{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":160230725,"defaultBranch":"master","name":"ntEdit","ownerLogin":"bcgsc","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2018-12-03T17:45:09.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/2319317?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1715444053.0","currentOid":""},"activityList":{"items":[{"before":"1ce1e5932c1cb10178c7c9ae824cf9af23e181dc","after":"9524ed716ae8177b54e8f1824d9fc6b76ae9b2d1","ref":"refs/heads/new_l_approach","pushedAt":"2024-05-21T20:23:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"},"commit":{"message":"Refactoring code","shortMessageHtmlLink":"Refactoring code"}},{"before":"93b1d22055eb8185baf260a584cfc5b9263c9a41","after":"1ce1e5932c1cb10178c7c9ae824cf9af23e181dc","ref":"refs/heads/new_l_approach","pushedAt":"2024-05-17T23:16:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"},"commit":{"message":"Retain INFO column from --vcf","shortMessageHtmlLink":"Retain INFO column from --vcf"}},{"before":"9496cd4d9dd36bd0ea602c02f4a5f64858caa6ba","after":"1e3260a808b6e58957f736fc84f7bfd3d80ce77c","ref":"refs/heads/master","pushedAt":"2024-05-14T01:00:37.000Z","pushType":"pr_merge","commitsCount":5,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Merge pull request #64 from bcgsc/warrenlr-patch-3\n\nUpdate ntedit.cpp","shortMessageHtmlLink":"Merge pull request #64 from bcgsc/warrenlr-patch-3"}},{"before":"751b199a829e482a02898a25d830d82d5c686f52","after":"34c19d2a0b0556709359405f677952eb1a14bf33","ref":"refs/heads/warrenlr-patch-3","pushedAt":"2024-05-14T00:55:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"},"commit":{"message":"ntedit.cpp fixes for clang-format","shortMessageHtmlLink":"ntedit.cpp fixes for clang-format"}},{"before":"0a14e3818492d0696b80a1928705f0c0c4fa5d2b","after":"751b199a829e482a02898a25d830d82d5c686f52","ref":"refs/heads/warrenlr-patch-3","pushedAt":"2024-05-14T00:42:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Update ntedit.cpp","shortMessageHtmlLink":"Update ntedit.cpp"}},{"before":"42d0428dc2f1924e562906cab56b3b1a4580c6c3","after":"0a14e3818492d0696b80a1928705f0c0c4fa5d2b","ref":"refs/heads/warrenlr-patch-3","pushedAt":"2024-05-14T00:34:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Update ntedit.cpp","shortMessageHtmlLink":"Update ntedit.cpp"}},{"before":null,"after":"42d0428dc2f1924e562906cab56b3b1a4580c6c3","ref":"refs/heads/warrenlr-patch-3","pushedAt":"2024-05-11T16:14:13.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Update ntedit.cpp\n\nadding VCF header to be VCF-compliant","shortMessageHtmlLink":"Update ntedit.cpp"}},{"before":"c871bbcb33292f8be2a4cf8cefbb95575ef2581e","after":"9496cd4d9dd36bd0ea602c02f4a5f64858caa6ba","ref":"refs/heads/master","pushedAt":"2024-04-26T15:42:55.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Merge pull request #63 from bcgsc/warrenlr-patch-2\n\nUpdate README.md","shortMessageHtmlLink":"Merge pull request #63 from bcgsc/warrenlr-patch-2"}},{"before":null,"after":"659e7395c3f1bdae75f9d32dc73de60665598122","ref":"refs/heads/warrenlr-patch-2","pushedAt":"2024-04-26T14:03:43.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Update README.md\n\nadded link to ntroot","shortMessageHtmlLink":"Update README.md"}},{"before":"6882ab6dcf971ad7c6f1902ce7cda0b040b725a8","after":null,"ref":"refs/heads/l_polish_mode","pushedAt":"2024-04-26T02:45:37.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"}},{"before":"ab94419f3451f8d73f2b0891d63abded2d42ee84","after":"c871bbcb33292f8be2a4cf8cefbb95575ef2581e","ref":"refs/heads/master","pushedAt":"2024-04-25T22:40:19.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Merge pull request #62 from bcgsc/l_polish_mode\n\nAllow -l to be used in polish mode","shortMessageHtmlLink":"Merge pull request #62 from bcgsc/l_polish_mode"}},{"before":"473c0404ea472168f6834ba0830e23f5cf647e3f","after":"6882ab6dcf971ad7c6f1902ce7cda0b040b725a8","ref":"refs/heads/l_polish_mode","pushedAt":"2024-04-25T22:06:37.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"},"commit":{"message":"Allow -l to be used in polish mode","shortMessageHtmlLink":"Allow -l to be used in polish mode"}},{"before":"2829ff9d558882ffae9ce1e1603e0d868cc5543e","after":"ab94419f3451f8d73f2b0891d63abded2d42ee84","ref":"refs/heads/master","pushedAt":"2024-04-25T22:04:51.000Z","pushType":"pr_merge","commitsCount":10,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Merge pull request #61 from bcgsc/cross-reference_indels\n\nFix the ntedit base insertion(s) and deletion(s) output VCF and added support to natively cross-reference indels within ntedit","shortMessageHtmlLink":"Merge pull request #61 from bcgsc/cross-reference_indels"}},{"before":null,"after":"473c0404ea472168f6834ba0830e23f5cf647e3f","ref":"refs/heads/l_polish_mode","pushedAt":"2024-04-25T20:31:38.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"},"commit":{"message":"Allow -l to be used in polish mode","shortMessageHtmlLink":"Allow -l to be used in polish mode"}},{"before":"17488b9efbc3823bcee473519cdca1fcfca5258b","after":"bf2454ed3a4ad982dafced7cc081f30f0a300bbe","ref":"refs/heads/cross-reference_indels","pushedAt":"2024-04-25T15:56:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"},"commit":{"message":"Fix for clang-format","shortMessageHtmlLink":"Fix for clang-format"}},{"before":"4777208de061e9cbc10a15f562892680c4ede683","after":"17488b9efbc3823bcee473519cdca1fcfca5258b","ref":"refs/heads/cross-reference_indels","pushedAt":"2024-04-25T15:47:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"},"commit":{"message":"Update demo files, bump all versions to 2.0.2","shortMessageHtmlLink":"Update demo files, bump all versions to 2.0.2"}},{"before":"54b974edd64fcf25db7b0836f458933486b07063","after":"4777208de061e9cbc10a15f562892680c4ede683","ref":"refs/heads/cross-reference_indels","pushedAt":"2024-04-25T15:28:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"},"commit":{"message":"Fixes for clang-format, remove commented-out lines","shortMessageHtmlLink":"Fixes for clang-format, remove commented-out lines"}},{"before":"c71c4f38480584a196e2705fe8d9333e68190af7","after":"54b974edd64fcf25db7b0836f458933486b07063","ref":"refs/heads/cross-reference_indels","pushedAt":"2024-04-25T01:15:39.000Z","pushType":"pr_merge","commitsCount":3,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Merge pull request #60 from bcgsc/master\n\nrebasing cross-reference_indels branch","shortMessageHtmlLink":"Merge pull request #60 from bcgsc/master"}},{"before":"c430f56a4b467d708bb7b75fd577b1ce4baf12ca","after":"c71c4f38480584a196e2705fe8d9333e68190af7","ref":"refs/heads/cross-reference_indels","pushedAt":"2024-04-25T01:12:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jwcodee","name":"JW","path":"/jwcodee","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/34543031?s=80&v=4"},"commit":{"message":"ntedit: fix insertion string creation bug","shortMessageHtmlLink":"ntedit: fix insertion string creation bug"}},{"before":"52b67bdc13dd16c167dd59ab0d9c9738f088fe4b","after":"c430f56a4b467d708bb7b75fd577b1ce4baf12ca","ref":"refs/heads/cross-reference_indels","pushedAt":"2024-04-24T23:54:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jwcodee","name":"JW","path":"/jwcodee","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/34543031?s=80&v=4"},"commit":{"message":"ntedit: use correct base as draft when reporting insertions","shortMessageHtmlLink":"ntedit: use correct base as draft when reporting insertions"}},{"before":"ac46b85f30be18bdb8b9c58ec5532525feeeeae4","after":"52b67bdc13dd16c167dd59ab0d9c9738f088fe4b","ref":"refs/heads/cross-reference_indels","pushedAt":"2024-04-24T20:19:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Update ntedit.cpp\n\nadded indel XR variant code\r\n-still need to fix insertion draft base (outstanding)","shortMessageHtmlLink":"Update ntedit.cpp"}},{"before":"ad246000740d65e0e1657d3b078f95d29cfaf4f6","after":null,"ref":"refs/heads/fix_fasta","pushedAt":"2024-04-24T20:17:01.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"}},{"before":"aea2853cee0d9bef0cf7ed31bbfc57783751bb14","after":"2829ff9d558882ffae9ce1e1603e0d868cc5543e","ref":"refs/heads/master","pushedAt":"2024-04-24T20:03:10.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Merge pull request #59 from bcgsc/fix_fasta\n\nFix usage of fasta files for --reads, remove bg and zip as supported","shortMessageHtmlLink":"Merge pull request #59 from bcgsc/fix_fasta"}},{"before":null,"after":"ad246000740d65e0e1657d3b078f95d29cfaf4f6","ref":"refs/heads/fix_fasta","pushedAt":"2024-04-24T18:21:02.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"lcoombe","name":"Lauren Coombe","path":"/lcoombe","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11697335?s=80&v=4"},"commit":{"message":"Fix usage of fasta files for --reads, remove bg and zip as supported","shortMessageHtmlLink":"Fix usage of fasta files for --reads, remove bg and zip as supported"}},{"before":"8af22ac122bb99ad9761e9107d8180c969f99ce7","after":"ac46b85f30be18bdb8b9c58ec5532525feeeeae4","ref":"refs/heads/cross-reference_indels","pushedAt":"2024-04-24T03:04:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Update ntedit.cpp\n\nbump version","shortMessageHtmlLink":"Update ntedit.cpp"}},{"before":"aea2853cee0d9bef0cf7ed31bbfc57783751bb14","after":"8af22ac122bb99ad9761e9107d8180c969f99ce7","ref":"refs/heads/cross-reference_indels","pushedAt":"2024-04-24T03:04:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Update ntedit.cpp\n\nfixes the way insertions are reported in the output VCF: DRAFTBASE. DRAFTBASEinsertion\r\n\r\nalso fix the position of deletion in the changes.tsv to be consistent with that of the output VCF","shortMessageHtmlLink":"Update ntedit.cpp"}},{"before":null,"after":"aea2853cee0d9bef0cf7ed31bbfc57783751bb14","ref":"refs/heads/cross-reference_indels","pushedAt":"2024-04-24T02:24:47.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"warrenlr","name":"René","path":"/warrenlr","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5719157?s=80&v=4"},"commit":{"message":"Cross reference against vcf, if provided, when variant has lower allelic depth than draft (#58)\n\n* ntedit: xref when variant has less support than draft\r\n\r\n* ntedit: clang-format\r\n\r\n* azure: use env to run make check\r\n\r\n* ntedit: replace base when xfer if snv_mode_no_edit is false\r\n\r\n* ntedit: remove comments","shortMessageHtmlLink":"Cross reference against vcf, if provided, when variant has lower alle…"}},{"before":"48d933325fd029446a389ee0a9971d160fb4fceb","after":"aea2853cee0d9bef0cf7ed31bbfc57783751bb14","ref":"refs/heads/master","pushedAt":"2024-04-24T01:01:43.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"jwcodee","name":"JW","path":"/jwcodee","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/34543031?s=80&v=4"},"commit":{"message":"Cross reference against vcf, if provided, when variant has lower allelic depth than draft (#58)\n\n* ntedit: xref when variant has less support than draft\r\n\r\n* ntedit: clang-format\r\n\r\n* azure: use env to run make check\r\n\r\n* ntedit: replace base when xfer if snv_mode_no_edit is false\r\n\r\n* ntedit: remove comments","shortMessageHtmlLink":"Cross reference against vcf, if provided, when variant has lower alle…"}},{"before":"c2c155413df0d7fc18aea50e2dbab290c50793ba","after":"a5fabb7b33f0aacab2f15ac6db15582d33692f1e","ref":"refs/heads/vcf_xref_bug_fix","pushedAt":"2024-04-24T00:53:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jwcodee","name":"JW","path":"/jwcodee","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/34543031?s=80&v=4"},"commit":{"message":"ntedit: remove comments","shortMessageHtmlLink":"ntedit: remove comments"}},{"before":"23a1bc92c4ec6d8f202b7f6d4445e700c110a190","after":"c2c155413df0d7fc18aea50e2dbab290c50793ba","ref":"refs/heads/vcf_xref_bug_fix","pushedAt":"2024-04-23T21:29:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jwcodee","name":"JW","path":"/jwcodee","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/34543031?s=80&v=4"},"commit":{"message":"ntedit: replace base when xfer if snv_mode_no_edit is false","shortMessageHtmlLink":"ntedit: replace base when xfer if snv_mode_no_edit is false"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEUEH5_QA","startCursor":null,"endCursor":null}},"title":"Activity · bcgsc/ntEdit"}