{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":149824365,"defaultBranch":"master","name":"danbing-tk","ownerLogin":"ChaissonLab","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2018-09-21T22:22:13.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/35581706?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1712368482.0","currentOid":""},"activityList":{"items":[{"before":null,"after":"7621bd9db47aa0922014b46b472d26f325fa78b1","ref":"refs/heads/rarevar","pushedAt":"2024-04-06T01:54:42.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Added gapQC filter","shortMessageHtmlLink":"Added gapQC filter"}},{"before":"01439329d7077f8dc07bd82eea2b8d24c4e27bb9","after":"c1734d8ea5ebb7733631f73338995140c6bcea59","ref":"refs/heads/master","pushedAt":"2023-11-08T22:46:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Removed `H` in `ops`","shortMessageHtmlLink":"Removed H in ops"}},{"before":"564ed1eee486bdfd865a5358d67bfbd557a42882","after":"01439329d7077f8dc07bd82eea2b8d24c4e27bb9","ref":"refs/heads/master","pushedAt":"2023-11-08T22:44:16.000Z","pushType":"push","commitsCount":34,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Updated simmode=2. Added F1 score computation.","shortMessageHtmlLink":"Updated simmode=2. Added F1 score computation."}},{"before":null,"after":"4d4a1235fe4c8fd073a31c6300d94b5f189b43ad","ref":"refs/heads/master-sim2","pushedAt":"2023-11-08T20:24:46.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Fixed simmode=2","shortMessageHtmlLink":"Fixed simmode=2"}},{"before":"32f195258d5c6e3ad5e8cd0bc87e93fea87f73b2","after":"01439329d7077f8dc07bd82eea2b8d24c4e27bb9","ref":"refs/heads/threadingv1","pushedAt":"2023-11-06T18:50:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Updated simmode=2. Added F1 score computation.","shortMessageHtmlLink":"Updated simmode=2. Added F1 score computation."}},{"before":"a84886efd9780a5b85dc6e4b62c307d3fd4f3126","after":"32f195258d5c6e3ad5e8cd0bc87e93fea87f73b2","ref":"refs/heads/threadingv1","pushedAt":"2023-10-27T21:58:20.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Added logfile; code cleanup","shortMessageHtmlLink":"Added logfile; code cleanup"}},{"before":"39366b28a08a1b850c88085260577c4291074031","after":"a84886efd9780a5b85dc6e4b62c307d3fd4f3126","ref":"refs/heads/threadingv1","pushedAt":"2023-10-24T19:13:46.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Fixed bug in cerr msg","shortMessageHtmlLink":"Fixed bug in cerr msg"}},{"before":"2e5b422d3d6b9555386e61e2ff0dfa89a2049d17","after":"39366b28a08a1b850c88085260577c4291074031","ref":"refs/heads/threadingv1","pushedAt":"2023-10-18T18:36:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Fixed keq. Removed `'H'`. Better handling of `N` in read. Fixed `kmers` `cg.tr` bug in case of indel. Fixed edits merging/reversion. More debug message.","shortMessageHtmlLink":"Fixed keq. Removed 'H'. Better handling of N in read. Fixed `kmer…"}},{"before":"cd1ddd1a1b3420db91eb5bbd5c18cc077d89a67a","after":"2e5b422d3d6b9555386e61e2ff0dfa89a2049d17","ref":"refs/heads/threadingv1","pushedAt":"2023-09-29T03:35:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"CIGAR strings now consider merging adjacent edits or overlapping edits from forward/backward correction.\nFixed multiple bugs from overlapping/adjacent edits.\nFixed index error of `cg.es.insert`","shortMessageHtmlLink":"CIGAR strings now consider merging adjacent edits or overlapping edit…"}},{"before":"1a880b6a21ab48dd56c25b2a78f9a75a45e6a3e2","after":"cd1ddd1a1b3420db91eb5bbd5c18cc077d89a67a","ref":"refs/heads/threadingv1","pushedAt":"2023-09-26T05:10:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Fixed bugs in errorCorrection, CIGAR, TR annot, threadCheck. More debugging messages.","shortMessageHtmlLink":"Fixed bugs in errorCorrection, CIGAR, TR annot, threadCheck. More deb…"}},{"before":"75ea932f4ab1091f905b2ba328b62464478203d0","after":"1a880b6a21ab48dd56c25b2a78f9a75a45e6a3e2","ref":"refs/heads/threadingv1","pushedAt":"2023-09-23T00:20:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Added `ktools extract` to extract locus-RPGG from RPGG","shortMessageHtmlLink":"Added ktools extract to extract locus-RPGG from RPGG"}},{"before":"9c1e1c3629724cbb40348fa1c063eb4e796f83d2","after":"75ea932f4ab1091f905b2ba328b62464478203d0","ref":"refs/heads/threadingv1","pushedAt":"2023-09-19T21:25:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Updated usage and alignment output format","shortMessageHtmlLink":"Updated usage and alignment output format"}},{"before":"59f3d17f39679db70a43d351e31f42afb392acb1","after":"9c1e1c3629724cbb40348fa1c063eb4e796f83d2","ref":"refs/heads/threadingv1","pushedAt":"2023-09-19T21:20:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Fixed wrong CIGAR string in backward correction when there's indel\nAdded sanity check for CIGAR and aligned kmers","shortMessageHtmlLink":"Fixed wrong CIGAR string in backward correction when there's indel"}},{"before":"4f6bdc4beb82a992cf31c0796e40651c11dbf5d3","after":"59f3d17f39679db70a43d351e31f42afb392acb1","ref":"refs/heads/threadingv1","pushedAt":"2023-09-19T00:20:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Fixed bug where backward correction not fully patched with forward alignment","shortMessageHtmlLink":"Fixed bug where backward correction not fully patched with forward al…"}},{"before":"f2d19eaa374046136861c81fb57478ee3b368a40","after":"4f6bdc4beb82a992cf31c0796e40651c11dbf5d3","ref":"refs/heads/threadingv1","pushedAt":"2023-09-01T20:35:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"test","shortMessageHtmlLink":"test"}},{"before":"17b35f7cf61aab58fc48b17ac998caca7033d960","after":"f2d19eaa374046136861c81fb57478ee3b368a40","ref":"refs/heads/threadingv1","pushedAt":"2023-09-01T20:31:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"test","shortMessageHtmlLink":"test"}},{"before":"e022db67360879a80ed225c39ca57f63e1b108c0","after":"17b35f7cf61aab58fc48b17ac998caca7033d960","ref":"refs/heads/threadingv1","pushedAt":"2023-09-01T20:29:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Requires num of extended kmers in `errorCorrection` to be >= `MSC*edit.size()`\nFixed incorrect `nskip` in backward correction\nAdded threading sanity check `threadCheck`\nCode cleanup","shortMessageHtmlLink":"Requires num of extended kmers in errorCorrection to be >= `MSC*edi…"}},{"before":"2508ab69c07d91f4853a036aa3cc285e1d124ee3","after":"e022db67360879a80ed225c39ca57f63e1b108c0","ref":"refs/heads/threadingv1","pushedAt":"2023-08-30T18:15:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"test","shortMessageHtmlLink":"test"}},{"before":"defc490005c477dcebd19c493c0a10d76bf833fe","after":"2508ab69c07d91f4853a036aa3cc285e1d124ee3","ref":"refs/heads/threadingv1","pushedAt":"2023-08-30T18:01:18.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Added backward errorCorrection","shortMessageHtmlLink":"Added backward errorCorrection"}},{"before":"1dd9e9550e9b4e69eb5779f2b4688f1129f036c8","after":"defc490005c477dcebd19c493c0a10d76bf833fe","ref":"refs/heads/threadingv1","pushedAt":"2023-08-28T22:12:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Added common functions","shortMessageHtmlLink":"Added common functions"}},{"before":"22b78cb507fec5ec26f420c9f0d593b27d280854","after":"1dd9e9550e9b4e69eb5779f2b4688f1129f036c8","ref":"refs/heads/threadingv1","pushedAt":"2023-08-28T19:30:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Only output read header once for a read pair; Minor code cleaning/formatting","shortMessageHtmlLink":"Only output read header once for a read pair; Minor code cleaning/for…"}},{"before":"c3f2017ccb3fec4adc88fb51ad9c2891bd5305b2","after":"22b78cb507fec5ec26f420c9f0d593b27d280854","ref":"refs/heads/threadingv1","pushedAt":"2023-08-25T17:39:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Updated `.aln` file format","shortMessageHtmlLink":"Updated .aln file format"}},{"before":"af0067ecb15af451612b2707392c6de613bab2ce","after":"c3f2017ccb3fec4adc88fb51ad9c2891bd5305b2","ref":"refs/heads/threadingv1","pushedAt":"2023-08-23T23:46:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"writing aln operations/annotations in CIGAR string style","shortMessageHtmlLink":"writing aln operations/annotations in CIGAR string style"}},{"before":"f77d0a6696f8a3cff45c031a8f13a271d9cf06d0","after":"af0067ecb15af451612b2707392c6de613bab2ce","ref":"refs/heads/threadingv1","pushedAt":"2023-08-23T22:45:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Fixed indentation","shortMessageHtmlLink":"Fixed indentation"}},{"before":"022a9b20c0da274e5f9fbe8f3e5ea330b3f98074","after":"f77d0a6696f8a3cff45c031a8f13a271d9cf06d0","ref":"refs/heads/threadingv1","pushedAt":"2023-08-23T21:49:18.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Replaced `ops` with `cg.nt` and `cg.tr` for clearer nucleotide operations and TR annotation","shortMessageHtmlLink":"Replaced ops with cg.nt and cg.tr for clearer nucleotide operat…"}},{"before":"eebb58edfe28d6c02925e29392209c32716669d7","after":"022a9b20c0da274e5f9fbe8f3e5ea330b3f98074","ref":"refs/heads/threadingv1","pushedAt":"2023-08-22T17:28:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Set default `maxncorrection` = 4","shortMessageHtmlLink":"Set default maxncorrection = 4"}},{"before":"04b81256346c015f99967e572aedb2ed0d5bc3d1","after":"eebb58edfe28d6c02925e29392209c32716669d7","ref":"refs/heads/threadingv1","pushedAt":"2023-08-15T20:05:52.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Merge branch 'threadingv1' of https://github.com/ChaissonLab/danbing-tk into threadingv1","shortMessageHtmlLink":"Merge branch 'threadingv1' of https://github.com/ChaissonLab/danbing-tk…"}},{"before":"5609061bbc2995c99ff3dd4092308d01155b59a7","after":"04b81256346c015f99967e572aedb2ed0d5bc3d1","ref":"refs/heads/threadingv1","pushedAt":"2023-08-15T18:31:58.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Merge branch 'threadingv1' of https://github.com/ChaissonLab/danbing-tk into threadingv1\n\nConflicts:\n\tsrc/aQueryFasta_thread.cpp","shortMessageHtmlLink":"Merge branch 'threadingv1' of https://github.com/ChaissonLab/danbing-tk…"}},{"before":"410646a4e3a900d1a6c076537153eec49bc0ded2","after":"5609061bbc2995c99ff3dd4092308d01155b59a7","ref":"refs/heads/threadingv1","pushedAt":"2023-08-12T22:17:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Added a second parameter for . is now tunable.","shortMessageHtmlLink":"Added a second parameter for . is now tunable."}},{"before":"833f205db1c797f92215009783ab384748ef782f","after":"410646a4e3a900d1a6c076537153eec49bc0ded2","ref":"refs/heads/threadingv1","pushedAt":"2023-08-12T20:56:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"joyeuxnoel8","name":"Tsung-Yu Lu","path":"/joyeuxnoel8","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24736196?s=80&v=4"},"commit":{"message":"Fixed bug in leading edit operations. Now edits of nucleotides in the 1st kmer are shown.","shortMessageHtmlLink":"Fixed bug in leading edit operations. Now edits of nucleotides in the…"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEKWPtQwA","startCursor":null,"endCursor":null}},"title":"Activity · ChaissonLab/danbing-tk"}