{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":262302802,"defaultBranch":"master","name":"StORF-Reporter","ownerLogin":"NickJD","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2020-05-08T11:12:50.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/5814452?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1708975564.0","currentOid":""},"activityList":{"items":[{"before":"4ec58723552885c70bb402acbfd937952aa798d2","after":"427110bff4c15007e4dd352529afca4169f4d659","ref":"refs/heads/master","pushedAt":"2024-02-26T19:14:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.3.4: Some minor changes to UR-Extractor output handling\n\nUR-Extractor now conforms better to 'standard' FASTA and GFF formats.\nAdded 'Multi_Contig_Genome' test directory for testing fragmented genomes.","shortMessageHtmlLink":"v1.3.4: Some minor changes to UR-Extractor output handling"}},{"before":"a89e774d431c0bd71ba80e9ecaf57a12392f9a90","after":"4ec58723552885c70bb402acbfd937952aa798d2","ref":"refs/heads/master","pushedAt":"2024-02-08T17:58:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.3.3: Fixed Con-StORFs middle stop and more IO errors.\n\n* Fixed - Con-StORFs were incorrectly being reported with middle '*' when 'remove_stop' was set to True (default)\n* Fixed - In some instances, when using -odir with 'Multiple_Genomes', 'Multiple_Combined_GFFs' or 'Multiple_GFFs', the input directory name was being applied to the output filename.","shortMessageHtmlLink":"v1.3.3: Fixed Con-StORFs middle stop and more IO errors."}},{"before":"7915c28401d8105512286487a143d6225d5e49b5","after":"a89e774d431c0bd71ba80e9ecaf57a12392f9a90","ref":"refs/heads/master","pushedAt":"2024-02-08T00:01:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.3.2: Fixed an issue with the hashing of the StORF IDs.\n\nThe hashing of StORF IDs may have been different between GFF/DNA and the AA outputs. Now the hashing takes the GFF input filename or in the case of a Pyrodigal run, will take the input FASTA filename.","shortMessageHtmlLink":"v1.3.2: Fixed an issue with the hashing of the StORF IDs."}},{"before":"a2856e834a709f4dee154cbbd636ea0db801f185","after":"7915c28401d8105512286487a143d6225d5e49b5","ref":"refs/heads/master","pushedAt":"2024-01-21T22:08:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.3.1: Fixed FASTA output and empty dir handling for Multiple_Out_Dirs","shortMessageHtmlLink":"v1.3.1: Fixed FASTA output and empty dir handling for Multiple_Out_Dirs"}},{"before":"3459390f9e4d6bf75abfb0a09f49a2ebf7cd36db","after":"a2856e834a709f4dee154cbbd636ea0db801f185","ref":"refs/heads/master","pushedAt":"2023-12-20T19:21:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.3.0: 'Multiple_Out_Dirs' option added\n\nStORF-Reporter can now be run on a directory containing multiple Prokka/Bakta output directories.","shortMessageHtmlLink":"v1.3.0: 'Multiple_Out_Dirs' option added"}},{"before":"66083f7cb69dc4179eadd8d696bb5de9253295e7","after":"3459390f9e4d6bf75abfb0a09f49a2ebf7cd36db","ref":"refs/heads/master","pushedAt":"2023-12-18T23:18:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.2.0: Reworked user IO for more user-control and to be OS independent\n\nFinalised overhaul of user IO to accommodate user requests and become OS independent for StORF-Reporter.","shortMessageHtmlLink":"v1.2.0: Reworked user IO for more user-control and to be OS independent"}},{"before":"e2f2b9b4109aed22322e018b4ca572a8e3beefd7","after":"66083f7cb69dc4179eadd8d696bb5de9253295e7","ref":"refs/heads/master","pushedAt":"2023-12-17T00:36:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"Reworking StORF-Reporter IO to be more flexible and OS independent","shortMessageHtmlLink":"Reworking StORF-Reporter IO to be more flexible and OS independent"}},{"before":"d242179d8fac5964b93a0d6feac13bd307c0f20f","after":"e2f2b9b4109aed22322e018b4ca572a8e3beefd7","ref":"refs/heads/master","pushedAt":"2023-12-11T02:51:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"Pushed missing config changes for v.1.1.4","shortMessageHtmlLink":"Pushed missing config changes for v.1.1.4"}},{"before":"9ade72b2335971abab27e9cf8def2af1bec0715f","after":"d242179d8fac5964b93a0d6feac13bd307c0f20f","ref":"refs/heads/master","pushedAt":"2023-12-11T02:48:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.1.4: Fixed output IDs for Con-StORFs","shortMessageHtmlLink":"v1.1.4: Fixed output IDs for Con-StORFs"}},{"before":"843eb3cbd28ee3a9852fbf316ff211790fd84941","after":"9ade72b2335971abab27e9cf8def2af1bec0715f","ref":"refs/heads/master","pushedAt":"2023-12-11T01:07:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.1.3: Fixed output format for StORF-Extractor\n\nFixed output format of StORF-Extractor to be more consistent with StORF-Reporter/Finder.","shortMessageHtmlLink":"v1.1.3: Fixed output format for StORF-Extractor"}},{"before":"f70d5f98ad3c29845097e4b54a1769fca6cebc96","after":"843eb3cbd28ee3a9852fbf316ff211790fd84941","ref":"refs/heads/master","pushedAt":"2023-12-09T18:49:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.1.2: Fixed a number of output bugs and reworked/simplified some code.\n\nBug link: https://github.com/NickJD/StORF-Reporter/issues/3#issue-2015619725","shortMessageHtmlLink":"v1.1.2: Fixed a number of output bugs and reworked/simplified some code."}},{"before":"8991c5a0383b32d8ee2b56e46e7e709fac2ccb5e","after":"f70d5f98ad3c29845097e4b54a1769fca6cebc96","ref":"refs/heads/master","pushedAt":"2023-11-06T00:34:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"Added Visual Abstract to README","shortMessageHtmlLink":"Added Visual Abstract to README"}},{"before":"f6e1dea53f7c93226edfce390db86ec0f0cc56c6","after":"8991c5a0383b32d8ee2b56e46e7e709fac2ccb5e","ref":"refs/heads/master","pushedAt":"2023-11-04T21:18:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.1.1: API handle changed to reflect Pyrodigal update","shortMessageHtmlLink":"v1.1.1: API handle changed to reflect Pyrodigal update"}},{"before":"f90832253c8b5ff4a6d4ada1f46f7295e8bdf11d","after":"f6e1dea53f7c93226edfce390db86ec0f0cc56c6","ref":"refs/heads/master","pushedAt":"2023-10-29T17:31:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"Updated readme to reflect publication of StORF-Reporter in NAR.","shortMessageHtmlLink":"Updated readme to reflect publication of StORF-Reporter in NAR."}},{"before":"5ff1fcd09b47e6d99477785bf9e9495facdc0410","after":"f90832253c8b5ff4a6d4ada1f46f7295e8bdf11d","ref":"refs/heads/master","pushedAt":"2023-08-21T19:30:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.1.0: Fixes and additional options for StORF-Extractor/Finder","shortMessageHtmlLink":"v1.1.0: Fixes and additional options for StORF-Extractor/Finder"}},{"before":"0600d03078d394e4e58329204adfbe058f36026e","after":"5ff1fcd09b47e6d99477785bf9e9495facdc0410","ref":"refs/heads/master","pushedAt":"2023-07-10T21:07:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.0.2: bug fixed to account for GFFs with spaces in 'source' entries","shortMessageHtmlLink":"v1.0.2: bug fixed to account for GFFs with spaces in 'source' entries"}},{"before":"c4804fded35a4da607e2be0aada09ecc1ce0f93b","after":"0600d03078d394e4e58329204adfbe058f36026e","ref":"refs/heads/master","pushedAt":"2023-07-10T20:51:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.0.2: Minor bugfix to outfile handling","shortMessageHtmlLink":"v1.0.2: Minor bugfix to outfile handling"}},{"before":"b4807f41a9ef51ca51279ca5d5e82c44fc53b959","after":"c4804fded35a4da607e2be0aada09ecc1ce0f93b","ref":"refs/heads/master","pushedAt":"2023-07-03T16:57:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"Updated readme and fixed StORF-Extractor bug","shortMessageHtmlLink":"Updated readme and fixed StORF-Extractor bug"}},{"before":"31f56013b8b0a77ea1ec11b3175c6a37b1ef1516","after":"b4807f41a9ef51ca51279ca5d5e82c44fc53b959","ref":"refs/heads/master","pushedAt":"2023-06-06T02:47:07.069Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.0.1: Bug fix for calling StORF-Reporter on multiple Bakta/Prokka GFFs","shortMessageHtmlLink":"v1.0.1: Bug fix for calling StORF-Reporter on multiple Bakta/Prokka GFFs"}},{"before":"203490a15eaeadefd638c362dba576d610221e5c","after":"31f56013b8b0a77ea1ec11b3175c6a37b1ef1516","ref":"refs/heads/master","pushedAt":"2023-05-28T21:03:55.492Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v1.0.0: First full release of StORF-Reporter with additions & bug fixes\n\nThis release includes a number of bug fixes, especially for file IO handling and new subpackages for managing StORFs after they have been extracted and added to a new GFF.","shortMessageHtmlLink":"v1.0.0: First full release of StORF-Reporter with additions & bug fixes"}},{"before":"2c6f9564a12e05065ebf89de958fe1c111a9edba","after":"203490a15eaeadefd638c362dba576d610221e5c","ref":"refs/heads/master","pushedAt":"2023-05-28T14:27:38.637Z","pushType":"push","commitsCount":2,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'origin/master'","shortMessageHtmlLink":"Merge remote-tracking branch 'origin/master'"}},{"before":"540bb6d5d9206e91ce08781d8616f98ea6ca7240","after":"2c6f9564a12e05065ebf89de958fe1c111a9edba","ref":"refs/heads/master","pushedAt":"2023-05-14T21:31:03.739Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"Added new tool - StORF-Remover\n\nStORF-Remover can be used to remove StORFs from extended GFF files which do not have a Diamond/BLAST user-defined bit score.","shortMessageHtmlLink":"Added new tool - StORF-Remover"}},{"before":"2b3ab21d492939b550d9d773ee8eb1ad846e49c9","after":"540bb6d5d9206e91ce08781d8616f98ea6ca7240","ref":"refs/heads/master","pushedAt":"2023-04-05T21:01:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"Updated Genome UR and StORF files and aux scripts updated","shortMessageHtmlLink":"Updated Genome UR and StORF files and aux scripts updated"}},{"before":"0c2ae14966636be1e6d6ca7c8d1ddb38113fd612","after":"2b3ab21d492939b550d9d773ee8eb1ad846e49c9","ref":"refs/heads/master","pushedAt":"2023-03-10T12:14:10.930Z","pushType":"push","commitsCount":1,"pusher":{"login":"NickJD","name":"Nick Dimonaco","path":"/NickJD","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5814452?s=80&v=4"},"commit":{"message":"v0.7.4: Fixed bug in filename handling.","shortMessageHtmlLink":"v0.7.4: Fixed bug in filename handling."}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEBcGGlAA","startCursor":null,"endCursor":null}},"title":"Activity ยท NickJD/StORF-Reporter"}