{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":41131628,"defaultBranch":"master","name":"canu","ownerLogin":"marbl","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2015-08-21T03:10:42.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/6492934?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1718602546.0","currentOid":""},"activityList":{"items":[{"before":"0d51e7d344082dbe1ad0e7f1c812a57a27998fb6","after":"39ef0f2ff77d4252bd12bdbad621568fc8723c87","ref":"refs/heads/master","pushedAt":"2024-09-24T18:49:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"skoren","name":"Sergey Koren","path":"/skoren","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/923478?s=80&v=4"},"commit":{"message":"update to allow per-contig trim setting in utgcns","shortMessageHtmlLink":"update to allow per-contig trim setting in utgcns"}},{"before":"bce488fa4771cdb8a5e988f25c4a0e1aebf55f08","after":"0d51e7d344082dbe1ad0e7f1c812a57a27998fb6","ref":"refs/heads/master","pushedAt":"2024-09-17T14:08:26.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"skoren","name":"Sergey Koren","path":"/skoren","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/923478?s=80&v=4"},"commit":{"message":"fix too low padding","shortMessageHtmlLink":"fix too low padding"}},{"before":"338af7ac60d7148615ca7b4ecf26fa588d2b4c6c","after":"bce488fa4771cdb8a5e988f25c4a0e1aebf55f08","ref":"refs/heads/master","pushedAt":"2024-09-09T17:23:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"skoren","name":"Sergey Koren","path":"/skoren","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/923478?s=80&v=4"},"commit":{"message":"fail if mkfifo fails","shortMessageHtmlLink":"fail if mkfifo fails"}},{"before":"f405dd3da2c7ea00a405d95363152944de6f84e8","after":"338af7ac60d7148615ca7b4ecf26fa588d2b4c6c","ref":"refs/heads/master","pushedAt":"2024-08-16T02:06:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"skoren","name":"Sergey Koren","path":"/skoren","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/923478?s=80&v=4"},"commit":{"message":"fix missing caExit include (issue #2334)","shortMessageHtmlLink":"fix missing caExit include (issue <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2459728022\" data-permission-text=\"Title is private\" data-url=\"https://github.com/marbl/canu/issues/2334\" data-hovercard-type=\"issue\" data-hovercard-url=\"/marbl/canu/issues/2334/hovercard\" href=\"https://github.com/marbl/canu/issues/2334\">#2334</a>)"}},{"before":"f1cfd2a61068b45f5ad89578b58912f2ce65767f","after":"f405dd3da2c7ea00a405d95363152944de6f84e8","ref":"refs/heads/master","pushedAt":"2024-07-24T14:28:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"skoren","name":"Sergey Koren","path":"/skoren","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/923478?s=80&v=4"},"commit":{"message":"minor fixes utgcns, properly handle skip bases in layouts","shortMessageHtmlLink":"minor fixes utgcns, properly handle skip bases in layouts"}},{"before":"a5e7910628fc454ee07e0a42256f74cbc28d712b","after":"f1cfd2a61068b45f5ad89578b58912f2ce65767f","ref":"refs/heads/master","pushedAt":"2024-07-24T14:03:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"skoren","name":"Sergey Koren","path":"/skoren","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/923478?s=80&v=4"},"commit":{"message":"fix confusion between lowqual vs skipcns flags, move constants to top of file","shortMessageHtmlLink":"fix confusion between lowqual vs skipcns flags, move constants to top…"}},{"before":"ee6d277b5a83ca77e5f5204ea014336caef6599d","after":"a5e7910628fc454ee07e0a42256f74cbc28d712b","ref":"refs/heads/master","pushedAt":"2024-07-23T17:30:43.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Remove parens around return values, ;'s at end of methods.","shortMessageHtmlLink":"Remove parens around return values, ;'s at end of methods."}},{"before":"5e923bf889b612bcbff77c58720f3080fb86ca8d","after":"ee6d277b5a83ca77e5f5204ea014336caef6599d","ref":"refs/heads/master","pushedAt":"2024-07-23T15:43:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Fix a few issues detecting when coverage is too low (or zero).  Issue #2320.","shortMessageHtmlLink":"Fix a few issues detecting when coverage is too low (or zero). Issue <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2343145598\" data-permission-text=\"Title is private\" data-url=\"https://github.com/marbl/canu/issues/2320\" data-hovercard-type=\"issue\" data-hovercard-url=\"/marbl/canu/issues/2320/hovercard\" href=\"https://github.com/marbl/canu/issues/2320\">#…</a>"}},{"before":"60609787f7488d33d28a4dc32c0f6a8f9d18ce68","after":"5e923bf889b612bcbff77c58720f3080fb86ca8d","ref":"refs/heads/master","pushedAt":"2024-07-22T21:16:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Don't check haplotyping resources unless haplotyping is enabled.  Issue #1911.","shortMessageHtmlLink":"Don't check haplotyping resources unless haplotyping is enabled. Issue <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"821437752\" data-permission-text=\"Title is private\" data-url=\"https://github.com/marbl/canu/issues/1911\" data-hovercard-type=\"issue\" data-hovercard-url=\"/marbl/canu/issues/1911/hovercard\" href=\"https://github.com/marbl/canu/issues/1911\">…</a>"}},{"before":"2aa139ec7eb4857a383425500ccf205d94f3af7d","after":"60609787f7488d33d28a4dc32c0f6a8f9d18ce68","ref":"refs/heads/master","pushedAt":"2024-07-22T16:18:37.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Warn against using 'ovl' for correction; remove 'overlapper=' parameter alias.  Issue 1924.","shortMessageHtmlLink":"Warn against using 'ovl' for correction; remove 'overlapper=' paramet…"}},{"before":"1449b1a7e8e0d35deaf1a444a21d7817b8e0f977","after":"2aa139ec7eb4857a383425500ccf205d94f3af7d","ref":"refs/heads/master","pushedAt":"2024-07-21T12:35:40.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Use more reliable slope-based histogram min detection in splitHaplotype.  Issue #2189.","shortMessageHtmlLink":"Use more reliable slope-based histogram min detection in splitHaploty…"}},{"before":"8a09ff58bf7fafd0dc6df341c622743cfb471bc5","after":"1449b1a7e8e0d35deaf1a444a21d7817b8e0f977","ref":"refs/heads/master","pushedAt":"2024-07-18T17:07:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"skoren","name":"Sergey Koren","path":"/skoren","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/923478?s=80&v=4"},"commit":{"message":"don't split in the middle of a read for trio inputs","shortMessageHtmlLink":"don't split in the middle of a read for trio inputs"}},{"before":"e3ec0ab33fe6671ec5e699f48b64555798b6f084","after":"8a09ff58bf7fafd0dc6df341c622743cfb471bc5","ref":"refs/heads/master","pushedAt":"2024-07-17T20:37:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Drop bogart memory requirements, especially for HiFi.  Issue #1788.","shortMessageHtmlLink":"Drop bogart memory requirements, especially for HiFi. Issue <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"692842532\" data-permission-text=\"Title is private\" data-url=\"https://github.com/marbl/canu/issues/1788\" data-hovercard-type=\"issue\" data-hovercard-url=\"/marbl/canu/issues/1788/hovercard\" href=\"https://github.com/marbl/canu/issues/1788\">#1788</a>."}},{"before":"e4386f9ca5452d059cffb0b7e7f19e2e1521bb63","after":"e3ec0ab33fe6671ec5e699f48b64555798b6f084","ref":"refs/heads/master","pushedAt":"2024-07-17T19:28:17.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Create seqStore outside of correction/trimming stages so we can detect pre-corrected/pre-trimmed reads.  Issue #1781.","shortMessageHtmlLink":"Create seqStore outside of correction/trimming stages so we can detec…"}},{"before":"afd271c87e18a48a8dbc904d2f0e526addbed188","after":"e4386f9ca5452d059cffb0b7e7f19e2e1521bb63","ref":"refs/heads/master","pushedAt":"2024-07-17T19:01:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"skoren","name":"Sergey Koren","path":"/skoren","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/923478?s=80&v=4"},"commit":{"message":"initialize tpos to appropriate value not 0","shortMessageHtmlLink":"initialize tpos to appropriate value not 0"}},{"before":"7ca774a6a3a7ed07237f55bba368195bfef5c446","after":"afd271c87e18a48a8dbc904d2f0e526addbed188","ref":"refs/heads/master","pushedAt":"2024-07-17T13:31:56.000Z","pushType":"push","commitsCount":21,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Merge 'bamoutput' into master.","shortMessageHtmlLink":"Merge 'bamoutput' into master."}},{"before":"e870a815cbd730d8e6338ed3708773295f08f2f1","after":"b871d94c72d7553861b67c3b7d855305f74dce53","ref":"refs/heads/bamoutput","pushedAt":"2024-07-17T13:20:06.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Save aligned CIGAR to .cns output files for later dumping to .bam files; options cnsAlign and bamOutput control this.  Bump on-disk tig format version to 2.","shortMessageHtmlLink":"Save aligned CIGAR to .cns output files for later dumping to .bam fil…"}},{"before":"c61ebbb7a5f90abb9c034650e2fd95642138de31","after":"7ca774a6a3a7ed07237f55bba368195bfef5c446","ref":"refs/heads/master","pushedAt":"2024-07-15T18:51:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"skoren","name":"Sergey Koren","path":"/skoren","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/923478?s=80&v=4"},"commit":{"message":"don't skip the last tig","shortMessageHtmlLink":"don't skip the last tig"}},{"before":"1121ee7e35ce4efaeaaec9ed7d87c8d6ffb052ec","after":"e870a815cbd730d8e6338ed3708773295f08f2f1","ref":"refs/heads/bamoutput","pushedAt":"2024-07-15T09:50:54.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Save aligned CIGAR to .cns output files for later dumping to .bam files; options cnsAlign and bamOutput control this.  Bump on-disk tig format version to 2.","shortMessageHtmlLink":"Save aligned CIGAR to .cns output files for later dumping to .bam fil…"}},{"before":"bae6426223a5542d23da245fda57286da7c3ef4b","after":"1121ee7e35ce4efaeaaec9ed7d87c8d6ffb052ec","ref":"refs/heads/bamoutput","pushedAt":"2024-07-11T02:29:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Accept samtools/htslib version strings of x.y.z or x.y (or even XYZ) when checking if they can run.","shortMessageHtmlLink":"Accept samtools/htslib version strings of x.y.z or x.y (or even XYZ) …"}},{"before":"343bcf1d8a95add5e6eebe0dabd296c7661cff58","after":"bae6426223a5542d23da245fda57286da7c3ef4b","ref":"refs/heads/bamoutput","pushedAt":"2024-07-07T21:17:19.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Update utility to get SAM/FASTQ and HTSlib fixes.","shortMessageHtmlLink":"Update utility to get SAM/FASTQ and HTSlib fixes."}},{"before":"4085852a1381aa0da1373b0cdcbd052cafe8c89d","after":"343bcf1d8a95add5e6eebe0dabd296c7661cff58","ref":"refs/heads/bamoutput","pushedAt":"2024-06-28T15:39:30.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Add script to compile using all compilers.  FreeBSD specific.","shortMessageHtmlLink":"Add script to compile using all compilers. FreeBSD specific."}},{"before":"fc09baea532435389a39083b28aab059ef97bed9","after":"4085852a1381aa0da1373b0cdcbd052cafe8c89d","ref":"refs/heads/bamoutput","pushedAt":"2024-06-24T08:19:16.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Fix adjustPosition() exceeding length of _templateToCNS[] by one.","shortMessageHtmlLink":"Fix adjustPosition() exceeding length of _templateToCNS[] by one."}},{"before":"2a092294c49c51517925c269828065d818ed28c7","after":"fc09baea532435389a39083b28aab059ef97bed9","ref":"refs/heads/bamoutput","pushedAt":"2024-06-20T09:19:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Fix memory leaks, logging, handle unaligned reads in BAM output.","shortMessageHtmlLink":"Fix memory leaks, logging, handle unaligned reads in BAM output."}},{"before":null,"after":"2a092294c49c51517925c269828065d818ed28c7","ref":"refs/heads/bamoutput","pushedAt":"2024-06-17T05:35:46.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Add support for BAM output of consensus pseudo-multi-align.","shortMessageHtmlLink":"Add support for BAM output of consensus pseudo-multi-align."}},{"before":"5ae8521e519cd6872efe5eb2617cef9e07c94896","after":"c61ebbb7a5f90abb9c034650e2fd95642138de31","ref":"refs/heads/master","pushedAt":"2024-04-19T17:31:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"skoren","name":"Sergey Koren","path":"/skoren","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/923478?s=80&v=4"},"commit":{"message":"Fix going out of bounds when adjusting bounds off the end (verkko issue #247)","shortMessageHtmlLink":"Fix going out of bounds when adjusting bounds off the end (verkko issue "}},{"before":"8e5787df59722212881c2c9017bb10b17606a3d3","after":"5ae8521e519cd6872efe5eb2617cef9e07c94896","ref":"refs/heads/master","pushedAt":"2024-03-14T06:04:14.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Remove kmers-v2 from build; update submodules to get new FASTQ-or-SAM heuristic.","shortMessageHtmlLink":"Remove kmers-v2 from build; update submodules to get new FASTQ-or-SAM…"}},{"before":"9fc7610eea58f52e48d22ee6db587f55a82a77d0","after":"8e5787df59722212881c2c9017bb10b17606a3d3","ref":"refs/heads/master","pushedAt":"2024-03-06T18:36:52.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Add two stale but possibly useful comments on findErrors.","shortMessageHtmlLink":"Add two stale but possibly useful comments on findErrors."}},{"before":"6b86fef7a7862f75d1d0d7cdcf229ae0e9d0c93e","after":"9fc7610eea58f52e48d22ee6db587f55a82a77d0","ref":"refs/heads/master","pushedAt":"2024-03-05T15:03:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Add SAM/BAM/CRAM support.","shortMessageHtmlLink":"Add SAM/BAM/CRAM support."}},{"before":"1a3d82fd004d865bf5192c8c006818536dc4d51f","after":"6b86fef7a7862f75d1d0d7cdcf229ae0e9d0c93e","ref":"refs/heads/master","pushedAt":"2024-02-13T15:50:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"brianwalenz","name":"Brian Walenz","path":"/brianwalenz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8249720?s=80&v=4"},"commit":{"message":"Handle recursive make in submodules; version number in main.mk; one-off custom targets in main.mk.","shortMessageHtmlLink":"Handle recursive make in submodules; version number in main.mk; one-o…"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yNFQxODo0OToxMC4wMDAwMDBazwAAAAS_hJRW","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wMi0xM1QxNTo1MDoyNy4wMDAwMDBazwAAAAP5qKh1"}},"title":"Activity · marbl/canu"}