{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":501744163,"defaultBranch":"main","name":"UnsupervisedPeakCaller","ownerLogin":"Tuteja-Lab","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-06-09T17:15:59.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/37884178?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1669319079.5410402","currentOid":""},"activityList":{"items":[{"before":"1afd39d92c31bff7028cddb83b20045e9fcbf8dc","after":"818ce278db744d69a0b8b3e61f0a64af54082021","ref":"refs/heads/main","pushedAt":"2023-12-02T18:32:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Polishing README.md","shortMessageHtmlLink":"Polishing README.md"}},{"before":"7037668596bdf82e312c733f4c3494bfb34ed863","after":"1afd39d92c31bff7028cddb83b20045e9fcbf8dc","ref":"refs/heads/main","pushedAt":"2023-12-02T18:32:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Polishing README.md","shortMessageHtmlLink":"Polishing README.md"}},{"before":"962dd37124024e8d9bee32e770ddb34ad859b7d6","after":"7037668596bdf82e312c733f4c3494bfb34ed863","ref":"refs/heads/main","pushedAt":"2023-12-02T18:29:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Polishing README.md","shortMessageHtmlLink":"Polishing README.md"}},{"before":"1f5b2bba7c17464cd6f1ae2a084bdf7a879dd6c5","after":"962dd37124024e8d9bee32e770ddb34ad859b7d6","ref":"refs/heads/main","pushedAt":"2023-12-02T18:29:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Polishing README.md","shortMessageHtmlLink":"Polishing README.md"}},{"before":"83c679a7d5a6acf0c8a59513af49856beb7358cd","after":"1f5b2bba7c17464cd6f1ae2a084bdf7a879dd6c5","ref":"refs/heads/main","pushedAt":"2023-12-02T18:26:18.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Polishing README.md","shortMessageHtmlLink":"Polishing README.md"}},{"before":"9fbcf956640ee6cf894dd2e5c0eaacbeacb8b300","after":"83c679a7d5a6acf0c8a59513af49856beb7358cd","ref":"refs/heads/main","pushedAt":"2023-12-02T18:23:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Polishing README.md","shortMessageHtmlLink":"Polishing README.md"}},{"before":"089b796286cf756238832d2f9e67a3c1821aed8d","after":"9fbcf956640ee6cf894dd2e5c0eaacbeacb8b300","ref":"refs/heads/main","pushedAt":"2023-12-02T18:22:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Polishing README.md","shortMessageHtmlLink":"Polishing README.md"}},{"before":"6de0aa76be32586a74a5d4208eeedccdc2299890","after":"089b796286cf756238832d2f9e67a3c1821aed8d","ref":"refs/heads/main","pushedAt":"2023-12-02T18:20:31.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Polishing the tutorial and adding description of run_rcl.sh command line options.","shortMessageHtmlLink":"Polishing the tutorial and adding description of run_rcl.sh command l…"}},{"before":"a836b6ef78502f4be3da1f364330c1d5228ace48","after":"6de0aa76be32586a74a5d4208eeedccdc2299890","ref":"refs/heads/main","pushedAt":"2023-12-02T06:08:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Allow pytorch lightning Trainer to use gpus argument in version < 2.0","shortMessageHtmlLink":"Allow pytorch lightning Trainer to use gpus argument in version < 2.0"}},{"before":"a70b2943e86947278054aec877bbf042d352de8d","after":"a836b6ef78502f4be3da1f364330c1d5228ace48","ref":"refs/heads/main","pushedAt":"2023-12-02T05:44:30.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Added test for already sorted BAM files in preprocessing.bash and removed option -S. Warn user when BAM files are sorted by the program.","shortMessageHtmlLink":"Added test for already sorted BAM files in preprocessing.bash and rem…"}},{"before":"4038a8fbeda26be2ed469a10f8721df16574d690","after":"a70b2943e86947278054aec877bbf042d352de8d","ref":"refs/heads/main","pushedAt":"2023-11-29T01:42:17.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Fixed a bug due to change in the way pandas.merge() works that affected RCL with more than 2 replicates.","shortMessageHtmlLink":"Fixed a bug due to change in the way pandas.merge() works that affect…"}},{"before":"676fd03722f290c7ede68008580dcee8aefab82d","after":"4038a8fbeda26be2ed469a10f8721df16574d690","ref":"refs/heads/main","pushedAt":"2023-11-25T03:09:16.000Z","pushType":"push","commitsCount":6,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Many updates to preprocessing.bash\n- add exclude (-e) command line option to exclude certain chromosomes from analysis; use as -e \"_\" for example\n- add zerowrite (-z) command line option to overwrite intermediate files that are currently size 0; some intermediate files are legitimately size 0\n- introduced stages 0 through 8 to describe the steps in the preprocessing code\n- add argument to overwrite (-w INT) and zerowrite (-z INT) flags to only overwrite intermediate files at or after the stage named INT\n- fixed bug in blacklist filtering that did not allow reference sequence names starting with chr\n- fixed bug in getCountFiles.R that did not correctly name segments when sequence names start with chr","shortMessageHtmlLink":"Many updates to preprocessing.bash"}},{"before":"13cf28cfdf9e487c53b4a03fb625df6e57cfe725","after":"676fd03722f290c7ede68008580dcee8aefab82d","ref":"refs/heads/main","pushedAt":"2023-11-22T18:25:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Polishing quickstart.","shortMessageHtmlLink":"Polishing quickstart."}},{"before":"66d375d584fa7e79ba419dfd61b08df8be13b8e2","after":"13cf28cfdf9e487c53b4a03fb625df6e57cfe725","ref":"refs/heads/main","pushedAt":"2023-11-22T18:24:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Linking tutorial steps together.","shortMessageHtmlLink":"Linking tutorial steps together."}},{"before":"0d2e77c69ae95380f85a19a548112b7511729279","after":"66d375d584fa7e79ba419dfd61b08df8be13b8e2","ref":"refs/heads/main","pushedAt":"2023-11-22T18:23:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Linking tutorial steps together.","shortMessageHtmlLink":"Linking tutorial steps together."}},{"before":"939919d5b5faa5bb6dd18a8d08696e1c5d31f615","after":"0d2e77c69ae95380f85a19a548112b7511729279","ref":"refs/heads/main","pushedAt":"2023-11-22T18:17:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Polishing quickstart section","shortMessageHtmlLink":"Polishing quickstart section"}},{"before":"d20030d6f113f382cad2042c48abcab31891040d","after":"939919d5b5faa5bb6dd18a8d08696e1c5d31f615","ref":"refs/heads/main","pushedAt":"2023-11-22T18:11:03.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Merge branch 'main' of https://github.com/Tuteja-Lab/UnsupervisedPeakCaller","shortMessageHtmlLink":"Merge branch 'main' of https://github.com/Tuteja-Lab/UnsupervisedPeak…"}},{"before":"8bdabee6adb3b4a9d024cbd84426ece669ca2936","after":"d20030d6f113f382cad2042c48abcab31891040d","ref":"refs/heads/main","pushedAt":"2023-11-22T18:03:24.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Merge branch 'main' of https://github.com/Tuteja-Lab/UnsupervisedPeakCaller","shortMessageHtmlLink":"Merge branch 'main' of https://github.com/Tuteja-Lab/UnsupervisedPeak…"}},{"before":"07ef8e3ba7d9d478922378138ab4e71a8fbe912b","after":"8bdabee6adb3b4a9d024cbd84426ece669ca2936","ref":"refs/heads/main","pushedAt":"2023-11-22T17:53:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Removing matplotlib dependency.","shortMessageHtmlLink":"Removing matplotlib dependency."}},{"before":"58c2bdb0acf16b0130d0ba3bf22a52cc7fdc3e63","after":"07ef8e3ba7d9d478922378138ab4e71a8fbe912b","ref":"refs/heads/main","pushedAt":"2023-11-22T17:18:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Fixing typo in preprocessing script.","shortMessageHtmlLink":"Fixing typo in preprocessing script."}},{"before":"1ebf9d4c15585cdaed195a685a2a555fe4d5c405","after":"58c2bdb0acf16b0130d0ba3bf22a52cc7fdc3e63","ref":"refs/heads/main","pushedAt":"2023-11-22T16:15:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Updating README.md","shortMessageHtmlLink":"Updating README.md"}},{"before":"593d11355c4174efd51da56887a3e59fc9095868","after":"1ebf9d4c15585cdaed195a685a2a555fe4d5c405","ref":"refs/heads/main","pushedAt":"2023-11-22T16:13:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Updating README.md","shortMessageHtmlLink":"Updating README.md"}},{"before":"8a0ed2698121526d43529d9ccea81e0fb1cec368","after":"593d11355c4174efd51da56887a3e59fc9095868","ref":"refs/heads/main","pushedAt":"2023-11-22T16:10:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Updating README.md","shortMessageHtmlLink":"Updating README.md"}},{"before":"be89d64e3b46083647ff21791f74fe1c80574898","after":"8a0ed2698121526d43529d9ccea81e0fb1cec368","ref":"refs/heads/main","pushedAt":"2023-11-22T16:08:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Updating README.md","shortMessageHtmlLink":"Updating README.md"}},{"before":"eac4024f749f90d0f9123ab0fd745916bfda8254","after":"be89d64e3b46083647ff21791f74fe1c80574898","ref":"refs/heads/main","pushedAt":"2023-11-22T15:59:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Updating README.md","shortMessageHtmlLink":"Updating README.md"}},{"before":"312b206c4ddca8a0cc5f0765f5ec6e01638786ac","after":"eac4024f749f90d0f9123ab0fd745916bfda8254","ref":"refs/heads/main","pushedAt":"2023-11-22T15:56:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Updating README.md","shortMessageHtmlLink":"Updating README.md"}},{"before":"821ef4a158a64f5ce6eed415ac5abccda96a26fe","after":"312b206c4ddca8a0cc5f0765f5ec6e01638786ac","ref":"refs/heads/main","pushedAt":"2023-11-22T15:53:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Updating README.md","shortMessageHtmlLink":"Updating README.md"}},{"before":"cc36ab006f5bf74d98f08ef312af3e5d03a8e1f1","after":"821ef4a158a64f5ce6eed415ac5abccda96a26fe","ref":"refs/heads/main","pushedAt":"2023-11-22T15:52:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Updating README.md","shortMessageHtmlLink":"Updating README.md"}},{"before":"d9ece2e3383c0059ea885c0ef538e245f1032dd1","after":"cc36ab006f5bf74d98f08ef312af3e5d03a8e1f1","ref":"refs/heads/main","pushedAt":"2023-11-22T15:51:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Adding tutorial section.","shortMessageHtmlLink":"Adding tutorial section."}},{"before":"217ff53de762fd4c8ba4892d8145b1de44d7ecdc","after":"d9ece2e3383c0059ea885c0ef538e245f1032dd1","ref":"refs/heads/main","pushedAt":"2023-11-22T15:48:28.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"kdorman","name":null,"path":"/kdorman","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4072500?s=80&v=4"},"commit":{"message":"Merge branch 'main' of https://github.com/Tuteja-Lab/UnsupervisedPeakCaller","shortMessageHtmlLink":"Merge branch 'main' of https://github.com/Tuteja-Lab/UnsupervisedPeak…"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAADvmUjgwA","startCursor":null,"endCursor":null}},"title":"Activity · Tuteja-Lab/UnsupervisedPeakCaller"}