{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":472945373,"defaultBranch":"master","name":"vcfdist","ownerLogin":"TimD1","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-03-22T21:37:01.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/13918078?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1715200269.0","currentOid":""},"activityList":{"items":[{"before":"25e6d7e999337c74bd38e047e42d731130bfbfcd","after":"92db7b547a8ebbfacaa87f29896045bcdac2410b","ref":"refs/heads/master","pushedAt":"2024-05-08T20:28:54.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"version bump (v2.5.2)","shortMessageHtmlLink":"version bump (v2.5.2)"}},{"before":"ec324c6e0745ee8b7a7a0ae9c2a1f41e7019a397","after":"b9e95aff1067d5859904dcbbee6f108de3d962f9","ref":"refs/heads/dev","pushedAt":"2024-04-05T17:56:51.000Z","pushType":"push","commitsCount":7,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Variant information is merged across haplotypes\n\n - this occurs after clustering but before superclustering\n - this will allow graph generation, with genotype information\n - introduced add_callset_vars()\n - added variantData->nc, moved ctg_variants to callset_vars","shortMessageHtmlLink":"Variant information is merged across haplotypes"}},{"before":"c641bee5cc82f56525cbad559fd83ac14ee08f08","after":"25e6d7e999337c74bd38e047e42d731130bfbfcd","ref":"refs/heads/master","pushedAt":"2024-03-25T16:20:03.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"version bump (v2.5.1)","shortMessageHtmlLink":"version bump (v2.5.1)"}},{"before":"c641bee5cc82f56525cbad559fd83ac14ee08f08","after":"ec324c6e0745ee8b7a7a0ae9c2a1f41e7019a397","ref":"refs/heads/dev","pushedAt":"2024-03-22T14:30:26.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Ignoring JSON.","shortMessageHtmlLink":"Ignoring JSON."}},{"before":"a9a8be1463d7bf85ff39fbce4d8b7c173c1e2820","after":"c641bee5cc82f56525cbad559fd83ac14ee08f08","ref":"refs/heads/dev","pushedAt":"2024-03-11T19:49:06.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"version bump (v2.5.0)","shortMessageHtmlLink":"version bump (v2.5.0)"}},{"before":"35dd9a3075933308fde3eb1d92a30b5beef8a522","after":"c641bee5cc82f56525cbad559fd83ac14ee08f08","ref":"refs/heads/master","pushedAt":"2024-03-11T19:48:41.000Z","pushType":"push","commitsCount":16,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"version bump (v2.5.0)","shortMessageHtmlLink":"version bump (v2.5.0)"}},{"before":"06696f630c91b97141f0b4be14cdce97057256d1","after":"a9a8be1463d7bf85ff39fbce4d8b7c173c1e2820","ref":"refs/heads/dev","pushedAt":"2024-03-11T13:33:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Removed `-s, --smallest-variant` option\n\n - There's no real reason to ever use this; people would be better off\n modifying the `--sv_threshold` to focus on variants of interest\n - setting this value will impact measured performance (prob unexpectedly)","shortMessageHtmlLink":"Removed -s, --smallest-variant option"}},{"before":"c27e47bd07e82b7cebbc1112eb835cb6a1c50cae","after":"06696f630c91b97141f0b4be14cdce97057256d1","ref":"refs/heads/dev","pushedAt":"2024-02-23T18:40:34.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Fixed (all?) bugs with new sync points\n\n - Valgrind finds no memory errors now\n - Fixed bug with new TP maximization, involving using `ref_query_ptrs`\n instead of `query_ref_ptrs` for calculating `is_tp`.\n - Removed complex logic for truth and query variant skipping when doing\n backwards parsing in `calc_prec_recall`, no longer needed!","shortMessageHtmlLink":"Fixed (all?) bugs with new sync points"}},{"before":"fdf650d6c7db97de3999b9b38528d46b6330ad48","after":"c27e47bd07e82b7cebbc1112eb835cb6a1c50cae","ref":"refs/heads/dev","pushedAt":"2024-02-19T22:16:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Fix old_ed vs ref_ed naming.","shortMessageHtmlLink":"Fix old_ed vs ref_ed naming."}},{"before":"c16c4784882bd01833c43e61d37c8ac254499cb4","after":"fdf650d6c7db97de3999b9b38528d46b6330ad48","ref":"refs/heads/dev","pushedAt":"2024-02-19T22:11:31.000Z","pushType":"push","commitsCount":53,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Merge several months of updates.","shortMessageHtmlLink":"Merge several months of updates."}},{"before":"0e19b4e954ce0f0c02b4fc911b88dcf0b73322a9","after":"35dd9a3075933308fde3eb1d92a30b5beef8a522","ref":"refs/heads/master","pushedAt":"2024-02-19T21:49:49.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Updated phab analysis.","shortMessageHtmlLink":"Updated phab analysis."}},{"before":"049320821aebe5494454e58e48e3ded464853c96","after":"0e19b4e954ce0f0c02b4fc911b88dcf0b73322a9","ref":"refs/heads/master","pushedAt":"2024-02-19T02:07:11.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Merge branch 'master' of github.com:TimD1/vcfdist","shortMessageHtmlLink":"Merge branch 'master' of github.com:TimD1/vcfdist"}},{"before":"ab1aa6ce826adad484b3248be816ab3d4c7bcddd","after":"049320821aebe5494454e58e48e3ded464853c96","ref":"refs/heads/master","pushedAt":"2024-02-18T20:46:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Update README.md\n\nvcfdist has been added to bioconda","shortMessageHtmlLink":"Update README.md"}},{"before":"b29d65584735fba226815f6c964e212cc3da724a","after":"ab1aa6ce826adad484b3248be816ab3d4c7bcddd","ref":"refs/heads/master","pushedAt":"2024-02-17T14:59:50.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"version bump (v2.4.0)","shortMessageHtmlLink":"version bump (v2.4.0)"}},{"before":"199f0cac5b2e4bebaebf4714074f9e2cb076fae4","after":"b29d65584735fba226815f6c964e212cc3da724a","ref":"refs/heads/master","pushedAt":"2024-02-15T16:32:29.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"version bump (v2.3.4)","shortMessageHtmlLink":"version bump (v2.3.4)"}},{"before":"aaecae99c2b1e38bd6ea6de6a67775684d5a4cb2","after":"199f0cac5b2e4bebaebf4714074f9e2cb076fae4","ref":"refs/heads/master","pushedAt":"2024-02-10T20:26:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Updated README.","shortMessageHtmlLink":"Updated README."}},{"before":"ebec11dd09f919e0b89296acaef0f04816971827","after":"aaecae99c2b1e38bd6ea6de6a67775684d5a4cb2","ref":"refs/heads/master","pushedAt":"2024-02-10T19:40:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Added docs/ for cached wiki.","shortMessageHtmlLink":"Added docs/ for cached wiki."}},{"before":"df4c9726b9e7dcd583db5f533a4a6c75d0b5efce","after":"ebec11dd09f919e0b89296acaef0f04816971827","ref":"refs/heads/master","pushedAt":"2024-02-10T19:28:17.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Reorganized project structure.\n\n - pushed old pipeline and data into analysis directory","shortMessageHtmlLink":"Reorganized project structure."}},{"before":"9838e17b053e27573b6b0d3cfb852cfc47ba899c","after":"df4c9726b9e7dcd583db5f533a4a6c75d0b5efce","ref":"refs/heads/master","pushedAt":"2024-02-09T16:03:56.000Z","pushType":"push","commitsCount":12,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"version bump (v2.3.3)","shortMessageHtmlLink":"version bump (v2.3.3)"}},{"before":"f7affd8f1d7c5c6393e5fc14dc1feb1a12aa7f20","after":"9838e17b053e27573b6b0d3cfb852cfc47ba899c","ref":"refs/heads/master","pushedAt":"2024-02-05T15:45:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Update output.txt","shortMessageHtmlLink":"Update output.txt"}},{"before":"078dff969d816769f51320199997eb7b51b06107","after":"f7affd8f1d7c5c6393e5fc14dc1feb1a12aa7f20","ref":"refs/heads/master","pushedAt":"2024-02-05T15:40:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Update README.md\n\nAdded new citation.","shortMessageHtmlLink":"Update README.md"}},{"before":"9c4ba310a2b027519f6a1376597825864daed7a0","after":"078dff969d816769f51320199997eb7b51b06107","ref":"refs/heads/master","pushedAt":"2024-02-02T21:55:54.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Fixed segfault when no variants are present.","shortMessageHtmlLink":"Fixed segfault when no variants are present."}},{"before":"6b4f3bc54dfd90556523895849274126f8a939fe","after":"9c4ba310a2b027519f6a1376597825864daed7a0","ref":"refs/heads/master","pushedAt":"2024-01-30T16:42:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Small updates to Makefile and README\n\n - lstdc++fs linking depends on GCC/LLVM versions (linking is still\n required even though it's in the standard C++17 library for old\n versions)\n - added `make install` command, placing vcfdist in INSTALLDIR\n (/usr/local/bin)\n - updated README\n - updated demo (THRESHOLD column, ../src/vcfdist -> vcfdist)","shortMessageHtmlLink":"Small updates to Makefile and README"}},{"before":"5cb2532ac2bbd82440aabffcf74e4535dba75ef6","after":"6b4f3bc54dfd90556523895849274126f8a939fe","ref":"refs/heads/master","pushedAt":"2024-01-29T20:56:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Minor updates to precision-recall summary printing\n\n - fixes #15, precision-recall-summary.tsv formatting tab bug\n - add \"THRESHOLD\" column to explain duplicate results (BEST/NONE)","shortMessageHtmlLink":"Minor updates to precision-recall summary printing"}},{"before":"573b0a26a36327714e8eb9d381f5128592d1ae48","after":"c16c4784882bd01833c43e61d37c8ac254499cb4","ref":"refs/heads/dev","pushedAt":"2024-01-29T20:56:34.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Added debug printing in case of error","shortMessageHtmlLink":"Added debug printing in case of error"}},{"before":"62b77a34f93606c406b0703951ec92b7305457f5","after":"5cb2532ac2bbd82440aabffcf74e4535dba75ef6","ref":"refs/heads/master","pushedAt":"2024-01-18T21:40:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Update docs.","shortMessageHtmlLink":"Update docs."}},{"before":"4c1890d5c275c1778931221dd530d688b5303097","after":"62b77a34f93606c406b0703951ec92b7305457f5","ref":"refs/heads/master","pushedAt":"2024-01-18T21:38:52.000Z","pushType":"push","commitsCount":22,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"version bump (v2.3.2)","shortMessageHtmlLink":"version bump (v2.3.2)"}},{"before":"95366e536e240723439123c69609952ec9d18244","after":"4c1890d5c275c1778931221dd530d688b5303097","ref":"refs/heads/master","pushedAt":"2024-01-18T20:30:57.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Merge pull request #14 from allyssonallan/patch-1\n\nexcluding lstdc++fs","shortMessageHtmlLink":"Merge pull request #14 from allyssonallan/patch-1"}},{"before":"6102090e668a52f7a7badfac96e98aad8d5bff0e","after":"95366e536e240723439123c69609952ec9d18244","ref":"refs/heads/master","pushedAt":"2023-12-10T17:47:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Updated citation.","shortMessageHtmlLink":"Updated citation."}},{"before":"6102090e668a52f7a7badfac96e98aad8d5bff0e","after":"573b0a26a36327714e8eb9d381f5128592d1ae48","ref":"refs/heads/dev","pushedAt":"2023-11-29T22:24:51.000Z","pushType":"push","commitsCount":13,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Work in progress: major backtracking updates\n\ngenerate_ptrs_strs()\n - +1 base to string end\n - +1 to INS pointers positions\n - added PTR_DEL_NXT, PTR_INS_LOC\n\nget_prec_recall_path_sync()\n - entirely removed dependency on ref_loc_sync; this loosens the\n restriction to allow sync points within complex variants when there\n is more than one possible path, as long as it happens on the diagonal\n - prohibit syncs at ref locations with INSs\n\ncalc_prec_recall()\n - work in progress, still has major bugs\n - edits/sync are now fenceposts to bases\n - added ref_truth_ptrs, will probably delete later\n - added next_i, may also delete\n - moved other WARNings to before edit dist is reset when shouldn't be\n zero\n - prev_i now precedes i","shortMessageHtmlLink":"Work in progress: major backtracking updates"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAERQRd8QA","startCursor":null,"endCursor":null}},"title":"Activity ยท TimD1/vcfdist"}