{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":610474938,"defaultBranch":"main","name":"rna2d3d","ownerLogin":"whl-usc","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2023-03-06T21:07:01.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/67292323?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1678136841.794262","currentOid":""},"activityList":{"items":[{"before":"30573c0de038b45858549a9a09a9fcb36d9635f7","after":"025bcb413906fba11ffe2e65ca573c406143852f","ref":"refs/heads/main","pushedAt":"2024-07-03T17:40:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update rna2d3d tools folder.\n\nMoved scripts from cris_tools for organization.","shortMessageHtmlLink":"Update rna2d3d tools folder."}},{"before":"5b19fb35e709999467e35497ddbd59104aa6f780","after":"30573c0de038b45858549a9a09a9fcb36d9635f7","ref":"refs/heads/main","pushedAt":"2024-03-23T00:33:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update for version notes formatting.","shortMessageHtmlLink":"Update for version notes formatting."}},{"before":"339849e6776dedc1fe4f503ebf218f28384828b3","after":"5b19fb35e709999467e35497ddbd59104aa6f780","ref":"refs/heads/main","pushedAt":"2024-03-22T21:16:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update crssant.py\n\nFixed typos in functions and added versioning element.","shortMessageHtmlLink":"Update crssant.py"}},{"before":"45a2b845084534a9a66ed51ec99586deb4c61bd6","after":"339849e6776dedc1fe4f503ebf218f28384828b3","ref":"refs/heads/main","pushedAt":"2024-03-20T22:58:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Updated crssant.py\n\nFixed issues with handling read coverage that extends into scientific notation.","shortMessageHtmlLink":"Updated crssant.py"}},{"before":"f883f720e14bfdd50b3262adfa8b64b8e26000bc","after":"45a2b845084534a9a66ed51ec99586deb4c61bd6","ref":"refs/heads/main","pushedAt":"2024-03-18T22:46:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Changed working for printed statements.","shortMessageHtmlLink":"Changed working for printed statements."}},{"before":"22d7a2aac49aa9f6fe881ec9a1605ef593929cb1","after":"f883f720e14bfdd50b3262adfa8b64b8e26000bc","ref":"refs/heads/main","pushedAt":"2024-03-18T22:06:26.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Updated crssant.py to time functions.\n\nAdded section for clustering time.","shortMessageHtmlLink":"Updated crssant.py to time functions."}},{"before":"f0100f1704118f22c3f2e29b9e9a8cdd90d7098b","after":"22d7a2aac49aa9f6fe881ec9a1605ef593929cb1","ref":"refs/heads/main","pushedAt":"2024-03-18T19:04:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Renamed crssant script, added versioning.","shortMessageHtmlLink":"Renamed crssant script, added versioning."}},{"before":"7b1096d4805fac31de9d07f7919c208f11df7679","after":"f0100f1704118f22c3f2e29b9e9a8cdd90d7098b","ref":"refs/heads/main","pushedAt":"2024-03-18T19:00:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Fixed typo in script timing.","shortMessageHtmlLink":"Fixed typo in script timing."}},{"before":"3a8edd0ec0e3c47e0ec2aaf11af87d94e6443907","after":"7b1096d4805fac31de9d07f7919c208f11df7679","ref":"refs/heads/main","pushedAt":"2024-03-18T18:46:26.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Merge branch 'main' of https://github.com/whl-usc/rna2d3d","shortMessageHtmlLink":"Merge branch 'main' of https://github.com/whl-usc/rna2d3d"}},{"before":"2ca4029621470ecac58a5ce4b60d68dcdeb553b9","after":"3a8edd0ec0e3c47e0ec2aaf11af87d94e6443907","ref":"refs/heads/main","pushedAt":"2024-03-07T23:13:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Updated crssant.sh\n\nFound typo in the description of the shell script.","shortMessageHtmlLink":"Updated crssant.sh"}},{"before":"f0c2638b55f9369b3aec7e5b9c6429c9f3845ecf","after":"2ca4029621470ecac58a5ce4b60d68dcdeb553b9","ref":"refs/heads/main","pushedAt":"2024-02-19T22:54:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update bamget.py\n\nFixed error in the file removal option.","shortMessageHtmlLink":"Update bamget.py"}},{"before":"57eeb40af34de251786a8a3af8c3d56f9f876d95","after":"f0c2638b55f9369b3aec7e5b9c6429c9f3845ecf","ref":"refs/heads/main","pushedAt":"2024-02-19T22:34:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update bamget.py\n\nFixed issue with the writeout to bed file.","shortMessageHtmlLink":"Update bamget.py"}},{"before":"858608976a716f29287f6a0d8e31011fa9cfa40b","after":"57eeb40af34de251786a8a3af8c3d56f9f876d95","ref":"refs/heads/main","pushedAt":"2024-02-19T22:21:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update bamget.py\n\nFixed typo in help text and description.","shortMessageHtmlLink":"Update bamget.py"}},{"before":"a075599cfd63dc79356a7ce04fb9fab79fdacf51","after":"858608976a716f29287f6a0d8e31011fa9cfa40b","ref":"refs/heads/main","pushedAt":"2024-02-19T22:16:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Updated bamget.py\n\nRemove error lines.","shortMessageHtmlLink":"Updated bamget.py"}},{"before":"47ab7803c7d1a025f4c619d34f8c5eb140fd0c3d","after":"a075599cfd63dc79356a7ce04fb9fab79fdacf51","ref":"refs/heads/main","pushedAt":"2024-02-19T22:14:35.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Updated mapping_v2.sh\n\n#SBATCH commands incorrect.","shortMessageHtmlLink":"Updated mapping_v2.sh"}},{"before":"b6594277c0b8656ecdb16fd2ddef960a1702685f","after":"47ab7803c7d1a025f4c619d34f8c5eb140fd0c3d","ref":"refs/heads/main","pushedAt":"2024-02-16T22:48:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update bamget.py\n\nFixed missing import of package.","shortMessageHtmlLink":"Update bamget.py"}},{"before":"792a9579df0cf8a0d39ce63933f01d47b7c7208b","after":"b6594277c0b8656ecdb16fd2ddef960a1702685f","ref":"refs/heads/main","pushedAt":"2024-02-16T22:46:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Updated mapping_v2.sh\n\nAddressed issue with SLURM scripting for memory for tasks.","shortMessageHtmlLink":"Updated mapping_v2.sh"}},{"before":"f2dc11f17f32e92e4e3708deb503a68335165061","after":"792a9579df0cf8a0d39ce63933f01d47b7c7208b","ref":"refs/heads/main","pushedAt":"2024-02-16T22:08:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update bamget.py\n\nFixed the file removal issue.","shortMessageHtmlLink":"Update bamget.py"}},{"before":"6d5bc8666e62dae726d349fe57b306a9422778c4","after":"f2dc11f17f32e92e4e3708deb503a68335165061","ref":"refs/heads/main","pushedAt":"2024-02-15T23:25:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Updated bamget.py\n\nModified write_bed_file to append for pre-existing files.","shortMessageHtmlLink":"Updated bamget.py"}},{"before":"5d98347556fb0f71bc81d936dba8b19bf9eefbdd","after":"6d5bc8666e62dae726d349fe57b306a9422778c4","ref":"refs/heads/main","pushedAt":"2024-02-15T22:14:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update bamget.py\n\nFixed the remove_files function calling.","shortMessageHtmlLink":"Update bamget.py"}},{"before":"6cbd3e78a4e069795e977989112f23ad1e2ad608","after":"5d98347556fb0f71bc81d936dba8b19bf9eefbdd","ref":"refs/heads/main","pushedAt":"2024-02-15T21:43:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Created bamget.py\n\nAdded a new tool for creating a BED file for CRSSANT analysis. Can be incorporated into a shell script.","shortMessageHtmlLink":"Created bamget.py"}},{"before":"bf0bfa5d607fce24c21baab4ff49298f14e00fc3","after":"6cbd3e78a4e069795e977989112f23ad1e2ad608","ref":"refs/heads/main","pushedAt":"2024-01-16T19:21:03.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Merge branch 'main' of https://github.com/whl-usc/rna2d3d","shortMessageHtmlLink":"Merge branch 'main' of https://github.com/whl-usc/rna2d3d"}},{"before":"ead8a95966d8dc2ef134d39cc40144d187a64be3","after":"bf0bfa5d607fce24c21baab4ff49298f14e00fc3","ref":"refs/heads/main","pushedAt":"2024-01-16T02:21:32.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Merge branch 'main' of https://github.com/whl-usc/rna2d3d","shortMessageHtmlLink":"Merge branch 'main' of https://github.com/whl-usc/rna2d3d"}},{"before":"d22c1bed6d31723cfe6b562296149afe07d799e4","after":"ead8a95966d8dc2ef134d39cc40144d187a64be3","ref":"refs/heads/main","pushedAt":"2024-01-12T21:21:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update seqstats.py\n\nAdjusting for error handling in slurm.out file search.\n\nInclude more information about the script in docstrings.","shortMessageHtmlLink":"Update seqstats.py"}},{"before":"48f7a6ed82d2e304d9aeac75e88d9206271384ec","after":"d22c1bed6d31723cfe6b562296149afe07d799e4","ref":"refs/heads/main","pushedAt":"2024-01-12T01:11:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Update seqstats.py\n\nFix the fastq counting error. , added docstrings for all functions.","shortMessageHtmlLink":"Update seqstats.py"}},{"before":"1dd4d0fd46f9b37612c304a2b16cec4fc6e4f164","after":"48f7a6ed82d2e304d9aeac75e88d9206271384ec","ref":"refs/heads/main","pushedAt":"2024-01-11T01:21:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Updated seqstats.py\n\nFixed typo in index column check.\n\nAdded comment to remind user that script must be run within parent directory of where directory_name folder exists.\n\nAddresses variations in slurm-*.out files. Rewrote function to work with files that have extra newlines.","shortMessageHtmlLink":"Updated seqstats.py"}},{"before":"7c550257a39dd0a58f89e12fdbae1e5c4416b74b","after":"1dd4d0fd46f9b37612c304a2b16cec4fc6e4f164","ref":"refs/heads/main","pushedAt":"2024-01-10T21:21:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Add new tool, seqstats.py\n\nUsed for extracting information about read counts, mapping statistics, details of gaptype and gapfilter analysis from the CRSSANT pipeline.","shortMessageHtmlLink":"Add new tool, seqstats.py"}},{"before":"dfe318fb57eb71c27835e37c63640e1f93da9da5","after":"7c550257a39dd0a58f89e12fdbae1e5c4416b74b","ref":"refs/heads/main","pushedAt":"2023-12-01T23:44:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Removed repeated printout.","shortMessageHtmlLink":"Removed repeated printout."}},{"before":"32bc6bea612ff62577821da5ba0a874cac5fdf41","after":"dfe318fb57eb71c27835e37c63640e1f93da9da5","ref":"refs/heads/main","pushedAt":"2023-12-01T23:42:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Fixing merger_sams.py again for file comprehension issue.","shortMessageHtmlLink":"Fixing merger_sams.py again for file comprehension issue."}},{"before":"a731122ce4006c1e82fb7d5b0de587807d01b165","after":"32bc6bea612ff62577821da5ba0a874cac5fdf41","ref":"refs/heads/main","pushedAt":"2023-12-01T19:25:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"whl-usc","name":"Wilson H Lee","path":"/whl-usc","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/67292323?s=80&v=4"},"commit":{"message":"Fixing the merger_sams.py f-string issue.","shortMessageHtmlLink":"Fixing the merger_sams.py f-string issue."}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEdihfOAA","startCursor":null,"endCursor":null}},"title":"Activity ยท whl-usc/rna2d3d"}