{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":140724152,"defaultBranch":"master","name":"xTea","ownerLogin":"parklab","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2018-07-12T14:26:48.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/1216524?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1718213674.0","currentOid":""},"activityList":{"items":[{"before":"a376179433c9f9194734d86aa2db661f15b43fa6","after":"a3bad185e3c3ecda7c9a237cc4c4a641ad633356","ref":"refs/heads/cli","pushedAt":"2024-06-27T20:49:51.000Z","pushType":"pr_merge","commitsCount":16,"pusher":{"login":"corinsexton","name":"Corinne Sexton","path":"/corinsexton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13277644?s=80&v=4"},"commit":{"message":"Merge pull request #117 from corinsexton/cli\n\nMatch up germline xTea results","shortMessageHtmlLink":"Merge pull request #117 from corinsexton/cli"}},{"before":"a79ca5d959246a2d7165eb3504eb6992e36fd39e","after":"a376179433c9f9194734d86aa2db661f15b43fa6","ref":"refs/heads/cli","pushedAt":"2024-06-13T02:45:22.000Z","pushType":"pr_merge","commitsCount":6,"pusher":{"login":"corinsexton","name":"Corinne Sexton","path":"/corinsexton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13277644?s=80&v=4"},"commit":{"message":"Merge pull request #115 from corinsexton/cli\n\nSync results of original xTea with cli xTea","shortMessageHtmlLink":"Merge pull request #115 from corinsexton/cli"}},{"before":null,"after":"fb24abdd9a3801062159e38263c37691e9270e50","ref":"refs/heads/unit_tests","pushedAt":"2024-06-12T17:34:34.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"TuanTrain","name":null,"path":"/TuanTrain","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6004105?s=80&v=4"},"commit":{"message":"convert toml file to setup.py","shortMessageHtmlLink":"convert toml file to setup.py"}},{"before":"2030bc9717292ee6447c8fd059ffafdf2c2fbe62","after":"a79ca5d959246a2d7165eb3504eb6992e36fd39e","ref":"refs/heads/cli","pushedAt":"2024-06-12T16:53:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"corinsexton","name":"Corinne Sexton","path":"/corinsexton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13277644?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"41a7d6a742c7cc393a32168b5abdf07d0da2da10","after":"2030bc9717292ee6447c8fd059ffafdf2c2fbe62","ref":"refs/heads/cli","pushedAt":"2024-06-12T15:26:41.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"corinsexton","name":"Corinne Sexton","path":"/corinsexton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13277644?s=80&v=4"},"commit":{"message":"Merge pull request #114 from corinsexton/cli\n\nAdd setup.py","shortMessageHtmlLink":"Merge pull request #114 from corinsexton/cli"}},{"before":"86812ebbf0cc3d5a037057c06f8b652a694d6c1c","after":"41a7d6a742c7cc393a32168b5abdf07d0da2da10","ref":"refs/heads/cli","pushedAt":"2024-06-11T20:41:04.000Z","pushType":"pr_merge","commitsCount":103,"pusher":{"login":"corinsexton","name":"Corinne Sexton","path":"/corinsexton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13277644?s=80&v=4"},"commit":{"message":"Merge pull request #113 from corinsexton/cli\n\nAdd model file and clean up extraneous files","shortMessageHtmlLink":"Merge pull request #113 from corinsexton/cli"}},{"before":"f6350246c15f8353061204b9d0af82b983c57387","after":"86812ebbf0cc3d5a037057c06f8b652a694d6c1c","ref":"refs/heads/cli","pushedAt":"2024-06-11T19:59:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"corinsexton","name":"Corinne Sexton","path":"/corinsexton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13277644?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"bbb9144059a60bd301331ee26773d476fc413f3d","after":"f6350246c15f8353061204b9d0af82b983c57387","ref":"refs/heads/cli","pushedAt":"2024-06-11T19:58:44.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"corinsexton","name":"Corinne Sexton","path":"/corinsexton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13277644?s=80&v=4"},"commit":{"message":"First commit refactoring command line interface (#111)\n\n* rearrange src; add pyproject.toml\r\n\r\n* src package structure\r\n\r\n* comment out TELocator code;start adding tests;clean recipes dir\r\n\r\n* remove unused code\r\n\r\n* move preprocess out of main script\r\n\r\n* create run_xtea.py; move clip and disc to locate_insertions\r\n\r\n* add import\r\n\r\n* mv locate insertions\r\n\r\n* add package name\r\n\r\n* add package name\r\n\r\n* add package name\r\n\r\n* add package name all\r\n\r\n* test clip function\r\n\r\n* add cmdline params clip-disc\r\n\r\n* parser\r\n\r\n* fix global_values\r\n\r\n* change list of bams from file to list object\r\n\r\n* fix cores str issue\r\n\r\n* fix type in intermediateSites\r\n\r\n* add coverage\r\n\r\n* add coverage\r\n\r\n* remove 10x functionality, remove file input\r\n\r\n* fix indent\r\n\r\n* fix self.sf_list\r\n\r\n* fix rep_lib_annot paths\r\n\r\n* add / to dir\r\n\r\n* add missing fx in clip_read\r\n\r\n* convert paths to absolute file paths\r\n\r\n* add '/' to dir\r\n\r\n* fix mosaic param\r\n\r\n* add n_disc\r\n\r\n* fix bam file input to list\r\n\r\n* fix global values\r\n\r\n* fix mean_is\r\n\r\n* add coverage default 40 (HARD CODE)\r\n\r\n* add int_files flag\r\n\r\n* fix if\r\n\r\n* add -K 10000 to bwa mem for reproducibility\r\n\r\n* add flag T/F\r\n\r\n* fix bwa reprod\r\n\r\n* fix bwa mem\r\n\r\n* add print for cutoffs\r\n\r\n* fix cutoff issue; add to cli\r\n\r\n* remove print\r\n\r\n* syntax error\r\n\r\n* separate clip and disc steps\r\n\r\n* add filter_csn step\r\n\r\n* add mod name\r\n\r\n* add tuple return\r\n\r\n* fix return indent; always attempt rcd calc\r\n\r\n* change sf_bam_list to list, not file\r\n\r\n* fix sf_list\r\n\r\n* fix bug changing files\r\n\r\n* fix global_values bug; start adding transduction\r\n\r\n* transduction call\r\n\r\n* add test TODO and cleanup dir\r\n\r\n* add more main functions to run_xtea\r\n\r\n* sm\r\n\r\n* sm\r\n\r\n* fix\r\n\r\n* annot_paths typo\r\n\r\n* add missing fx\r\n\r\n* add fx\r\n\r\n* fix file to list\r\n\r\n* add fx\r\n\r\n* file to list\r\n\r\n* int to str\r\n\r\n* fix int issue\r\n\r\n* typo\r\n\r\n* typo annot\r\n\r\n* mv file typo\r\n\r\n* add timing\r\n\r\n* fix wuote\r\n\r\n* fix timings\r\n\r\n* fix time\r\n\r\n* fix tuple assignments\r\n\r\n* add missing functions\r\n\r\n* fix code typo\r\n\r\n* uncomment funcs\r\n\r\n* add annotation step\r\n\r\n* add resume\r\n\r\n* add resume to filter\r\n\r\n* add extend\r\n\r\n* add gzip support\r\n\r\n* add resume sib step; annotate fix\r\n\r\n* gzip file support\r\n\r\n* remove print\r\n\r\n* add sklearn model\r\n\r\n* load pickle\r\n\r\n* add onnx support for model\r\n\r\n* fix spacing\r\n\r\n* fix minor mosaic code issues\r\n\r\n* fix rep_type vcf output\r\n\r\n* add README; add executable\r\n\r\n* update README\r\n\r\n* update README\r\n\r\n* update README","shortMessageHtmlLink":"First commit refactoring command line interface (#111)"}},{"before":null,"after":"bbb9144059a60bd301331ee26773d476fc413f3d","ref":"refs/heads/cli","pushedAt":"2024-06-11T19:23:43.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"corinsexton","name":"Corinne Sexton","path":"/corinsexton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13277644?s=80&v=4"},"commit":{"message":"add CHM13v2.0 support","shortMessageHtmlLink":"add CHM13v2.0 support"}},{"before":"8abdc7ecacfa1db415a2908ceb5181ed7d6d4dce","after":"ed962e0331563c003160f55497dbfc2a21c3e23b","ref":"refs/heads/xtea_mosaic","pushedAt":"2023-10-13T22:46:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"simoncchu","name":"Simon C Chu","path":"/simoncchu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/3340363?s=80&v=4"},"commit":{"message":"update readme","shortMessageHtmlLink":"update readme"}},{"before":"bbb9144059a60bd301331ee26773d476fc413f3d","after":"8abdc7ecacfa1db415a2908ceb5181ed7d6d4dce","ref":"refs/heads/xtea_mosaic","pushedAt":"2023-10-13T22:40:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"simoncchu","name":"Simon C Chu","path":"/simoncchu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/3340363?s=80&v=4"},"commit":{"message":"add version for mosaic TE insertion calling","shortMessageHtmlLink":"add version for mosaic TE insertion calling"}},{"before":null,"after":"bbb9144059a60bd301331ee26773d476fc413f3d","ref":"refs/heads/xtea_mosaic","pushedAt":"2023-10-13T22:10:57.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"simoncchu","name":"Simon C Chu","path":"/simoncchu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/3340363?s=80&v=4"},"commit":{"message":"add CHM13v2.0 support","shortMessageHtmlLink":"add CHM13v2.0 support"}},{"before":"20c7e9fbecbe4c0e35eb0766c4c7b4e6125fe71e","after":"bbb9144059a60bd301331ee26773d476fc413f3d","ref":"refs/heads/master","pushedAt":"2023-06-12T13:20:55.443Z","pushType":"push","commitsCount":2,"pusher":{"login":"simoncchu","name":"Simon C Chu","path":"/simoncchu","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/3340363?s=80&v=4"},"commit":{"message":"add CHM13v2.0 support","shortMessageHtmlLink":"add CHM13v2.0 support"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEcUBXmwA","startCursor":null,"endCursor":null}},"title":"Activity ยท parklab/xTea"}