 'develop' of github.com:samtools/bcftools into develop","shortMessageHtmlLink":"Merge branch 'develop' of github.com:samtools/bcftools into develop"}},{"before":"e5687163acc091fb9803d005a4842d161a8736b1","after":"f313599887a647df4b35b0799cb154c050c722c4","ref":"refs/heads/develop","pushedAt":"2024-06-03T11:19:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Percent-encode characters with special meaning\n\nwhen adding Type=String annotations from a tab-delimited file.\n\nINFO\n    ; .. %3B\n    = .. %3D\nFORMAT\n    : .. %3A\n\nResolves #2202","shortMessageHtmlLink":"Percent-encode characters with special meaning"}},{"before":"5aa522b76988b0c4e954bf1d4e6b9691256bc67a","after":"e5687163acc091fb9803d005a4842d161a8736b1","ref":"refs/heads/develop","pushedAt":"2024-05-31T12:37:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Update documentation on -A, --count-orphans option","shortMessageHtmlLink":"Update documentation on -A, --count-orphans option"}},{"before":"5d48dbc3188fb0d182218bd7f17f6b1cf22c37c1","after":"5aa522b76988b0c4e954bf1d4e6b9691256bc67a","ref":"refs/heads/develop","pushedAt":"2024-05-31T12:12:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Add the `-i/-e` filtering options to select records for normalization.\n\nNote duplicate removal ignores this option.\n\nAlso in this commit the filtering expression ILEN changed so that it can\nbe positive (insertion), negative (deletion), zero (balanced substitutions),\nor set to missing value (symbolic alleles). Previously substitutions would\nbe set to missing value and symbolic alleles would be processed as simple\nstrings","shortMessageHtmlLink":"Add the <code>-i/-e</code> filtering options to select records for normalization."}},{"before":"30c64434edd753850d273e40580b9722f6023b00","after":"061112dca3b732a229a9ad6182d205b18df4459e","ref":"refs/heads/gh-pages","pushedAt":"2024-05-31T08:37:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Add FAQ item: XYZ not defined in the header","shortMessageHtmlLink":"Add FAQ item: XYZ not defined in the header"}},{"before":"bc37b8b2a662dbac5ae7b6e22b5d34a133f7fd79","after":"5d48dbc3188fb0d182218bd7f17f6b1cf22c37c1","ref":"refs/heads/develop","pushedAt":"2024-05-29T09:33:44.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Fix typos","shortMessageHtmlLink":"Fix typos"}},{"before":"310a6097298cb48ac8ac7902debe2785c6f386c7","after":"30c64434edd753850d273e40580b9722f6023b00","ref":"refs/heads/gh-pages","pushedAt":"2024-05-29T09:30:51.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Misc","shortMessageHtmlLink":"Misc"}},{"before":"62142f3d939aa40ce81ad19fdad0e29480a5a29d","after":"bc37b8b2a662dbac5ae7b6e22b5d34a133f7fd79","ref":"refs/heads/develop","pushedAt":"2024-05-29T09:29:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Remove an overly strict sanity check\n\nIf VCF variant goes beyond the fasta reference sequence, simply\ndon't apply it, rather than exiting with an error\n\nFixes #2191","shortMessageHtmlLink":"Remove an overly strict sanity check"}},{"before":"81c2643888bb29462faa5549a130de2d026001e6","after":"62142f3d939aa40ce81ad19fdad0e29480a5a29d","ref":"refs/heads/develop","pushedAt":"2024-05-27T09:48:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Support multiple semicolon-separated strings when filtering by ID\n\nPreviously the following expressions\n\n    ID=\"@testid\"\n    ID=\"rs123\"\n    ID!=\"rs123\"\n\nwould not match the ID string \"rs123;rs456\" as expected.\n\nResolves #2190","shortMessageHtmlLink":"Support multiple semicolon-separated strings when filtering by ID"}},{"before":"0452ef2138b7e3ef05b77deefe71f878e95eabcd","after":"81c2643888bb29462faa5549a130de2d026001e6","ref":"refs/heads/develop","pushedAt":"2024-05-24T16:33:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Update test for 379e1b6","shortMessageHtmlLink":"Update test for <a class=\"commit-link\" data-hovercard-type=\"commit\" data-hovercard-url=\"https://github.com/samtools/bcftools/commit/379e1b6f66721e3f39e80c6c408d806f59befaf4/hovercard\" href=\"https://github.com/samtools/bcftools/commit/379e1b6f66721e3f39e80c6c408d806f59befaf4\"><tt>379e1b6</tt></a>"}},{"before":"379e1b6f66721e3f39e80c6c408d806f59befaf4","after":"0452ef2138b7e3ef05b77deefe71f878e95eabcd","ref":"refs/heads/develop","pushedAt":"2024-05-24T16:29:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Add `-S, --sort` switch to optionally sort output records by allele\n\nResolves #1484","shortMessageHtmlLink":"Add <code>-S, --sort</code> switch to optionally sort output records by allele"}},{"before":"de86675cdfa30f334d78d7c937dd28ef260e0fcc","after":"379e1b6f66721e3f39e80c6c408d806f59befaf4","ref":"refs/heads/develop","pushedAt":"2024-05-24T14:32:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Extend file format description","shortMessageHtmlLink":"Extend file format description"}},{"before":"57b90721e0abc45de861361f3f175ae0edd1e715","after":"de86675cdfa30f334d78d7c937dd28ef260e0fcc","ref":"refs/heads/develop","pushedAt":"2024-05-24T13:22:18.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Add FORMAT/AD annotation by default, disable with `-a -AD`","shortMessageHtmlLink":"Add FORMAT/AD annotation by default, disable with <code>-a -AD</code>"}},{"before":"4ad2efd995a5528dd056b48128297576ab9cbd43","after":"57b90721e0abc45de861361f3f175ae0edd1e715","ref":"refs/heads/develop","pushedAt":"2024-05-24T07:18:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Propagate bam_mplp_auto() error code, throw an error on truncated bam/cram files","shortMessageHtmlLink":"Propagate bam_mplp_auto() error code, throw an error on truncated bam…"}},{"before":"6d53540567e0241ebb53c723e1352c71d571ca46","after":"4ad2efd995a5528dd056b48128297576ab9cbd43","ref":"refs/heads/develop","pushedAt":"2024-05-21T09:25:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"[MINOR] Print correct index in the header","shortMessageHtmlLink":"[MINOR] Print correct index in the header"}},{"before":"5d61fceb204ba8ec5127548bf5277412945fa18d","after":"6d53540567e0241ebb53c723e1352c71d571ca46","ref":"refs/heads/develop","pushedAt":"2024-05-15T14:45:48.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Better support of duplicate removal of symbolic alleles\n\nFor example, these variants should not be removed with `-d exact`\n\n    POS=1 ALT=<DEL> SVLEN=-1000\n    POS=1 ALT=<DEL> SVLEN=-2000\n    POS=1 ALT=<DEL> SVLEN=-3000\n\nResolves #2182","shortMessageHtmlLink":"Better support of duplicate removal of symbolic alleles"}},{"before":"cf150c96eda3e3b2063f72679cfe371c1eadda76","after":"310a6097298cb48ac8ac7902debe2785c6f386c7","ref":"refs/heads/gh-pages","pushedAt":"2024-05-15T13:41:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Add +setGT documentation","shortMessageHtmlLink":"Add +setGT documentation"}},{"before":"18439d1d0b847ca55c01d062bf9912404924c37f","after":"5d61fceb204ba8ec5127548bf5277412945fa18d","ref":"refs/heads/develop","pushedAt":"2024-05-15T13:17:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Fix a segfault with --no-HWE-prob\n\nThe bug was introduced with the output format change in 1.19\nwhich replaced the DC section with DCv2\nhttps://github.com/samtools/bcftools/commit/983e610ab\n\nFixes #2180","shortMessageHtmlLink":"Fix a segfault with --no-HWE-prob"}},{"before":"f3d1ca39a1720cade434b2ef186c9b2dcf1914e5","after":"18439d1d0b847ca55c01d062bf9912404924c37f","ref":"refs/heads/develop","pushedAt":"2024-05-05T17:58:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Allow combining genotypes with different ploidy\n\nThe command `bcftools norm -m+` will not work when the merged\ngenotypes have different ploidy. This commit attempts to fix that,\nbut note that it is experimental and I am having doubts if it should\nbe supported at all, given it may interfere with partially missing\ngenotypes produces by atomization\n\nResolves #1962","shortMessageHtmlLink":"Allow combining genotypes with different ploidy"}},{"before":"206c80ebe9239926e3b5207ec24fae9001c9514c","after":"f3d1ca39a1720cade434b2ef186c9b2dcf1914e5","ref":"refs/heads/develop","pushedAt":"2024-05-04T13:56:14.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Work around ubuntu's latest clang compiler missing address sanitizer\n\nWe move this to gcc instead.","shortMessageHtmlLink":"Work around ubuntu's latest clang compiler missing address sanitizer"}},{"before":"4bd57e53a9e46bc34e47e6459a0af4871de0b451","after":"206c80ebe9239926e3b5207ec24fae9001c9514c","ref":"refs/heads/develop","pushedAt":"2024-05-04T13:55:52.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Add mpileup_bench/run_multi.sh for multi-sample evaluations\n\nThis doesn't change the test harness at all.  It's simply extra\ndocumentation and scripts to aid with large scale evaluation of\nmpileup changes.","shortMessageHtmlLink":"Add mpileup_bench/run_multi.sh for multi-sample evaluations"}},{"before":"4ff13623b3e4733a918daad2bfad3980a6738670","after":"4bd57e53a9e46bc34e47e6459a0af4871de0b451","ref":"refs/heads/develop","pushedAt":"2024-04-30T07:58:06.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Merge branch 'develop' of github.com:samtools/bcftools into develop","shortMessageHtmlLink":"Merge branch 'develop' of github.com:samtools/bcftools into develop"}},{"before":"5977f1f3c42ff444f2cd292bdd595f62010816b6","after":"4ff13623b3e4733a918daad2bfad3980a6738670","ref":"refs/heads/develop","pushedAt":"2024-04-29T14:32:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Add `norm --verbose` option and update documentation","shortMessageHtmlLink":"Add <code>norm --verbose</code> option and update documentation"}},{"before":"bdff51c2bffa67cba8ca180b217e231399e82d55","after":"cf150c96eda3e3b2063f72679cfe371c1eadda76","ref":"refs/heads/gh-pages","pushedAt":"2024-04-29T07:12:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Update man page","shortMessageHtmlLink":"Update man page"}},{"before":"89c4b7b92ab561ae1e9b0caf4853891f36743394","after":"5977f1f3c42ff444f2cd292bdd595f62010816b6","ref":"refs/heads/develop","pushedAt":"2024-04-27T17:53:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Fix in reporting reference allele genotypes with `--multi-overlaps .`\n\nResolves #2160","shortMessageHtmlLink":"Fix in reporting reference allele genotypes with <code>--multi-overlaps .</code>"}},{"before":"2ed881cbe1948a385cfe01cec2c74e99bdb6c6dc","after":"bdff51c2bffa67cba8ca180b217e231399e82d55","ref":"refs/heads/gh-pages","pushedAt":"2024-04-27T15:51:18.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Clarify documentation","shortMessageHtmlLink":"Clarify documentation"}},{"before":"abf8f73d1ef435bf722349ea8037e159a9a75ce5","after":"89c4b7b92ab561ae1e9b0caf4853891f36743394","ref":"refs/heads/develop","pushedAt":"2024-04-27T15:22:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Document the VariantKey %VKX format,\n\nsee https://github.com/tecnickcom/variantkey\n\nResolves #2157","shortMessageHtmlLink":"Document the VariantKey %VKX format,"}},{"before":"4ae52d9c62f927a6bef18f2434a83c7635163c7a","after":"abf8f73d1ef435bf722349ea8037e159a9a75ce5","ref":"refs/heads/develop","pushedAt":"2024-04-27T10:49:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Write to tbi rather than csi with -m 0\n\nResolves #2153","shortMessageHtmlLink":"Write to tbi rather than csi with -m 0"}},{"before":"ad818b1544a567dc3d923e039ce8b4d700f0f51a","after":"4ae52d9c62f927a6bef18f2434a83c7635163c7a","ref":"refs/heads/develop","pushedAt":"2024-04-27T10:25:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Support realignment of symbolic <DUP.*> alleles,\n\nsimilarly to symbolic <DEL.*> alleles added previously (7040c10)\n\nResolves #2145","shortMessageHtmlLink":"Support realignment of symbolic &lt;DUP.*&gt; alleles,"}},{"before":"a4e70017dee87607c5b310752131c2731e355baa","after":"ad818b1544a567dc3d923e039ce8b4d700f0f51a","ref":"refs/heads/develop","pushedAt":"2024-04-19T14:29:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pd3","name":"Petr Danecek","path":"/pd3","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/524074?s=80&v=4"},"commit":{"message":"Support dynamic variables read from a tab-delimited annotation file\n\nFor example, in the two cases below the field 'STR' from the -a file is required to match\nthe INFO/TAG in VCF. In the first example the alleles REF,ALT must match, in the second\nexample they are ignored. The option -k is required to output also records that were not\nannotated:\n\n    bcftools annotate -a ann.tsv.gz -c CHROM,POS,REF,ALT,SCORE,~STR -i'TAG={STR}' -k in.vcf\n    bcftools annotate -a ann.tsv.gz -c CHROM,POS,-,-,SCORE,~STR     -i'TAG={STR}' -k in.vcf\n\nResolves #2151","shortMessageHtmlLink":"Support dynamic variables read from a tab-delimited annotation file"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEXUZInAA","startCursor":null,"endCursor":null}},"title":"Activity · samtools/bcftools"}