{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":115191883,"defaultBranch":"main","name":"CoverM","ownerLogin":"wwood","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2017-12-23T11:43:13.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/15348?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1726606797.0","currentOid":""},"activityList":{"items":[{"before":"0a19d7a261e68ed86b04919a391838a2e49890b6","after":"2cf3baa5a412672a86ffed1f541c9f22196d0fe2","ref":"refs/heads/strobealign-aemb","pushedAt":"2024-09-17T21:09:43.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"contig: strobealign-aemb: Initial efforts.","shortMessageHtmlLink":"contig: strobealign-aemb: Initial efforts."}},{"before":null,"after":"0a19d7a261e68ed86b04919a391838a2e49890b6","ref":"refs/heads/strobealign-aemb","pushedAt":"2024-09-17T20:59:57.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"contig: strobealign-aemb: Initial efforts.","shortMessageHtmlLink":"contig: strobealign-aemb: Initial efforts."}},{"before":"2f775baccea87b3b3dd26bde7db3b15a583ba129","after":"35e21af57b6acbeadb827929ecd58b76ddcfebc0","ref":"refs/heads/main","pushedAt":"2024-09-17T08:23:48.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"actions: osx: Skip strobealign.","shortMessageHtmlLink":"actions: osx: Skip strobealign."}},{"before":"35e21af57b6acbeadb827929ecd58b76ddcfebc0","after":null,"ref":"refs/heads/actions_fixing2","pushedAt":"2024-09-17T08:23:34.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"}},{"before":"a1f7fea4170e756e5c87cfdec6ba5392551364ee","after":"35e21af57b6acbeadb827929ecd58b76ddcfebc0","ref":"refs/heads/actions_fixing2","pushedAt":"2024-09-17T06:31:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"actions: osx: Skip strobealign.","shortMessageHtmlLink":"actions: osx: Skip strobealign."}},{"before":"57037eb636105f51f67e63cca2e52b3a2f87fc98","after":"a1f7fea4170e756e5c87cfdec6ba5392551364ee","ref":"refs/heads/actions_fixing2","pushedAt":"2024-09-17T06:28:05.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"cargo.toml: Update deps.","shortMessageHtmlLink":"cargo.toml: Update deps."}},{"before":"f62adf7e1990eed2815349592a11105b583226d6","after":"57037eb636105f51f67e63cca2e52b3a2f87fc98","ref":"refs/heads/actions_fixing2","pushedAt":"2024-09-17T06:23:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"tests: test_cmdline: Use minimap2 as standard for osx action.","shortMessageHtmlLink":"tests: test_cmdline: Use minimap2 as standard for osx action."}},{"before":null,"after":"f62adf7e1990eed2815349592a11105b583226d6","ref":"refs/heads/actions_fixing2","pushedAt":"2024-09-17T05:50:07.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"actions: osx: Install less.","shortMessageHtmlLink":"actions: osx: Install less."}},{"before":null,"after":"dc11996ff9dcaed2b0c5953d820dc3db3b1d3f59","ref":"refs/heads/mapq2","pushedAt":"2024-09-17T05:37:36.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"mapq filtering: Implement it.\n\nFixes #219.\n\nSuggested by: @SDmetagenomics.","shortMessageHtmlLink":"mapq filtering: Implement it."}},{"before":"c1e225f5121d7b81fd4fce732b8177b552d92bb3","after":"9cf7a008dc8ac1bdbe341f575bf16c3e524de1cb","ref":"refs/heads/mapq","pushedAt":"2024-09-17T05:34:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"mapq filtering: Implement it.\n\nFixes #219.\n\nSuggested by: @SDmetagenomics.","shortMessageHtmlLink":"mapq filtering: Implement it."}},{"before":null,"after":"c1e225f5121d7b81fd4fce732b8177b552d92bb3","ref":"refs/heads/mapq","pushedAt":"2024-09-16T22:43:22.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"filter: Towards MAPQ filtering.","shortMessageHtmlLink":"filter: Towards MAPQ filtering."}},{"before":"f79a354f3a227362f58ea28699ce374fc26d8206","after":"2f775baccea87b3b3dd26bde7db3b15a583ba129","ref":"refs/heads/main","pushedAt":"2024-07-08T06:31:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"docs: Say that supplied --reference can be gzip.\n\nSuggested by: @jvollme\n\nCloses #218","shortMessageHtmlLink":"docs: Say that supplied --reference can be gzip."}},{"before":"42826ef3578f55fb3143e1197f319a92052b2def","after":null,"ref":"refs/heads/fix-mapping-help","pushedAt":"2024-06-12T05:55:08.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"}},{"before":"c0eb05ffaab21486ede946ef5a4941b4947b7529","after":"f79a354f3a227362f58ea28699ce374fc26d8206","ref":"refs/heads/main","pushedAt":"2024-06-12T05:55:02.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"add strobealign to mappers in help (#214)\n\n* add strobealign to mappers in help\r\n\r\n* change default mapper to strobealign\r\n\r\n* fix tests\r\n\r\n* change env file path\r\n\r\n* change env file path again\r\n\r\n* switch back to mamba\r\n\r\n* readd checkout step\r\n\r\n* fix macosx test workflow\r\n\r\n* extra options needed?\r\n\r\n* revert previous commit\r\n\r\n* use bash -el shell for test\r\n\r\n* fix macosx runs too\r\n\r\n* trim carriage return (\\r) from contig names\r\nseems to happen with strobealign for some reason\r\n\r\n* trim carriage return (\\r) in print_sparse_cached_coverage_taker too","shortMessageHtmlLink":"add strobealign to mappers in help (#214)"}},{"before":"a80d4ebb06249f465b8ee338443075fe69dfbb29","after":"42826ef3578f55fb3143e1197f319a92052b2def","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-06-11T05:44:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"trim carriage return (\\r) in print_sparse_cached_coverage_taker too","shortMessageHtmlLink":"trim carriage return (\\r) in print_sparse_cached_coverage_taker too"}},{"before":"411f5b254d0729fd7e9dce6b00844337b97ff773","after":"a80d4ebb06249f465b8ee338443075fe69dfbb29","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-06-11T00:14:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"trim carriage return (\\r) from contig names\nseems to happen with strobealign for some reason","shortMessageHtmlLink":"trim carriage return (\\r) from contig names"}},{"before":"acd9f6d3410d541935d88fa0c2466896415802be","after":"411f5b254d0729fd7e9dce6b00844337b97ff773","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-06-02T23:54:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"fix macosx runs too","shortMessageHtmlLink":"fix macosx runs too"}},{"before":"b2a8cd34a873f81b2d96a668bcea8b013f0838b7","after":"acd9f6d3410d541935d88fa0c2466896415802be","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-06-02T23:41:37.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"use bash -el shell for test","shortMessageHtmlLink":"use bash -el shell for test"}},{"before":"56022d82f2c272b98a80d36c238a3609e96ca9b6","after":"b2a8cd34a873f81b2d96a668bcea8b013f0838b7","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-06-02T23:25:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"extra options needed?","shortMessageHtmlLink":"extra options needed?"}},{"before":"c8971741df909929337d484409cfcdb755c5c9af","after":"56022d82f2c272b98a80d36c238a3609e96ca9b6","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-05-31T04:39:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"fix macosx test workflow","shortMessageHtmlLink":"fix macosx test workflow"}},{"before":"3a8990e31ba3dbcb329f859e2b5c4e1fd42d52ac","after":"c8971741df909929337d484409cfcdb755c5c9af","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-05-31T04:23:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"readd checkout step","shortMessageHtmlLink":"readd checkout step"}},{"before":"334e9a80d05b9f3ec3c9d5a60b2deb0eaa2b185c","after":"3a8990e31ba3dbcb329f859e2b5c4e1fd42d52ac","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-05-31T04:12:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"switch back to mamba","shortMessageHtmlLink":"switch back to mamba"}},{"before":"3ab9af7ce81f9a7a0a56f1c1387087cfa38c2343","after":"334e9a80d05b9f3ec3c9d5a60b2deb0eaa2b185c","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-05-31T04:08:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"change env file path again","shortMessageHtmlLink":"change env file path again"}},{"before":"f6d57fec493cc90c05c744b0913d069d372a19ef","after":"3ab9af7ce81f9a7a0a56f1c1387087cfa38c2343","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-05-31T04:07:58.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"change env file path","shortMessageHtmlLink":"change env file path"}},{"before":"7dae171d6af4a0345acc69a27333071848d9cdc8","after":"f6d57fec493cc90c05c744b0913d069d372a19ef","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-05-31T03:44:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"change default mapper to strobealign","shortMessageHtmlLink":"change default mapper to strobealign"}},{"before":null,"after":"7dae171d6af4a0345acc69a27333071848d9cdc8","ref":"refs/heads/fix-mapping-help","pushedAt":"2024-05-31T03:20:04.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"AroneyS","name":"Samuel Aroney","path":"/AroneyS","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/41124903?s=80&v=4"},"commit":{"message":"add strobealign to mappers in help","shortMessageHtmlLink":"add strobealign to mappers in help"}},{"before":"b2829fb32c01248ce4673e9cc7e027a785fba9d3","after":"4b2093c73307faf8d3bedc8a8045aef25e485230","ref":"refs/heads/actions_fixing","pushedAt":"2024-05-23T06:29:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"actions","shortMessageHtmlLink":"actions"}},{"before":"aeadc5c8b3cf3ba8ff8b14266d069d36edc7b92b","after":"b2829fb32c01248ce4673e9cc7e027a785fba9d3","ref":"refs/heads/actions_fixing","pushedAt":"2024-05-23T06:27:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"actions","shortMessageHtmlLink":"actions"}},{"before":"43863923285d2e6bc8a0339572f0f3e6642ae745","after":"aeadc5c8b3cf3ba8ff8b14266d069d36edc7b92b","ref":"refs/heads/actions_fixing","pushedAt":"2024-05-23T06:27:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"actions","shortMessageHtmlLink":"actions"}},{"before":null,"after":"43863923285d2e6bc8a0339572f0f3e6642ae745","ref":"refs/heads/actions_fixing","pushedAt":"2024-05-23T06:22:53.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"wwood","name":"Ben J Woodcroft","path":"/wwood","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/15348?s=80&v=4"},"commit":{"message":"actions: Attempt to fix env file path.","shortMessageHtmlLink":"actions: Attempt to fix env file path."}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEuP4PmQA","startCursor":null,"endCursor":null}},"title":"Activity ยท wwood/CoverM"}