{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":821442545,"defaultBranch":"master","name":"regtools","ownerLogin":"fulcrumgenomics","currentUserCanPush":false,"isFork":true,"isEmpty":false,"createdAt":"2024-06-28T14:47:52.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/13546013?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1720038925.0","currentOid":""},"activityList":{"items":[{"before":"409a49257f0523233690ef81aa0141ce12526e2e","after":"548b60efb7091478c5587016ac2b68185362e30c","ref":"refs/heads/189/td/flag-and-quality-filtering","pushedAt":"2024-09-19T18:32:25.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"feat: added per-read flag and map quality filtering\n\n - closes #183, flag based filtering\n - closes #189, mapping quality based filtering\n - option '-F' filters reads containing any of these flags\n - option '-f' filters reads not containing all these flags\n - option '-q' filters reads below this mapping quality","shortMessageHtmlLink":"feat: added per-read flag and map quality filtering"}},{"before":"1260bf9f5c42c5b863d68fd1077f188f4df9d9e4","after":"b82980e48b31d912552bc3075c5677a5061bb5d7","ref":"refs/heads/188/td/min-intron-length-init","pushedAt":"2024-09-19T18:26:32.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: min_intron_length_ initialization in JunctionsExtractor\n\n - fixes #188, min_intron_length_ was accidentally set from min_anchor_len_","shortMessageHtmlLink":"fix: min_intron_length_ initialization in JunctionsExtractor"}},{"before":"1e2c426f59604e9a6299de190ab2be586838291e","after":"1260bf9f5c42c5b863d68fd1077f188f4df9d9e4","ref":"refs/heads/188/td/min-intron-length-init","pushedAt":"2024-09-19T15:12:30.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: min_intron_length_ initialization in JunctionsExtractor\n\n - fixes #188, min_intron_length_ was accidentally set from min_anchor_len_","shortMessageHtmlLink":"fix: min_intron_length_ initialization in JunctionsExtractor"}},{"before":"4056950cd2ca9a22656c076ab4dbacd76b1d7dc8","after":"1e3080c02dfa3493293863dc136a421dc8ea6226","ref":"refs/heads/186/td/read-min-anchor-len","pushedAt":"2024-09-19T15:12:30.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"feat: added per-read anchor requirement to junction extract\n\n - closes #186, reads now only 'support' a junction if they have at least\n a given minimum anchor length, supplied with the '-A' flag (default 0)","shortMessageHtmlLink":"feat: added per-read anchor requirement to junction extract"}},{"before":"bab8723a30c59def50fa0d1220916bd8627d5eef","after":"409a49257f0523233690ef81aa0141ce12526e2e","ref":"refs/heads/189/td/flag-and-quality-filtering","pushedAt":"2024-09-19T15:12:30.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"feat: added per-read flag and map quality filtering\n\n - closes #183, flag based filtering\n - closes #189, mapping quality based filtering\n - option '-F' filters reads containing any of these flags\n - option '-f' filters reads not containing all these flags\n - option '-q' filters reads below this mapping quality","shortMessageHtmlLink":"feat: added per-read flag and map quality filtering"}},{"before":"24dd431e9eeee3b55ad6a24cd19fe11ce7c28908","after":"435e8b88b02c7e71ce70bc4c024e4191ae28428c","ref":"refs/heads/176/td/fix-mac-build","pushedAt":"2024-09-19T15:12:30.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: CMake build errors on Mac resolved\n\n - closes #176, CMake was including `src/utils/bedtools/gzstream/version`\n as a C++ source file, when it was a simple text file containing version info\n - I moved this version info into `src/utils/bedtools/gzstream/README`","shortMessageHtmlLink":"fix: CMake build errors on Mac resolved"}},{"before":"17b6cf456169ded4fad9cc4243a02981fb1cbb74","after":"c1ba2a2ebc6bdb4cd8d08b2613a9e46204f58290","ref":"refs/heads/master","pushedAt":"2024-09-19T15:12:30.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"Update index.md\n\nupdated test data description","shortMessageHtmlLink":"Update index.md"}},{"before":"2c64af197600c5953d7672476c8fd3d0326522ce","after":"9f5e456ea7176ff39b03546482cb4314459e596f","ref":"refs/heads/187/td/no-double-read-support","pushedAt":"2024-09-19T15:11:54.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: junctions extractor count overlapping read pairs once\n\n - closes #187, implemented by adding set of `reads` to `Junction`, and\n only incrementing `read_count` if read has not been seen yet\n - this commit should also increase RegTools speed by removing the barcode\n updating bottleneck caused by repeatedly copying the barcode map\n - updated regtools to v1.1.0","shortMessageHtmlLink":"fix: junctions extractor count overlapping read pairs once"}},{"before":"a59e829a4b6527279f35290d195f16065dc29a82","after":"24dd431e9eeee3b55ad6a24cd19fe11ce7c28908","ref":"refs/heads/176/td/fix-mac-build","pushedAt":"2024-09-19T14:47:57.000Z","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":"Merge branch 'griffithlab:master' into 176/td/fix-mac-build","shortMessageHtmlLink":"Merge branch 'griffithlab:master' into 176/td/fix-mac-build"}},{"before":"892f8490f0822ab5f2280f6cd1c09efa3b8dcc66","after":"4056950cd2ca9a22656c076ab4dbacd76b1d7dc8","ref":"refs/heads/186/td/read-min-anchor-len","pushedAt":"2024-09-19T14:47:43.000Z","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":"Merge branch 'griffithlab:master' into 186/td/read-min-anchor-len","shortMessageHtmlLink":"Merge branch 'griffithlab:master' into 186/td/read-min-anchor-len"}},{"before":"0e7ae9b407665105f666f19ea3667a0eb143b3b8","after":"2c64af197600c5953d7672476c8fd3d0326522ce","ref":"refs/heads/187/td/no-double-read-support","pushedAt":"2024-09-19T14:47:31.000Z","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":"Merge branch 'griffithlab:master' into 187/td/no-double-read-support","shortMessageHtmlLink":"Merge branch 'griffithlab:master' into 187/td/no-double-read-support"}},{"before":"e8d31f69253441c13b42231e241bb5063ebdfd14","after":"1e2c426f59604e9a6299de190ab2be586838291e","ref":"refs/heads/188/td/min-intron-length-init","pushedAt":"2024-09-19T14:47:20.000Z","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":"Merge branch 'griffithlab:master' into 188/td/min-intron-length-init","shortMessageHtmlLink":"Merge branch 'griffithlab:master' into 188/td/min-intron-length-init"}},{"before":"ae608f6ea1d75e57ded96cf6b89f2235172c5857","after":"bab8723a30c59def50fa0d1220916bd8627d5eef","ref":"refs/heads/189/td/flag-and-quality-filtering","pushedAt":"2024-09-19T14:47:06.000Z","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":"Merge branch 'griffithlab:master' into 189/td/flag-and-quality-filtering","shortMessageHtmlLink":"Merge branch 'griffithlab:master' into 189/td/flag-and-quality-filtering"}},{"before":"c1ba2a2ebc6bdb4cd8d08b2613a9e46204f58290","after":"17b6cf456169ded4fad9cc4243a02981fb1cbb74","ref":"refs/heads/master","pushedAt":"2024-09-19T14:46:45.000Z","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":"Update mkdocs.yml","shortMessageHtmlLink":"Update mkdocs.yml"}},{"before":"404f97634fedcb40553d76472d8f966bf90e706f","after":null,"ref":"refs/heads/186/td/anchors-and-filtering","pushedAt":"2024-07-03T20:35:25.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"}},{"before":"70fd322dad0bb474c94aaa46d29a4d792ca81d80","after":"0e7ae9b407665105f666f19ea3667a0eb143b3b8","ref":"refs/heads/187/td/no-double-read-support","pushedAt":"2024-07-03T20:34:57.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: junctions extractor count overlapping read pairs once\n\n - closes #187, implemented by adding set of `reads` to `Junction`, and\n only incrementing `read_count` if read has not been seen yet\n - this commit should also increase RegTools speed by removing the barcode\n updating bottleneck caused by repeatedly copying the barcode map\n - updated regtools to v1.1.0","shortMessageHtmlLink":"fix: junctions extractor count overlapping read pairs once"}},{"before":null,"after":"892f8490f0822ab5f2280f6cd1c09efa3b8dcc66","ref":"refs/heads/186/td/read-min-anchor-len","pushedAt":"2024-07-03T20:34:57.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"feat: added per-read anchor requirement to junction extract\n\n - closes #186, reads now only 'support' a junction if they have at least\n a given minimum anchor length, supplied with the '-A' flag (default 0)","shortMessageHtmlLink":"feat: added per-read anchor requirement to junction extract"}},{"before":null,"after":"ae608f6ea1d75e57ded96cf6b89f2235172c5857","ref":"refs/heads/189/td/flag-and-quality-filtering","pushedAt":"2024-07-03T20:34:57.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"feat: added per-read flag and map quality filtering\n\n - closes #183, flag based filtering\n - closes #189, mapping quality based filtering\n - option '-F' filters reads containing any of these flags\n - option '-f' filters reads not containing all these flags\n - option '-q' filters reads below this mapping quality","shortMessageHtmlLink":"feat: added per-read flag and map quality filtering"}},{"before":"77451c4feda4b5e8bf9e58957b73a3f34b8b3036","after":"404f97634fedcb40553d76472d8f966bf90e706f","ref":"refs/heads/186/td/anchors-and-filtering","pushedAt":"2024-07-02T20:44:40.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"feat: added per-read anchor requirement to junction extract\n\n - closes #186, reads now only 'support' a junction if they have at least\n a given minimum anchor length, supplied with the '-A' flag (default 0)","shortMessageHtmlLink":"feat: added per-read anchor requirement to junction extract"}},{"before":"19644c15c6cdbf631635eb4acd494ea3d1c6f25d","after":"70fd322dad0bb474c94aaa46d29a4d792ca81d80","ref":"refs/heads/187/td/no-double-read-support","pushedAt":"2024-07-02T20:44:40.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: junctions extractor count overlapping read pairs once\n\n - closes #187, implemented by adding set of `reads` to `Junction`, and\n only incrementing `read_count` if read has not been seen yet\n - this commit should also increase RegTools speed by removing the barcode\n updating bottleneck caused by repeatedly copying the barcode map","shortMessageHtmlLink":"fix: junctions extractor count overlapping read pairs once"}},{"before":null,"after":"a59e829a4b6527279f35290d195f16065dc29a82","ref":"refs/heads/176/td/fix-mac-build","pushedAt":"2024-07-02T20:44:40.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: CMake build errors on Mac resolved\n\n - closes #176, CMake was including `src/utils/bedtools/gzstream/version`\n as a C++ source file, when it was a simple text file containing version info\n - I moved this version info into `src/utils/bedtools/gzstream/README`","shortMessageHtmlLink":"fix: CMake build errors on Mac resolved"}},{"before":"0a9373acc9fb3dc568e892231122ae744add0477","after":"e8d31f69253441c13b42231e241bb5063ebdfd14","ref":"refs/heads/188/td/min-intron-length-init","pushedAt":"2024-07-02T20:44:40.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: min_intron_length_ initialization in JunctionsExtractor\n\n - fixes #188, min_intron_length_ was accidentaly set from min_anchor_len_","shortMessageHtmlLink":"fix: min_intron_length_ initialization in JunctionsExtractor"}},{"before":"9040ecb18acf4aad4dfe826125f1840ad932c4cc","after":"77451c4feda4b5e8bf9e58957b73a3f34b8b3036","ref":"refs/heads/186/td/anchors-and-filtering","pushedAt":"2024-07-02T19:52:50.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"feat: added per-read anchor requirement to junction extract\n\n - closes #186, reads now only 'support' a junction if they have at least\n a given minimum anchor length, supplied with the '-A' flag (default 0)","shortMessageHtmlLink":"feat: added per-read anchor requirement to junction extract"}},{"before":"13a3e443aa69307e3f92bb2ed78615391c2a97b0","after":"19644c15c6cdbf631635eb4acd494ea3d1c6f25d","ref":"refs/heads/187/td/no-double-read-support","pushedAt":"2024-07-02T19:52:33.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: junctions extractor count overlapping read pairs once\n\n - closes #187, implemented by adding set of `reads` to `Junction`, and\n only incrementing `read_count` if read has not been seen yet\n - this commit should also increase RegTools speed by removing the barcode\n updating bottleneck caused by repeatedly copying the barcode map","shortMessageHtmlLink":"fix: junctions extractor count overlapping read pairs once"}},{"before":null,"after":"0a9373acc9fb3dc568e892231122ae744add0477","ref":"refs/heads/188/td/min-intron-length-init","pushedAt":"2024-07-02T19:40:04.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: min_intron_length_ initialization in JunctionsExtractor\n\n - fixes #188, min_intron_length_ was accidentaly set from min_anchor_len_","shortMessageHtmlLink":"fix: min_intron_length_ initialization in JunctionsExtractor"}},{"before":"bd7df5afbefc8441ec83f7289099398739ba3e38","after":"9040ecb18acf4aad4dfe826125f1840ad932c4cc","ref":"refs/heads/186/td/anchors-and-filtering","pushedAt":"2024-07-02T19:39:30.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"feat: added per-read anchor requirement to junction extract\n\n - closes #186, reads now only 'support' a junction if they have at least\n a given minimum anchor length, supplied with the '-A' flag (default 0)","shortMessageHtmlLink":"feat: added per-read anchor requirement to junction extract"}},{"before":"4209eb698d1e5e71fc349cb7239b53ef6dcb4a3b","after":"13a3e443aa69307e3f92bb2ed78615391c2a97b0","ref":"refs/heads/187/td/no-double-read-support","pushedAt":"2024-07-02T19:38:08.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: junctions extractor count overlapping read pairs once\n\n - closes #187, implemented by adding set of `reads` to `Junction`, and\n only incrementing `read_count` if read has not been seen yet\n - this commit should also increase RegTools speed by removing the barcode\n updating bottleneck caused by repeatedly copying the barcode map","shortMessageHtmlLink":"fix: junctions extractor count overlapping read pairs once"}},{"before":null,"after":"4209eb698d1e5e71fc349cb7239b53ef6dcb4a3b","ref":"refs/heads/187/td/no-double-read-support","pushedAt":"2024-07-01T20:55:16.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"fix: junctions extractor count overlapping read pairs once\n\n - closes #187, implemented by adding set of `reads` to `Junction`, and\n only incrementing `read_count` if read has not been seen yet\n - this commit should also increase RegTools speed by removing the barcode\n updating bottleneck caused by repeatedly copying the barcode map","shortMessageHtmlLink":"fix: junctions extractor count overlapping read pairs once"}},{"before":"fb6098d81092e17e49d5540bbbff768cd88e187f","after":"bd7df5afbefc8441ec83f7289099398739ba3e38","ref":"refs/heads/186/td/anchors-and-filtering","pushedAt":"2024-07-01T13:27:34.000Z","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":"feat: added per-read anchor requirement to junction extract\n\n - closes #186, reads now only 'support' a junction if they have at least\n a given minimum anchor length, supplied with the '-A' flag","shortMessageHtmlLink":"feat: added per-read anchor requirement to junction extract"}},{"before":null,"after":"fb6098d81092e17e49d5540bbbff768cd88e187f","ref":"refs/heads/186/td/anchors-and-filtering","pushedAt":"2024-06-28T20:46:11.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"TimD1","name":"Tim Dunn","path":"/TimD1","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13918078?s=80&v=4"},"commit":{"message":"feat: added per-read flag and map quality filtering\n\n - option '-F' filters reads containing any of these flags\n - option '-f' filters reads not containing all these flags\n - option '-q' filters reads below this mapping quality","shortMessageHtmlLink":"feat: added per-read flag and map quality filtering"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0xOVQxODozMjoyNS4wMDAwMDBazwAAAAS7M47E","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNi0yOFQyMDo0NjoxMS4wMDAwMDBazwAAAARyN2Vi"}},"title":"Activity ยท fulcrumgenomics/regtools"}