{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":297981304,"defaultBranch":"master","name":"fDOG","ownerLogin":"BIONF","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2020-09-23T13:37:25.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/21359313?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1717667214.0","currentOid":""},"activityList":{"items":[{"before":"3a3081e052e14fe0b019167573c22b85292cadc6","after":"01c94ba08c8d5217356943bb21f5f714c592cae7","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2024-06-20T14:16:52.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"bugfix using --strict (#48)","shortMessageHtmlLink":"bugfix using --strict (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2364575182\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BIONF/fDOG/issues/48\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BIONF/fDOG/pull/48/hovercard\" href=\"https://github.com/BIONF/fDOG/pull/48\">#48</a>)"}},{"before":"dddd57a1dcde85b525624ddd508b94f72610e757","after":"3a3081e052e14fe0b019167573c22b85292cadc6","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2024-06-18T12:57:30.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"Improvements fdog.addAssembly script (#47)\n\n* Updated fdog.addAssembly module\r\n\r\n* improved call of main fuction\r\n\r\n* Improved help function","shortMessageHtmlLink":"Improvements fdog.addAssembly script (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2359803337\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BIONF/fDOG/issues/47\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BIONF/fDOG/pull/47/hovercard\" href=\"https://github.com/BIONF/fDOG/pull/47\">#47</a>)"}},{"before":"c38687e927c0bdc9a9db4442cf2e17e9cb3f18f0","after":"dddd57a1dcde85b525624ddd508b94f72610e757","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2024-06-13T11:20:17.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"v 0.1.5.1 (#45)\n\n* bug fix debug mode\r\n\r\n* updated check_ref_spec function\r\n\r\n* updated check_ref_spec function, added region output if augustus is used\r\n\r\n* update get_distance_function\r\n\r\n* bug fix check_ref_spec function\r\n\r\n* v 0.1.5.1\r\n\r\n* update output containing candidate regions\r\n\r\n* bugfix\r\n\r\n---------\r\n\r\nCo-authored-by: trvinh <trvinh@gmail.com>","shortMessageHtmlLink":"v 0.1.5.1 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2350879679\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BIONF/fDOG/issues/45\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BIONF/fDOG/pull/45/hovercard\" href=\"https://github.com/BIONF/fDOG/pull/45\">#45</a>)"}},{"before":"60ae899fe228e83a616fb8593af72d15d8a888ea","after":"c38687e927c0bdc9a9db4442cf2e17e9cb3f18f0","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2024-06-13T09:29:42.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"Update of some functions to improve I/O operations  (#44)","shortMessageHtmlLink":"Update of some functions to improve I/O operations (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2350653407\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BIONF/fDOG/issues/44\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BIONF/fDOG/pull/44/hovercard\" href=\"https://github.com/BIONF/fDOG/pull/44\">#44</a>)"}},{"before":"3893e6610f2c913ae0c440d34aded88ae2b36e95","after":"e9340cf9fa9b5fd30c1fc3a895362075909b6d4f","ref":"refs/heads/master","pushedAt":"2024-06-06T09:46:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"check duplicated ids in mergeOutput for fasta files","shortMessageHtmlLink":"check duplicated ids in mergeOutput for fasta files"}},{"before":"29afb5261976dd96b3de689ee0e12e43ba52f76d","after":"3893e6610f2c913ae0c440d34aded88ae2b36e95","ref":"refs/heads/master","pushedAt":"2024-06-03T09:40:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"added option to use user-defined annotool file","shortMessageHtmlLink":"added option to use user-defined annotool file"}},{"before":"a6019906a84e96d4e4fe587a3cc30a0aca1cb187","after":"29afb5261976dd96b3de689ee0e12e43ba52f76d","ref":"refs/heads/master","pushedAt":"2024-04-22T13:09:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"changed error msg for seed ident","shortMessageHtmlLink":"changed error msg for seed ident"}},{"before":"359e739c37e9f9e9d20ecd93e3fe84807ac48ece","after":"a6019906a84e96d4e4fe587a3cc30a0aca1cb187","ref":"refs/heads/master","pushedAt":"2024-03-14T08:08:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"fixed mergeOutput","shortMessageHtmlLink":"fixed mergeOutput"}},{"before":"1b4a778e87d5de167a44d100e67b961027525a26","after":"359e739c37e9f9e9d20ecd93e3fe84807ac48ece","ref":"refs/heads/master","pushedAt":"2024-03-12T10:26:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"fixed mergeOutput for domains files","shortMessageHtmlLink":"fixed mergeOutput for domains files"}},{"before":"5b437ce75e2e159a24daff8aa6f444e518f13510","after":null,"ref":"refs/heads/trvinh-patch-1","pushedAt":"2024-03-05T18:52:13.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"}},{"before":null,"after":"5b437ce75e2e159a24daff8aa6f444e518f13510","ref":"refs/heads/trvinh-patch-1","pushedAt":"2024-03-05T18:51:10.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"fixed typo in orthosearch.py","shortMessageHtmlLink":"fixed typo in orthosearch.py"}},{"before":"08510c06daee41f953b1d7f00de84137fe6181b5","after":"60ae899fe228e83a616fb8593af72d15d8a888ea","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2024-03-04T13:48:19.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"Fdog assembly (#42)\n\nUpdate fDOG version\r\nBug fix addAssembly user output\r\n\r\n---------\r\n\r\nCo-authored-by: trvinh <trvinh@gmail.com>","shortMessageHtmlLink":"Fdog assembly (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2166888659\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BIONF/fDOG/issues/42\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BIONF/fDOG/pull/42/hovercard\" href=\"https://github.com/BIONF/fDOG/pull/42\">#42</a>)"}},{"before":"05283e009be6d2c877d89b75ed6c96d0d97fb311","after":"08510c06daee41f953b1d7f00de84137fe6181b5","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2024-03-04T13:06:34.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"Fdog assembly (#41)\n\nfDOG-Assembly bug fix during distance calculation: AS U will be scored as C","shortMessageHtmlLink":"Fdog assembly (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2166806803\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BIONF/fDOG/issues/41\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BIONF/fDOG/pull/41/hovercard\" href=\"https://github.com/BIONF/fDOG/pull/41\">#41</a>)"}},{"before":"91edb370050e13657d1f07bca925ff9f42b3d232","after":"1b4a778e87d5de167a44d100e67b961027525a26","ref":"refs/heads/master","pushedAt":"2024-02-28T13:27:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"fixed bug identical geneIDs btw search and refspec","shortMessageHtmlLink":"fixed bug identical geneIDs btw search and refspec"}},{"before":"844c02d38afaf812bc247c34d741837dd668aa54","after":"05283e009be6d2c877d89b75ed6c96d0d97fb311","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2024-02-12T08:56:07.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"Fdog assembly (#40)","shortMessageHtmlLink":"Fdog assembly (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2129669190\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BIONF/fDOG/issues/40\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BIONF/fDOG/pull/40/hovercard\" href=\"https://github.com/BIONF/fDOG/pull/40\">#40</a>)"}},{"before":"82acd8229aca8691dcc8a3b5d0833d11d9d74a61","after":"91edb370050e13657d1f07bca925ff9f42b3d232","ref":"refs/heads/master","pushedAt":"2024-02-12T08:41:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"fixed search taxa list when using --coreTaxa","shortMessageHtmlLink":"fixed search taxa list when using --coreTaxa"}},{"before":"9983e30b4218b792d76cf5ca56b7c558c652388d","after":"844c02d38afaf812bc247c34d741837dd668aa54","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2024-02-09T15:38:37.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"Fdog assembly v0.1.5 (#39)\n\n* added fDOG-Assembly workflow\r\n\r\n* added fDOG-Assembly dependencies\r\n\r\n* adjustments to new muscle version and fDOG version\r\n\r\n* further changes to adapt to new fDOG version\r\n\r\n* script to produce msa and hmm in the format fDOG-Assembly requires from a fasta file\r\n\r\n* deactivate fas config output\r\n\r\n* Bugfix muscle v5 command in fdog.addCoreGroup\r\n\r\n* fixed augustus version\r\n\r\n* further updates to adapt fDOG-Assembly to the new fDOG version. Additionally bugfix in co-ortholog detection if MSA crashed due to too many sequences.\r\n\r\n* contig fasta files where delited from the tmp folder to save memory\r\n\r\n* add function to output only best isoform\r\n\r\n* added function to only output one isoform\r\n\r\n* new gff function, fixed problem that muscle can not work with path containing @ sysmbols, adapted mergeOutput that merges files with _og ending\r\n\r\n* Fixed bug where fDOG-Assembly does not terminate if FAS raises an error\r\n\r\n* bugfix createGff function\r\n\r\n* bugfix createGff function\r\n\r\n---------\r\n\r\nCo-authored-by: trvinh <trvinh@gmail.com>","shortMessageHtmlLink":"Fdog assembly v0.1.5 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2127377390\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BIONF/fDOG/issues/39\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BIONF/fDOG/pull/39/hovercard\" href=\"https://github.com/BIONF/fDOG/pull/39\">#39</a>)"}},{"before":"46b8c0541834f6f3b9af8d1ab3222c14d4dae1f2","after":"9983e30b4218b792d76cf5ca56b7c558c652388d","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2024-02-06T11:00:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"update block profile function","shortMessageHtmlLink":"update block profile function"}},{"before":"172ee24fb0343dc4c45b4b4287030bc0edf91837","after":"46b8c0541834f6f3b9af8d1ab3222c14d4dae1f2","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2024-02-05T11:53:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"bugfix block profile computation","shortMessageHtmlLink":"bugfix block profile computation"}},{"before":"e1f92f1f8054ac976d8218df91906f1a488641df","after":"82acd8229aca8691dcc8a3b5d0833d11d9d74a61","ref":"refs/heads/master","pushedAt":"2023-12-21T17:26:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"option to validate hmm hits by sequence score","shortMessageHtmlLink":"option to validate hmm hits by sequence score"}},{"before":"0404231cf5cc50bd796c3149f14e016dae266b55","after":"e1f92f1f8054ac976d8218df91906f1a488641df","ref":"refs/heads/master","pushedAt":"2023-12-20T17:02:26.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"option to validate hmm hits by sequence score","shortMessageHtmlLink":"option to validate hmm hits by sequence score"}},{"before":"9dc4fe92e004244ca68d37518b8b6d06b144e59a","after":"0404231cf5cc50bd796c3149f14e016dae266b55","ref":"refs/heads/master","pushedAt":"2023-12-20T15:04:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"option to validate hmm hits by sequence score","shortMessageHtmlLink":"option to validate hmm hits by sequence score"}},{"before":"26bba4720fc63a29f748e7e0c05ffe68be20e89a","after":"9dc4fe92e004244ca68d37518b8b6d06b144e59a","ref":"refs/heads/master","pushedAt":"2023-12-20T11:36:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"fixed bug identical geneIDs btw search and refspec","shortMessageHtmlLink":"fixed bug identical geneIDs btw search and refspec"}},{"before":"959e0a0fb1544654d99931686e09b69f70d6facc","after":"26bba4720fc63a29f748e7e0c05ffe68be20e89a","ref":"refs/heads/master","pushedAt":"2023-12-14T11:35:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"trvinh","name":"Vinh Tran","path":"/trvinh","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/19269760?s=80&v=4"},"commit":{"message":"fixed bug identical geneIDs btw search and refspec","shortMessageHtmlLink":"fixed bug identical geneIDs btw search and refspec"}},{"before":"90a4f20156c5b29d1a0cb1242fd7e305c1235ef6","after":"172ee24fb0343dc4c45b4b4287030bc0edf91837","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2023-12-11T14:37:03.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"bug fix run time error with --fasoff","shortMessageHtmlLink":"bug fix run time error with --fasoff"}},{"before":"8b1a58f61775235461b2c80724ee6869abe1e227","after":"90a4f20156c5b29d1a0cb1242fd7e305c1235ef6","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2023-11-20T15:25:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"renamed .extended.fa to _og.fa","shortMessageHtmlLink":"renamed .extended.fa to _og.fa"}},{"before":"d429ec9afb996a04d1f205099242474cb9402d71","after":"8b1a58f61775235461b2c80724ee6869abe1e227","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2023-11-20T13:22:12.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"Fdog assembly (#37)","shortMessageHtmlLink":"Fdog assembly (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2002191000\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BIONF/fDOG/issues/37\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BIONF/fDOG/pull/37/hovercard\" href=\"https://github.com/BIONF/fDOG/pull/37\">#37</a>)"}},{"before":"87c66f1bc4ba83146ed88df87593553fa0dc7477","after":"d429ec9afb996a04d1f205099242474cb9402d71","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2023-11-17T16:31:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"bug fix parallel computation","shortMessageHtmlLink":"bug fix parallel computation"}},{"before":"7f666b7f73aede70d5f09622e0ec11f4d30f129b","after":"87c66f1bc4ba83146ed88df87593553fa0dc7477","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2023-10-24T12:10:04.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"Fdog assembly v0.1.4 (#35)\n\nfDOG Assembly update to version v0.1.4\r\n\r\nA few bug fixes, cleaned up the output and added a script to compute MSA and pHMM of an ortholog group that can be used as input for fDOG-Assembly.","shortMessageHtmlLink":"Fdog assembly v0.1.4 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1957306465\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BIONF/fDOG/issues/35\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BIONF/fDOG/pull/35/hovercard\" href=\"https://github.com/BIONF/fDOG/pull/35\">#35</a>)"}},{"before":"b1a25aa450d31cc0a05776f5eaec554d15cfa686","after":"7f666b7f73aede70d5f09622e0ec11f4d30f129b","ref":"refs/heads/fdog_goes_assembly","pushedAt":"2023-10-24T12:06:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"HannahBioI","name":"Hannah Muelbaier","path":"/HannahBioI","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/47216555?s=80&v=4"},"commit":{"message":"Squashed commit of the following:\n\ncommit 3f2929b64ef28051f2f848914be50f024cdc64ef\nMerge: 7fb439f 959e0a0\nAuthor: Hannah Muelbaier <47216555+mueli94@users.noreply.github.com>\nDate:   Mon Oct 23 15:06:29 2023 +0200\n\n    Merge pull request #2 from BIONF/master\n\n    deactivate fas config output\n\ncommit 7fb439fa0e5e0e53d5db2f7e54550ec55885ed2f\nAuthor: mueli94 <hannah.muelbaier@gmail.com>\nDate:   Fri Oct 20 10:05:26 2023 +0200\n\n    Revert \"Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly into fdog-assembly\"\n\n    This reverts commit d688bbb6f9498d3e8e02a20a8321a91b9215a23d, reversing\n    changes made to 5068b7acf249209c0b4d951b23fa7c2d79af32ab.\n\ncommit d0d359f0afc52ca9f3a4b8782315b6ba56f00094\nMerge: 5068b7a d688bbb\nAuthor: mueli94 <hannah.muelbaier@gmail.com>\nDate:   Fri Oct 20 10:05:01 2023 +0200\n\n    Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly into fdog-assembly\n\ncommit d688bbb6f9498d3e8e02a20a8321a91b9215a23d\nMerge: 5068b7a 3b62945\nAuthor: mueli94 <hannah.muelbaier@gmail.com>\nDate:   Thu Oct 19 16:28:55 2023 +0200\n\n    Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly into fdog-assembly\n\ncommit 5068b7acf249209c0b4d951b23fa7c2d79af32ab\nAuthor: mueli94 <hannah.muelbaier@gmail.com>\nDate:   Thu Oct 19 16:20:18 2023 +0200\n\n    contig fasta files where delited from the tmp folder to save memory\n\ncommit 3b629458e9f12d7f60089385dd04d5a2a0284d9f\nAuthor: Hannah <47216555+mueli94@users.noreply.github.com>\nDate:   Thu Sep 21 16:31:17 2023 +0200\n\n    further updates to adapt fDOG-Assembly to the new fDOG version. Additionally bugfix in co-ortholog detection if MSA crashed due to too many sequences.\n\ncommit 41660e6d7e3d3ade28230d281bf3701fdaac7615\nAuthor: Hannah <47216555+mueli94@users.noreply.github.com>\nDate:   Wed Sep 20 10:34:56 2023 +0200\n\n    fixed augustus version\n\ncommit 5d77522b91c854cdb0e38502806b083ed8c8c403\nAuthor: mueli94 <hannah.muelbaier@gmail.com>\nDate:   Tue Sep 19 15:02:57 2023 +0200\n\n    Bugfix muscle v5 command in fdog.addCoreGroup\n\ncommit 959e0a0fb1544654d99931686e09b69f70d6facc\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Sep 19 14:49:48 2023 +0200\n\n    deactivate fas config output\n\ncommit ea40a0cd682f3b88392e7e7e92ba2e0df5735002\nMerge: 3140fc4 3cc809c\nAuthor: Hannah <47216555+mueli94@users.noreply.github.com>\nDate:   Mon Sep 18 17:27:04 2023 +0200\n\n    Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly into fdog-assembly\n\ncommit 3140fc40dad5b8d56ec4313608b90c42cad47835\nAuthor: Hannah <47216555+mueli94@users.noreply.github.com>\nDate:   Mon Sep 18 17:25:39 2023 +0200\n\n    script to produce msa and hmm in the format fDOG-Assembly requires from a fasta file\n\ncommit 3cc809c49bfd29c391d59e2eea7619d307c1358c\nAuthor: Hannah <47216555+mueli94@users.noreply.github.com>\nDate:   Mon Sep 18 17:21:07 2023 +0200\n\n    script to produce msa and hmm in the format fDOG-Assembly requires from a fasta file\n\ncommit ef5acb725a00fa6fc811a18aa5360ec137aacc2c\nAuthor: Hannah <47216555+mueli94@users.noreply.github.com>\nDate:   Mon Sep 18 17:20:09 2023 +0200\n\n    further changes to adapt to new fDOG version\n\ncommit a832824f2db3e23866463aceaa0f03a968bbb130\nAuthor: Hannah <47216555+mueli94@users.noreply.github.com>\nDate:   Mon Sep 18 13:17:11 2023 +0200\n\n    adjustments to new muscle version and fDOG version\n\ncommit 8df8a737fe06d7b2fc6739453594ce89eafbfa0b\nAuthor: Hannah <47216555+mueli94@users.noreply.github.com>\nDate:   Mon Sep 18 11:38:06 2023 +0200\n\n    added fDOG-Assembly dependencies\n\ncommit fc0ea453574efbff8cf8be31d18a68711709a346\nAuthor: Hannah <47216555+mueli94@users.noreply.github.com>\nDate:   Mon Sep 18 10:58:18 2023 +0200\n\n    added fDOG-Assembly workflow\n\ncommit 5ccf8242c5714fb17d6d73cd2d41f10496a17cb8\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Wed Aug 16 13:33:40 2023 +0200\n\n    check valid rank for refspec only\n\ncommit deeda8add38064e096368b3dd0d4f80369373203\nAuthor: Vinh Tran <trvinh@gmail.com>\nDate:   Wed Aug 16 13:19:31 2023 +0200\n\n    Update CHANGELOG.md\n\ncommit eb902a63d94ae59dd065688e58cc5db6ef7eb3fd\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Wed Aug 16 12:03:36 2023 +0200\n\n    option to not added all taxa\n\ncommit e6ce3d19bbb152a0906296e7ae0e5f4755cfbc76\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Wed Aug 16 11:50:10 2023 +0200\n\n    changed orthID NA to fdogMA for manually added taxa\n\ncommit 5cb0946e6c4dccd54f8dd5eda46e7228e3114564\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Wed Aug 16 09:57:26 2023 +0200\n\n    added all searchTaxa to phyloprofile\n\ncommit 3e0859b3753c497f9394b570f7d70c87708dc1c7\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Aug 15 15:39:54 2023 +0200\n\n    added check for invalid min-/maxDist; works with fasta36.3.8g\n\ncommit b7ec6fa437ece98f9aa25ce4f2001a12641b4d24\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Aug 15 15:19:36 2023 +0200\n\n    fixed worrking with old fasta36\n\ncommit 553cdaa442c3468ae86e503b45aa14cf46bf4f52\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Aug 15 12:44:18 2023 +0200\n\n    added check for invalid min-/maxDist; works with fasta36.3.8g\n\ncommit c756ab03eeea5f71f6685588a3c575f0c6415447\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Aug 15 11:48:59 2023 +0200\n\n    added check for invalid min-/maxDist; works with fasta36.3.8g\n\ncommit a746c8fa045d7fed7012f53ea7ab83bcac3d154c\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Aug 15 11:32:45 2023 +0200\n\n    added check for invalid min-/maxDist; works with fasta36.3.8g\n\ncommit 48372cf2ee93c21063a8138d27946b4152ac133a\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Jul 18 11:11:37 2023 +0200\n\n    added warning for no hmm hit\n\ncommit a8541f89e3b2317c29ac79f45767afb1aaffc35a\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu Jun 15 16:24:24 2023 +0200\n\n    set seqlen limit for muscle5\n\ncommit b06b3a12eb640a8442320781cf483523331f9e34\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Mon Jun 12 14:09:09 2023 +0200\n\n    fixed mapping file for addTaxon\n\ncommit c5ca07cf56935b5c0a5c3ba73f1bf2648aac38c2\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu May 25 14:13:45 2023 +0200\n\n    fixed output filename for muscle5\n\ncommit b014157c38bab799b08cffe92fb12385db5fb378\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu May 11 13:13:19 2023 +0200\n\n    check empty tmp dir before deleting in addTaxon\n\ncommit 052cf704d5406cc8ba1e79b989a49355b2580f4b\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Fri Mar 10 15:42:15 2023 +0100\n\n    muscle5,checkBlast,ignoreAnnoCheck\n\ncommit 7e6bfbc5a1f54e610c9f8d28b44175f1f97e3a99\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Wed Feb 22 09:57:23 2023 +0100\n\n    adapt evalue\n\ncommit 56995b147ce7a60de635e910f74f87a93c39a87c\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Wed Feb 22 09:56:40 2023 +0100\n\n    adapt evalue\n\ncommit 7798d15db810c9b06f13f56aea072c2af44679a5\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Mon Feb 20 13:50:31 2023 +0100\n\n    rename log fdogs.run\n\ncommit 03c9038595a18503724041b801b0122b74927fe0\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Fri Feb 17 14:29:03 2023 +0100\n\n    fix number of hmmhits core compilation\n\ncommit f7c4cf830b8ef2c69cdbee4314aaf623eddad107\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Feb 14 12:47:09 2023 +0100\n\n    fix check for pathconfig file\n\ncommit 57859800b224271805a6f5731fb26671661b7630\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Feb 14 11:14:23 2023 +0100\n\n    fix sorting hmm hits\n\ncommit bb185a3aaca3128a58e865a5ed60a43a655fb804\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Mon Feb 6 14:14:52 2023 +0100\n\n    add several options to work with data paths; resolves: #28\n\ncommit 8bd2359c366276fa9b1b811b1a7605d57367a485\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Mon Feb 6 14:04:01 2023 +0100\n\n    add several options to work with data paths; resolves: #28\n\ncommit 7c3191a75f4a762a91ea52f10cc53a7135a987e2\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Mon Feb 6 13:59:31 2023 +0100\n\n    add several options to work with data paths\n\ncommit ab5491b6e0c180722f367089b2d175b49b5fc741\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Fri Feb 3 15:46:46 2023 +0100\n\n    option to use different names for data folders\n\ncommit 198393dc31c89ef31df391b55933a905df605962\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Fri Feb 3 15:07:49 2023 +0100\n\n    add option to update json file to checkData\n\ncommit 4339bad93a84eefd090e579b679121b8422909ce\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu Feb 2 17:17:34 2023 +0100\n\n    accept old folder names\n\ncommit bfbc324aff95289d03663324d1a2f082ccf44854\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu Feb 2 16:39:34 2023 +0100\n\n    added fn desc\n\ncommit ad8741d5df55a49af642a49914238291139c0301\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu Feb 2 10:17:29 2023 +0100\n\n    v0.1.5 version bump\n\ncommit ad2cbbdac62a1525e0d99b8e74b92a2a2cf969db\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu Feb 2 10:06:53 2023 +0100\n\n    sort hmm hits using domain scores; correct tree walking; setup force not delete data; correct profile output with fasOff\n\ncommit 206def02f2cec7ad3aa5a3297001cc50d5f6a95c\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu Feb 2 10:04:18 2023 +0100\n\n    sort hmm hits using domain scores; correct tree walking; setup force not delete data; correct profile output with fasOff\n\ncommit 1edad42cbfb50150e7918f5bfac5c6cf39325671\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Fri Jan 27 09:33:58 2023 +0100\n\n    version bump\n\ncommit 8855db4d5a77c4f3085e8f9f66089f0b22e5de9b\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Fri Jan 27 09:33:38 2023 +0100\n\n    reduce evalue for identify seed ID\n\ncommit 83326905754032fae0e52640404656baeca8862c\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu Jan 26 14:48:27 2023 +0100\n\n    fix bug identify seed ID with reuseCore\n\ncommit 9edaf9ebc84f4f886b014b90de60f077953339d0\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu Jan 26 10:47:14 2023 +0100\n\n    speed up preparation in fdogs.run\n\ncommit 2405698b9b9037b3b8beedb9ef69d9fe020810a0\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu Jan 26 10:24:23 2023 +0100\n\n    save core jobs for fdogs.run to file\n\ncommit e72825223e8fb634a1277fb8e77fdcee337f24c5\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Thu Jan 26 09:51:00 2023 +0100\n\n    fix path to refspec fa; add amino to hmmbuild\n\ncommit f984b2665ad4dfc45d65fcdd5173a6d7f12c04b9\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Wed Jan 25 14:41:09 2023 +0100\n\n    added preparation runtime to fdogs.run\n\ncommit 8624f7dca706a3de6a0c9c7a5f2b77cbf245be5f\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Jan 24 14:23:03 2023 +0100\n\n    fixed kimura distance devide by 0\n\ncommit dd9a45cab14c12386204c64ade04c5b225cb84f8\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Jan 24 10:57:38 2023 +0100\n\n    updated README\n\ncommit 055051fcf4d2700a70e79dc35f5ce9e8ae76f302\nAuthor: Vinh Tran <trvinh@gmail.com>\nDate:   Tue Jan 24 10:21:08 2023 +0100\n\n    0.1.0 (#26)\n\n    * create v0.1.0\n\n    * simplfying hamstr.pl\n\n    * first python conversion\n\n    * modified addTaxon and addTaxa\n\n    * added install/check dependencies\n\n    * rename data folders\n\n    * added runtime for core complilation\n\ncommit d8eea1fe68efd6a497865aafb41ef2f82a0f2ede\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Wed Oct 12 09:10:56 2022 +0200\n\n    fixed addTaxon replacing pipe\n\ncommit 20aa839eb84cb6b5161140b443bc9850f1cf9287\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Mon Jun 13 10:19:40 2022 +0200\n\n    removed fdog assembly files\n\ncommit a0747e0f7388d4d26e848a764774976e050ba0c7\nAuthor: trvinh <trvinh@gmail.com>\nDate:   Tue Mar 15 14:19:32 2022 +0100\n\n    fdogs accepts dots in seed filename","shortMessageHtmlLink":"Squashed commit of the following:"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNi0yMFQxNDoxNjo1Mi4wMDAwMDBazwAAAARqptjl","endCursor":"Y3Vyc29yOnYyOpK7MjAyMy0xMC0yNFQxMjowNjowOC4wMDAwMDBazwAAAAOedm_y"}},"title":"Activity · BIONF/fDOG"}