{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":280272915,"defaultBranch":"master","name":"Captus","ownerLogin":"edgardomortiz","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2020-07-16T22:37:10.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/5767612?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1709408909.0","currentOid":""},"activityList":{"items":[{"before":"cbac8bc0635c486300224c9c610ed6a30caddc19","after":"cd5bfef48319820510ca97b6eeafc16daec29f69","ref":"refs/heads/master","pushedAt":"2024-08-02T05:15:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Path to 'CLR' was not set\n\nReally old bug, when no JSON reference file the path to 'CLR' was not set and produced a key error","shortMessageHtmlLink":"Path to 'CLR' was not set"}},{"before":"959f38a39975b5308b8eda20ed613c1b304f5962","after":"cbac8bc0635c486300224c9c610ed6a30caddc19","ref":"refs/heads/master","pushedAt":"2024-04-10T13:32:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"shigita","name":"Gentaro Shigita","path":"/shigita","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40628880?s=80&v=4"},"commit":{"message":"Update docs\n\n- Fix broken link to the tutorial data","shortMessageHtmlLink":"Update docs"}},{"before":"dd6d9d556a348bd293ec3ced2f64fbbf3f61de6b","after":"959f38a39975b5308b8eda20ed613c1b304f5962","ref":"refs/heads/master","pushedAt":"2024-04-09T11:39:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"shigita","name":"Gentaro Shigita","path":"/shigita","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40628880?s=80&v=4"},"commit":{"message":"Remove tutorial data","shortMessageHtmlLink":"Remove tutorial data"}},{"before":"070d0b883407c2fc2829be5c152347cd55d86173","after":"dd6d9d556a348bd293ec3ced2f64fbbf3f61de6b","ref":"refs/heads/master","pushedAt":"2024-04-08T12:36:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"shigita","name":"Gentaro Shigita","path":"/shigita","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40628880?s=80&v=4"},"commit":{"message":"Update README.md\n\n- Add logo","shortMessageHtmlLink":"Update README.md"}},{"before":"da21567af0b6e6d690c39808f8aa1cbb96a1f79d","after":"070d0b883407c2fc2829be5c152347cd55d86173","ref":"refs/heads/master","pushedAt":"2024-03-05T21:03:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Updates to recipe\n\n- Added version restriction to pandas (>=2.1.0)","shortMessageHtmlLink":"Updates to recipe"}},{"before":"c0b66f22ef5c7a1cd49502c35af8ce94a4664e6c","after":"da21567af0b6e6d690c39808f8aa1cbb96a1f79d","ref":"refs/heads/master","pushedAt":"2024-03-02T19:38:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Latest changes before releasing v1.0.1\n\n- Added option to `align` step to ``--collect_only` the extracted markers and exit\n-","shortMessageHtmlLink":"Latest changes before releasing v1.0.1"}},{"before":"176c617393b53763b5535871e754ff739fd9ddce","after":"c0b66f22ef5c7a1cd49502c35af8ce94a4664e6c","ref":"refs/heads/master","pushedAt":"2024-02-16T23:12:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Update extract.py\n\nMark MAFFT as \"not used\" when clustering is skipped during `extract`","shortMessageHtmlLink":"Update extract.py"}},{"before":"2f83164538ec4fe81b3aaf23f8b863ee8587792f","after":"176c617393b53763b5535871e754ff739fd9ddce","ref":"refs/heads/master","pushedAt":"2024-02-14T21:13:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Fix stripping of _R_ pattern\n\nUsing lstrip() led to unwanted behavior","shortMessageHtmlLink":"Fix stripping of _R_ pattern"}},{"before":"d2638d922f7f8f2f6df030832e0aa7f31553ba32","after":"2f83164538ec4fe81b3aaf23f8b863ee8587792f","ref":"refs/heads/master","pushedAt":"2024-02-14T15:40:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Added strand correction\n\nWhen creating a new DNA reference from clustering, each sequence in a reference locus can have different strands. We add a method to uniformize the strand per reference locus.","shortMessageHtmlLink":"Added strand correction"}},{"before":"c223e16f766454c6efbc8953d75d73a61f4d67e0","after":"d2638d922f7f8f2f6df030832e0aa7f31553ba32","ref":"refs/heads/master","pushedAt":"2024-02-01T12:50:54.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"shigita","name":"Gentaro Shigita","path":"/shigita","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40628880?s=80&v=4"},"commit":{"message":"Update report.py\n\n- Support for pandas 2.2.0","shortMessageHtmlLink":"Update report.py"}},{"before":"993ca443954c11216541472f34902ab3fd7df7cd","after":"c223e16f766454c6efbc8953d75d73a61f4d67e0","ref":"refs/heads/master","pushedAt":"2024-02-01T12:41:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"shigita","name":"Gentaro Shigita","path":"/shigita","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40628880?s=80&v=4"},"commit":{"message":"Update report.py\n\n- Support for pandas 2.2.0","shortMessageHtmlLink":"Update report.py"}},{"before":"fc8725e446a6cd6f5d20fcb3b26a828e7b260bac","after":"993ca443954c11216541472f34902ab3fd7df7cd","ref":"refs/heads/master","pushedAt":"2024-02-01T11:26:58.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Improved reference translation\n\n- Improved guessing of reading frame when translating a reference\n- Increase DNA_TOLERANCE_PID to 0.0333","shortMessageHtmlLink":"Improved reference translation"}},{"before":"e83aff7484e3897938cfad0141a1e3fdc201d8bb","after":"fc8725e446a6cd6f5d20fcb3b26a828e7b260bac","ref":"refs/heads/master","pushedAt":"2024-02-01T11:06:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Revert \"Revert \"Update report.py\"\"\n\nThis reverts commit e83aff7484e3897938cfad0141a1e3fdc201d8bb.","shortMessageHtmlLink":"Revert \"Revert \"Update report.py\"\""}},{"before":"76966bdca4ce572e435f15292b6e6440c03bd1dc","after":"e83aff7484e3897938cfad0141a1e3fdc201d8bb","ref":"refs/heads/master","pushedAt":"2024-02-01T10:57:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Revert \"Update report.py\"\n\nThis reverts commit 76966bdca4ce572e435f15292b6e6440c03bd1dc.","shortMessageHtmlLink":"Revert \"Update report.py\""}},{"before":"9954adf76d0066188abcab9dae085fd5ad8fd738","after":"76966bdca4ce572e435f15292b6e6440c03bd1dc","ref":"refs/heads/master","pushedAt":"2024-01-30T16:53:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"shigita","name":"Gentaro Shigita","path":"/shigita","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/40628880?s=80&v=4"},"commit":{"message":"Update report.py\n\n- Support for pandas 2.2.0","shortMessageHtmlLink":"Update report.py"}},{"before":"39fc10d56d26d98bb28e97fedd43ad0ce4ac646f","after":"9954adf76d0066188abcab9dae085fd5ad8fd738","ref":"refs/heads/master","pushedAt":"2024-01-30T01:35:26.000Z","pushType":"push","commitsCount":315,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Merge branch 'master' of https://github.com/edgardomortiz/Captus","shortMessageHtmlLink":"Merge branch 'master' of https://github.com/edgardomortiz/Captus"}},{"before":"993ca443954c11216541472f34902ab3fd7df7cd","after":"39fc10d56d26d98bb28e97fedd43ad0ce4ac646f","ref":"refs/heads/master","pushedAt":"2024-01-30T01:32:02.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Improved reference translation\n\n- Improved guessing of reading frame when translating a reference\n- Increase DNA_TOLERANCE_PID to 0.0333\n\n\nFormer-commit-id: 993ca443954c11216541472f34902ab3fd7df7cd","shortMessageHtmlLink":"Improved reference translation"}},{"before":"d19565432e7bb2c55341dd5c9f2bc88897f5516e","after":"993ca443954c11216541472f34902ab3fd7df7cd","ref":"refs/heads/master","pushedAt":"2024-01-30T01:05:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Improved reference translation\n\n- Improved guessing of reading frame when translating a reference\n- Increase DNA_TOLERANCE_PID to 0.0333","shortMessageHtmlLink":"Improved reference translation"}},{"before":"d626d6235c6b415c4f754e59af5cf3ba82b4256d","after":"d19565432e7bb2c55341dd5c9f2bc88897f5516e","ref":"refs/heads/master","pushedAt":"2024-01-22T12:19:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Reduce delta identity\n\nReduce the difference in identity percentage to the reference between two hits in order to be compatible from 5% to 2% or 1%","shortMessageHtmlLink":"Reduce delta identity"}},{"before":"a4e85ec777628397a668e4b9d15ae7a1e45de3f6","after":"d626d6235c6b415c4f754e59af5cf3ba82b4256d","ref":"refs/heads/master","pushedAt":"2023-12-11T13:58:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Fixing small bugs, updateing to v1.0.1\n\n- If `min_data_per_column` is equal to `num_seqs` in alignment, then `clipkit_gaps` should be 1 not 0\n- Remove paralogs from different marker types even if the loci names match between types\n- Fix division by zero error in expected tiling calculation","shortMessageHtmlLink":"Fixing small bugs, updateing to v1.0.1"}},{"before":"e253a6b24abe5110dd5d6292584ea9e4f12b8cf0","after":"a4e85ec777628397a668e4b9d15ae7a1e45de3f6","ref":"refs/heads/master","pushedAt":"2023-11-21T10:50:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Update version to 1.0.0","shortMessageHtmlLink":"Update version to 1.0.0"}},{"before":"008dedf293a474eea34f6b9d4e8d5042c4e1cba2","after":"e253a6b24abe5110dd5d6292584ea9e4f12b8cf0","ref":"refs/heads/master","pushedAt":"2023-11-21T10:01:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Update README.md\n\n- Add news about BUSCO lineages","shortMessageHtmlLink":"Update README.md"}},{"before":"9aeaf5894b977ff7000080ef37df6914a176cacd","after":"008dedf293a474eea34f6b9d4e8d5042c4e1cba2","ref":"refs/heads/master","pushedAt":"2023-11-19T09:16:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"722fc031c6675f26c718edb7eddef63d07469a53","after":"9aeaf5894b977ff7000080ef37df6914a176cacd","ref":"refs/heads/master","pushedAt":"2023-11-19T09:15:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Update README.md\n\nWarn about MEGAHIT broken version in Mac","shortMessageHtmlLink":"Update README.md"}},{"before":"bafe01bf3f3ea2a9b31c217217c8ec71d6de8240","after":"722fc031c6675f26c718edb7eddef63d07469a53","ref":"refs/heads/master","pushedAt":"2023-11-18T08:01:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Update bait.py","shortMessageHtmlLink":"Update bait.py"}},{"before":"7089c080ad6fdecf72e47a7d3a0690977572ea66","after":"bafe01bf3f3ea2a9b31c217217c8ec71d6de8240","ref":"refs/heads/master","pushedAt":"2023-11-18T07:59:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Make final baitset names unique\n\n- Make final baitset names unique","shortMessageHtmlLink":"Make final baitset names unique"}},{"before":"a000a4492989670f78776cd041cb3a5e58bd8c0b","after":"7089c080ad6fdecf72e47a7d3a0690977572ea66","ref":"refs/heads/master","pushedAt":"2023-11-18T07:39:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Saving shuffled FASTAs\n\n- Now FASTAs can be saved after shuffling the sequence headers, useful for sending a baitset for synthesis so all sequences have an equal prob of being made","shortMessageHtmlLink":"Saving shuffled FASTAs"}},{"before":"ba46e857501c843d1a0d4c0b936da25e927516be","after":"a000a4492989670f78776cd041cb3a5e58bd8c0b","ref":"refs/heads/master","pushedAt":"2023-11-18T02:41:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Update bait.py\n\n- Fix small mistakes","shortMessageHtmlLink":"Update bait.py"}},{"before":"e697c80e7e4746b741152ea268902c5dd9f9758b","after":"ba46e857501c843d1a0d4c0b936da25e927516be","ref":"refs/heads/master","pushedAt":"2023-11-18T02:33:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Update bait.py\n\n- Minor cosmetic changes","shortMessageHtmlLink":"Update bait.py"}},{"before":"dc11c8b543e18b9df0577b3129902f2ffa33fd0d","after":"e697c80e7e4746b741152ea268902c5dd9f9758b","ref":"refs/heads/master","pushedAt":"2023-11-18T02:21:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"edgardomortiz","name":"Edgardo M. Ortiz","path":"/edgardomortiz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5767612?s=80&v=4"},"commit":{"message":"Update bait.py\n\n- Cosmetic improvements","shortMessageHtmlLink":"Update bait.py"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEj8_G1AA","startCursor":null,"endCursor":null}},"title":"Activity ยท edgardomortiz/Captus"}