{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":460687047,"defaultBranch":"main","name":"ExonHunter","ownerLogin":"amirh-hajianpour","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-02-18T02:51:22.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/57235137?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1693497291.0","currentOid":""},"activityList":{"items":[{"before":"0de68d7179295c700ab56e3169ad5b17f56cd677","after":"67ae89a6222e378009badfb2e2e0bccc5656a5a3","ref":"refs/heads/new_version","pushedAt":"2024-04-13T03:37:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"score() no uses pyinterval for interval calculations. This fixes a bug where the overlap and consequently coverage were incorrectly calculated where there was more than two overlapping intervals.","shortMessageHtmlLink":"score() no uses pyinterval for interval calculations. This fixes a bu…"}},{"before":"dbcb5152262c3559e1880b7e5138ed86881a46cf","after":"0de68d7179295c700ab56e3169ad5b17f56cd677","ref":"refs/heads/new_version","pushedAt":"2024-04-13T03:00:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"evaluate_hit_set() bug fixes.","shortMessageHtmlLink":"evaluate_hit_set() bug fixes."}},{"before":"3f3b9ffa219c473253981b580d07153c7ff1e181","after":"dbcb5152262c3559e1880b7e5138ed86881a46cf","ref":"refs/heads/new_version","pushedAt":"2024-04-13T02:34:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"evaluate_hit_set() now handles per-exon, nucleotide-level, and also exon-level performance measures, correctly.","shortMessageHtmlLink":"evaluate_hit_set() now handles per-exon, nucleotide-level, and also e…"}},{"before":"def5a5cbf27aa5e6b15d2fd8a7463e0188f5ba6b","after":"3f3b9ffa219c473253981b580d07153c7ff1e181","ref":"refs/heads/new_version","pushedAt":"2024-04-12T21:07:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"minor changes.","shortMessageHtmlLink":"minor changes."}},{"before":"f593454a1af95d71d463878c94ccbe2ad0e6cdb2","after":"def5a5cbf27aa5e6b15d2fd8a7463e0188f5ba6b","ref":"refs/heads/new_version","pushedAt":"2024-04-12T18:41:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"evaluate_hit_set() now uses pyinterval module for interval-related calculations. evaluate_hit_set() now calculates the nucleotide-level statistics correctly.","shortMessageHtmlLink":"evaluate_hit_set() now uses pyinterval module for interval-related ca…"}},{"before":"9d2d18f043073c4bec03f33e30f08b83a012e031","after":"f593454a1af95d71d463878c94ccbe2ad0e6cdb2","ref":"refs/heads/new_version","pushedAt":"2024-04-11T20:22:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"get_overlap() now also returns the interval of overlap. get_overlap() now takes two lists, instead of four integers. Overlapping hits (of only two hits. three hits and more are not handled.) now are measured correctly; previously length of overlap of hits were added however hits might overlap with eachother. minor changes and improvements.","shortMessageHtmlLink":"get_overlap() now also returns the interval of overlap. get_overlap()…"}},{"before":"f8c1b83cc95cb4074f1fcd51201a16ff02c054d2","after":"9d2d18f043073c4bec03f33e30f08b83a012e031","ref":"refs/heads/new_version","pushedAt":"2024-04-10T18:55:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"ignoring intermediary files.","shortMessageHtmlLink":"ignoring intermediary files."}},{"before":"a97b28712a68cb3879f8769e89a2ceb00e7fde2b","after":"f8c1b83cc95cb4074f1fcd51201a16ff02c054d2","ref":"refs/heads/new_version","pushedAt":"2024-04-10T18:52:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"minor changes.","shortMessageHtmlLink":"minor changes."}},{"before":"52c7f00b1c844330e89a690f72f4550b3f2dc6d2","after":"a97b28712a68cb3879f8769e89a2ceb00e7fde2b","ref":"refs/heads/new_version","pushedAt":"2024-04-09T20:47:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"amino_to_nucleic() now accepts ranges starting from 1. evaluate_hit_set() now works correctly fro nucleotide-level stats. score() params are changed manually. is_exon(0 is removed.","shortMessageHtmlLink":"amino_to_nucleic() now accepts ranges starting from 1. evaluate_hit_s…"}},{"before":"03607337c44a9d1b0f6d2865e08cdc8e0827c5fd","after":"52c7f00b1c844330e89a690f72f4550b3f2dc6d2","ref":"refs/heads/new_version","pushedAt":"2024-04-04T14:22:33.000Z","pushType":"push","commitsCount":6,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"is_exon() is not overlap calculator. best_hit_set() is removed. get_gene_sequence() is added to get gene sequence from FASTA file. gene_to_protein() is added to translate a gene sequence. clustalo() is added as a wrapper of clustal-omega alignment software. proteins_to_faa() is added to make an FAA file from multiple protein sequences. exon_hunter() is removed and hunt() is added. hunt() basically only calls the utility functions and controls the pipeline. argparse feature is added to exon_hunter.py. old redundant manual argument parser is removed.","shortMessageHtmlLink":"is_exon() is not overlap calculator. best_hit_set() is removed. get_g…"}},{"before":"42ec36eb390cd952919cea05911d325746829b73","after":"03607337c44a9d1b0f6d2865e08cdc8e0827c5fd","ref":"refs/heads/new_version","pushedAt":"2024-02-28T18:15:03.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"added runner files.","shortMessageHtmlLink":"added runner files."}},{"before":"1b43d1df1a818a0ffc9f9c9e05b07f9ba7463c8d","after":"42ec36eb390cd952919cea05911d325746829b73","ref":"refs/heads/new_version","pushedAt":"2023-12-12T19:54:14.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"correct_mf_format() was added. read_mf() is not tested for revese genes. Other minor changes and improvements.","shortMessageHtmlLink":"correct_mf_format() was added. read_mf() is not tested for revese gen…"}},{"before":"40ffeebde3a07f50f6d3b52362e2813370e6738e","after":"1b43d1df1a818a0ffc9f9c9e05b07f9ba7463c8d","ref":"refs/heads/new_version","pushedAt":"2023-08-31T20:08:14.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"moved methods to separate files to increase modularity.","shortMessageHtmlLink":"moved methods to separate files to increase modularity."}},{"before":null,"after":"40ffeebde3a07f50f6d3b52362e2813370e6738e","ref":"refs/heads/new_version","pushedAt":"2023-08-31T15:54:51.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"amirh-hajianpour","name":"Amirhossein Hajianpour","path":"/amirh-hajianpour","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/57235137?s=80&v=4"},"commit":{"message":"removed output text files.","shortMessageHtmlLink":"removed output text files."}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNC0xM1QwMzozNzowNy4wMDAwMDBazwAAAAQvnN2N","startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNC0xM1QwMzozNzowNy4wMDAwMDBazwAAAAQvnN2N","endCursor":"Y3Vyc29yOnYyOpK7MjAyMy0wOC0zMVQxNTo1NDo1MS4wMDAwMDBazwAAAAN2xgvS"}},"title":"Activity · amirh-hajianpour/ExonHunter"}