https://sourceforge.net/p/harfang/activity/Recent activity for HarfangenThu, 28 Oct 2021 13:33:06 -0000https://sourceforge.net/p/harfang/code/ci/c2a572f55b93e3385fae68c14da323a28864ee41/Changed invocations of samtools, bgzip, and tabix to lookup executable pathIan ReidThu, 28 Oct 2021 13:33:06 -0000https://sourceforge.net/p/harfang/code/ci/c2a572f55b93e3385fae68c14da323a28864ee41/https://sourceforge.net/p/harfang/code/ci/7e0a67e84156e5eb6f2da0a229844f69afaf54b0/Removed find_read_islands.py from gitIan ReidThu, 28 Oct 2021 10:58:00 -0000https://sourceforge.net/p/harfang/code/ci/7e0a67e84156e5eb6f2da0a229844f69afaf54b0/https://sourceforge.net/p/harfang/code/ci/399a030a55fdca24333cdc16d6e65a6034f5ab62/Moved parse_wigline and trim block from find_read_islands.py to get_model_coverage.pyIan ReidThu, 28 Oct 2021 10:58:00 -0000https://sourceforge.net/p/harfang/code/ci/399a030a55fdca24333cdc16d6e65a6034f5ab62/https://sourceforge.net/p/harfang/code/ci/be62d0fdbf59bafe28c412638373d700146a2c31/Initial implementation of CoverArray classIan ReidThu, 28 Oct 2021 10:58:00 -0000https://sourceforge.net/p/harfang/code/ci/be62d0fdbf59bafe28c412638373d700146a2c31/https://sourceforge.net/p/harfang/code/ci/bb6d09c24163dbb6bfd269b1bafb03101d0068cb/Extracted CoverArray definition into coverarray.pyIan ReidThu, 28 Oct 2021 10:58:00 -0000https://sourceforge.net/p/harfang/code/ci/bb6d09c24163dbb6bfd269b1bafb03101d0068cb/https://sourceforge.net/p/harfang/code/ci/9d061126ec639e030b487eb054a6e45a3f43154e/Replaced uses of coverage tabix files with CoverArrayIan ReidThu, 28 Oct 2021 10:58:00 -0000https://sourceforge.net/p/harfang/code/ci/9d061126ec639e030b487eb054a6e45a3f43154e/https://sourceforge.net/p/harfang/code/ci/5ea5d995b580fb1f10d21d345546432375025a2a/Debugged use of np.nditer in get_model_coverage.get_coverblocksIan ReidThu, 28 Oct 2021 10:58:00 -0000https://sourceforge.net/p/harfang/code/ci/5ea5d995b580fb1f10d21d345546432375025a2a/https://sourceforge.net/p/harfang/code/ci/8143942d3372dfeec8d663a127f731ef4d92b29c/Implemented remove_untranslatable_CDS.pyIan ReidThu, 28 Oct 2021 10:58:00 -0000https://sourceforge.net/p/harfang/code/ci/8143942d3372dfeec8d663a127f731ef4d92b29c/https://sourceforge.net/p/harfang/code/ci/1abd890333566094ee95361f267b333132503651/Implemented remove_untranslatable_CDS.pyIan ReidThu, 28 Oct 2021 10:58:00 -0000https://sourceforge.net/p/harfang/code/ci/1abd890333566094ee95361f267b333132503651/https://sourceforge.net/p/harfang/code/ci/ff697a20bbe3f86119d536f421033e0e7f2e0ca5/Copied gff3-names.py from transcriptomicsIan ReidWed, 20 Oct 2021 12:06:45 -0000https://sourceforge.net/p/harfang/code/ci/ff697a20bbe3f86119d536f421033e0e7f2e0ca5/https://sourceforge.net/p/harfang/code/ci/1a259419c4ac2743f6fab9385aa7147ba7705ae0/Modified pool_gene_models.py to handle CDS records with no IDIan ReidWed, 20 Oct 2021 08:01:47 -0000https://sourceforge.net/p/harfang/code/ci/1a259419c4ac2743f6fab9385aa7147ba7705ae0/https://sourceforge.net/p/harfang/code/ci/38ff4eb5017b52c8b6a154ec73d8a0a408d2e36a/Cleaned up importsIan ReidTue, 19 Oct 2021 23:14:10 -0000https://sourceforge.net/p/harfang/code/ci/38ff4eb5017b52c8b6a154ec73d8a0a408d2e36a/https://sourceforge.net/p/harfang/code/ci/2212316dfda0f6dda64ad6e33525155d276f00c9/Cleaned up importsIan ReidTue, 19 Oct 2021 01:12:58 -0000https://sourceforge.net/p/harfang/code/ci/2212316dfda0f6dda64ad6e33525155d276f00c9/https://sourceforge.net/p/harfang/code/ci/bdd902469b408bc650276cbecaadc773a6ca19a4/Removed deprecated Bio.Alphabet import from gff3Record.pyIan ReidTue, 19 Oct 2021 00:06:16 -0000https://sourceforge.net/p/harfang/code/ci/bdd902469b408bc650276cbecaadc773a6ca19a4/https://sourceforge.net/p/harfang/code/ci/38350f0a4ae82c5e7014ca8102d2549794acaf40/modified gff3Record.get_score to always return a float valueIan ReidFri, 16 Oct 2020 01:25:50 -0000https://sourceforge.net/p/harfang/code/ci/38350f0a4ae82c5e7014ca8102d2549794acaf40/https://sourceforge.net/p/harfang/code/ci/58538b8533618618cd5268a07c00b2b269ab552f/Removed unused class AugustusConfigParser from run_Harfang.py and moved Augustus_config_parser.py to redundantIan ReidFri, 16 Oct 2020 01:25:50 -0000https://sourceforge.net/p/harfang/code/ci/58538b8533618618cd5268a07c00b2b269ab552f/https://sourceforge.net/p/harfang/code/ci/04fadf2cf5c2af3309c84f2999dfb736d0927005/Started implementing test_check_intron_structure.pyIan ReidFri, 16 Oct 2020 01:25:50 -0000https://sourceforge.net/p/harfang/code/ci/04fadf2cf5c2af3309c84f2999dfb736d0927005/https://sourceforge.net/p/harfang/code/ci/3649b92bbd75c2d5e9a7934b5dd6fc672a36e6e8/Refactored task_Extract_splice_junctionsIan ReidFri, 11 Sep 2020 12:24:29 -0000https://sourceforge.net/p/harfang/code/ci/3649b92bbd75c2d5e9a7934b5dd6fc672a36e6e8/https://sourceforge.net/p/harfang/code/ci/60648cda3fce84dd2b2a284e50bd6a2ad0ccb733/Refactored task_Extract_splice_junctionsIan ReidFri, 11 Sep 2020 12:08:30 -0000https://sourceforge.net/p/harfang/code/ci/60648cda3fce84dd2b2a284e50bd6a2ad0ccb733/https://sourceforge.net/p/harfang/code/ci/4f4a26ff9a203d7b0306d9abfc29aa67eb00290e/Added completed successfully message to task_Publish_accepted_modelsIan ReidFri, 11 Sep 2020 07:52:53 -0000https://sourceforge.net/p/harfang/code/ci/4f4a26ff9a203d7b0306d9abfc29aa67eb00290e/https://sourceforge.net/p/harfang/code/ci/713db1f1736519049c597a2f9bd4df5791bf3cd8/Fixed --out argument for format_accepted_models in run_Harfang.task_Select_models()Ian ReidFri, 11 Sep 2020 07:19:19 -0000https://sourceforge.net/p/harfang/code/ci/713db1f1736519049c597a2f9bd4df5791bf3cd8/https://sourceforge.net/p/harfang/code/ci/c87b6d976e22c0403251df3c6757cb5465e854ec/syntax corrections in run_Harfang:task_Map_reads()Ian ReidFri, 11 Sep 2020 00:28:06 -0000https://sourceforge.net/p/harfang/code/ci/c87b6d976e22c0403251df3c6757cb5465e854ec/https://sourceforge.net/p/harfang/code/ci/6a706b15ce805ba20e3335bb6929721f678ab0ec/syntax corrections in run_Harfang:task_Map_reads()Ian ReidFri, 11 Sep 2020 00:19:19 -0000https://sourceforge.net/p/harfang/code/ci/6a706b15ce805ba20e3335bb6929721f678ab0ec/https://sourceforge.net/p/harfang/code/ci/0cd718c06294caebe90eb1beac0c47213055bb63/syntax corrections in run_Harfang:task_Map_reads()Ian ReidThu, 10 Sep 2020 23:32:31 -0000https://sourceforge.net/p/harfang/code/ci/0cd718c06294caebe90eb1beac0c47213055bb63/https://sourceforge.net/p/harfang/code/ci/e00506f1d6f99e90dca4a90983327cc580ce4c73/syntax corrections in run_Harfang:task_Map_reads()Ian ReidThu, 10 Sep 2020 20:56:09 -0000https://sourceforge.net/p/harfang/code/ci/e00506f1d6f99e90dca4a90983327cc580ce4c73/https://sourceforge.net/p/harfang/code/ci/7abae86a1db26ffc0f4efdf20b421a9903a6a8f3/syntax corrections in run_Harfang:task_Map_reads()Ian ReidThu, 10 Sep 2020 17:13:10 -0000https://sourceforge.net/p/harfang/code/ci/7abae86a1db26ffc0f4efdf20b421a9903a6a8f3/https://sourceforge.net/p/harfang/code/ci/649166ae91cd6b0499065e0fb15e95d2a7299c11/syntax corrections in run_Harfang:task_Map_reads()Ian ReidThu, 10 Sep 2020 16:37:51 -0000https://sourceforge.net/p/harfang/code/ci/649166ae91cd6b0499065e0fb15e95d2a7299c11/https://sourceforge.net/p/harfang/code/ci/8732de073239e93ed8763047733706d790df604a/syntax corrections in run_Harfang:task_Map_reads()Ian ReidThu, 10 Sep 2020 15:55:16 -0000https://sourceforge.net/p/harfang/code/ci/8732de073239e93ed8763047733706d790df604a/https://sourceforge.net/p/harfang/code/ci/e56f1eacaf532d276a27aa26ebfce82e97b0ba37/syntax corrections in run_Harfang:task_Map_reads()Ian ReidThu, 10 Sep 2020 15:44:40 -0000https://sourceforge.net/p/harfang/code/ci/e56f1eacaf532d276a27aa26ebfce82e97b0ba37/https://sourceforge.net/p/harfang/code/ci/5a1fb380f857afa5079e6ad90858728536cdb460/syntax corrections in run_Harfang:task_Map_reads()Ian ReidThu, 10 Sep 2020 15:41:44 -0000https://sourceforge.net/p/harfang/code/ci/5a1fb380f857afa5079e6ad90858728536cdb460/https://sourceforge.net/p/harfang/code/ci/c4fd270642a1f2d792d8e0ad016c56e049a7fa77/syntax corrections in run_Harfang:task_Map_reads()Ian ReidThu, 10 Sep 2020 15:35:20 -0000https://sourceforge.net/p/harfang/code/ci/c4fd270642a1f2d792d8e0ad016c56e049a7fa77/https://sourceforge.net/p/harfang/code/ci/d524abed6fa880bdd77563e734e6768a4dd047dc/syntax corrections in run_Harfang:task_Map_reads()Ian ReidThu, 10 Sep 2020 15:32:01 -0000https://sourceforge.net/p/harfang/code/ci/d524abed6fa880bdd77563e734e6768a4dd047dc/https://sourceforge.net/p/harfang/code/ci/3dae612d8b78ca792ab46add19be90448cc525a6/syntax corrections in run_Harfang:task_Map_reads()Ian ReidThu, 10 Sep 2020 15:21:12 -0000https://sourceforge.net/p/harfang/code/ci/3dae612d8b78ca792ab46add19be90448cc525a6/https://sourceforge.net/p/harfang/code/ci/cebc8ee53eee8dea885981c5432d00d40d23a16d/Corrected STAR configIan ReidThu, 10 Sep 2020 15:11:58 -0000https://sourceforge.net/p/harfang/code/ci/cebc8ee53eee8dea885981c5432d00d40d23a16d/https://sourceforge.net/p/harfang/code/ci/7db067e7222bda06dd9531967f364d8f11c19007/Explicitly open files in text modeIan ReidThu, 10 Sep 2020 14:48:21 -0000https://sourceforge.net/p/harfang/code/ci/7db067e7222bda06dd9531967f364d8f11c19007/https://sourceforge.net/p/harfang/code/ci/320a043941c302d9c4cab0039eb40712dfa1a767/Added test for key presence in run_Harfang:get_args()Ian ReidThu, 10 Sep 2020 14:36:27 -0000https://sourceforge.net/p/harfang/code/ci/320a043941c302d9c4cab0039eb40712dfa1a767/https://sourceforge.net/p/harfang/code/ci/61f386566f921b05cf15c306a16677c0756ed9d2/Added format_accepted_models.pyIan ReidTue, 08 Sep 2020 18:42:18 -0000https://sourceforge.net/p/harfang/code/ci/61f386566f921b05cf15c306a16677c0756ed9d2/https://sourceforge.net/p/harfang/code/ci/b29cc784bd5a9e73feb30c724a41365e351c939e/Added external_predictions to count_contributions_to_final.shIan ReidThu, 03 Sep 2020 18:02:27 -0000https://sourceforge.net/p/harfang/code/ci/b29cc784bd5a9e73feb30c724a41365e351c939e/https://sourceforge.net/p/harfang/code/ci/3941dec044821732f53248d91df5a1266e696747/Corrected strand names in task_Unhinted_AugustusIan ReidThu, 03 Sep 2020 16:42:13 -0000https://sourceforge.net/p/harfang/code/ci/3941dec044821732f53248d91df5a1266e696747/https://sourceforge.net/p/harfang/code/ci/2e24ed0e2fd5e49f10436d05dfb147ee68ef8205/Corrected strand names in task_Unhinted_AugustusIan ReidThu, 03 Sep 2020 16:38:56 -0000https://sourceforge.net/p/harfang/code/ci/2e24ed0e2fd5e49f10436d05dfb147ee68ef8205/https://sourceforge.net/p/harfang/code/ci/338f166e8c36fbeb21e4335efcf22679749b74ea/Removed BAM_hint_dir from file_dep for task_Pool_ModelsIan ReidThu, 03 Sep 2020 15:58:25 -0000https://sourceforge.net/p/harfang/code/ci/338f166e8c36fbeb21e4335efcf22679749b74ea/https://sourceforge.net/p/harfang/code/ci/cc7892099d3273fb5ce1bdf657b7dc3099ffad2e/Added collect actions to task_Unhinted_AugustusIan ReidThu, 03 Sep 2020 15:34:36 -0000https://sourceforge.net/p/harfang/code/ci/cc7892099d3273fb5ce1bdf657b7dc3099ffad2e/https://sourceforge.net/p/harfang/code/ci/c8d08cf2d73b7cf9704c8303bc903b24fff6712a/Added collect actions to task_Unhinted_AugustusIan ReidThu, 03 Sep 2020 15:15:22 -0000https://sourceforge.net/p/harfang/code/ci/c8d08cf2d73b7cf9704c8303bc903b24fff6712a/https://sourceforge.net/p/harfang/code/ci/cf7962b632d4435f1c150759e4860017e8481312/Updates to task_Pool_Models and count_contributions_to_final.shIan ReidThu, 03 Sep 2020 08:25:42 -0000https://sourceforge.net/p/harfang/code/ci/cf7962b632d4435f1c150759e4860017e8481312/https://sourceforge.net/p/harfang/code/ci/6e0d24af5003858cb7d57dbac65bfd406c86844d/Updated script count_contributions_to_final.sh to match filenames in Unhinted_Augustus_ModelsIan ReidTue, 01 Sep 2020 16:31:41 -0000https://sourceforge.net/p/harfang/code/ci/6e0d24af5003858cb7d57dbac65bfd406c86844d/https://sourceforge.net/p/harfang/code/ci/80d6216839e4dbd18d28a82bcc5278f46c4c704a/Moved safe_cat to a separate python moduleIan ReidTue, 01 Sep 2020 11:23:04 -0000https://sourceforge.net/p/harfang/code/ci/80d6216839e4dbd18d28a82bcc5278f46c4c704a/https://sourceforge.net/p/harfang/code/ci/e82415ec8f266d8c59e7145b09383047bb00e883/Broke safe_cat in unsplit_ tasks into slices of 100 filenamesIan ReidTue, 01 Sep 2020 10:57:21 -0000https://sourceforge.net/p/harfang/code/ci/e82415ec8f266d8c59e7145b09383047bb00e883/https://sourceforge.net/p/harfang/code/ci/cacb33486661b8525867384a7ffc90d2da75d988/Corrected and added command logging to task_Complete_Score_ModelsIan ReidTue, 01 Sep 2020 09:42:20 -0000https://sourceforge.net/p/harfang/code/ci/cacb33486661b8525867384a7ffc90d2da75d988/https://sourceforge.net/p/harfang/code/ci/8799490bedb43680ff7bf37a9371bc36757ab1b3/Changed task_Pool_Models to put pooled models in Scored folderIan ReidTue, 01 Sep 2020 02:36:48 -0000https://sourceforge.net/p/harfang/code/ci/8799490bedb43680ff7bf37a9371bc36757ab1b3/https://sourceforge.net/p/harfang/code/ci/06e21c41eabe11fa52b3b666b093348a5e350ff2/Fixed translate_ORF_CDS_to_genome.py for transcripts on reverse strandIan ReidMon, 31 Aug 2020 23:49:51 -0000https://sourceforge.net/p/harfang/code/ci/06e21c41eabe11fa52b3b666b093348a5e350ff2/https://sourceforge.net/p/harfang/code/ci/600e9b52308c775b3053e0b00ea9f1f7d632703e/Added error messages to startup codeIan ReidMon, 31 Aug 2020 19:31:22 -0000https://sourceforge.net/p/harfang/code/ci/600e9b52308c775b3053e0b00ea9f1f7d632703e/https://sourceforge.net/p/harfang/code/ci/bce22b45282e9909e95ac84256fea3e53032b2f3/Extracted prepare function from run_Harfang.runIan ReidSat, 29 Aug 2020 01:47:41 -0000https://sourceforge.net/p/harfang/code/ci/bce22b45282e9909e95ac84256fea3e53032b2f3/https://sourceforge.net/p/harfang/code/ci/e71ef729520e92fc3dfff4ff79fbd8d999f832a1/Fixed bug in translate_ORF_CDS_to_genome.embed_orfs_in_1_transcript when CDS starts exactly at the start of an internal exonIan ReidSat, 29 Aug 2020 01:47:41 -0000https://sourceforge.net/p/harfang/code/ci/e71ef729520e92fc3dfff4ff79fbd8d999f832a1/https://sourceforge.net/p/harfang/code/ci/046249e750e4855d1f6cd381c1e90db7ed7b96e6/Added RM dolumns to extrinsic configuration filesIan ReidSun, 19 Jul 2020 00:14:40 -0000https://sourceforge.net/p/harfang/code/ci/046249e750e4855d1f6cd381c1e90db7ed7b96e6/https://sourceforge.net/p/harfang/code/ci/8fa65600a139e3d0a7c810a733d0d733ae0d1d9a/Corrected Braker option AUGUSTUS_ab_initioIan ReidSat, 18 Jul 2020 09:17:56 -0000https://sourceforge.net/p/harfang/code/ci/8fa65600a139e3d0a7c810a733d0d733ae0d1d9a/https://sourceforge.net/p/harfang/code/ci/8b3407bb965da5e0c0f02cc3411fa04881dbd2cd/Corrected Braker option AUGUSTUS_ab_initioIan ReidSat, 18 Jul 2020 08:47:23 -0000https://sourceforge.net/p/harfang/code/ci/8b3407bb965da5e0c0f02cc3411fa04881dbd2cd/https://sourceforge.net/p/harfang/code/ci/90a54f513f44cb6305db5d865d184894c944c81a/Added CONFIG checks for Braker etpmodeIan ReidSat, 18 Jul 2020 08:25:51 -0000https://sourceforge.net/p/harfang/code/ci/90a54f513f44cb6305db5d865d184894c944c81a/https://sourceforge.net/p/harfang/code/ci/3d4cf20651e4395c69dd9294d2741881e27b690e/Created stub for testGff32predictedTranscriptsAndProteins.pyIan ReidFri, 17 Jul 2020 23:33:54 -0000https://sourceforge.net/p/harfang/code/ci/3d4cf20651e4395c69dd9294d2741881e27b690e/https://sourceforge.net/p/harfang/code/ci/24f0a826f67d0fbbdfdcf8b5f7602e2718211374/Modified run_Harfang.task_Run_Braker to run harfang in etpmodeIan ReidFri, 17 Jul 2020 23:33:54 -0000https://sourceforge.net/p/harfang/code/ci/24f0a826f67d0fbbdfdcf8b5f7602e2718211374/https://sourceforge.net/p/harfang/code/ci/9087405ddc81620d157ff518c68f6cfe1f512266/Updated output formatting in collect_accepted_models_by_source.pyIan ReidFri, 17 Jul 2020 13:29:59 -0000https://sourceforge.net/p/harfang/code/ci/9087405ddc81620d157ff518c68f6cfe1f512266/https://sourceforge.net/p/harfang/code/ci/7d907d278234b9f4a94703a16dfc96c996ec37dc/Changed value of Braker_gff3 to avoid filename collision in run_Harfang.pyIan ReidMon, 13 Jul 2020 14:05:36 -0000https://sourceforge.net/p/harfang/code/ci/7d907d278234b9f4a94703a16dfc96c996ec37dc/https://sourceforge.net/p/harfang/code/ci/6bdd3fc86bbcf8590f32824f0db007b604f0d80a/Modified run_Harfang.py to eliminate score_coverage_homogeneityIan ReidTue, 07 Jul 2020 15:15:59 -0000https://sourceforge.net/p/harfang/code/ci/6bdd3fc86bbcf8590f32824f0db007b604f0d80a/https://sourceforge.net/p/harfang/code/ci/3368eb55c9d1cfe7189c445a5612bcb40200472c/MOdified renumber_models.py to avoid clobbering exon IDsIan ReidTue, 07 Jul 2020 14:48:32 -0000https://sourceforge.net/p/harfang/code/ci/3368eb55c9d1cfe7189c445a5612bcb40200472c/https://sourceforge.net/p/harfang/code/ci/32736ec5ddf9d493161fbcb523a90b64bab6800e/Increased MAX_OVERLAP to 50% in merge_strand_representatives.pyIan ReidMon, 06 Jul 2020 20:51:04 -0000https://sourceforge.net/p/harfang/code/ci/32736ec5ddf9d493161fbcb523a90b64bab6800e/https://sourceforge.net/p/harfang/code/ci/e82b28b144fc260da2c38f25cd04e5081d6fa39e/Modified gff32predictedTranscriptsAndProteins.py to handle transcripts with more than one ORFIan ReidMon, 06 Jul 2020 17:54:05 -0000https://sourceforge.net/p/harfang/code/ci/e82b28b144fc260da2c38f25cd04e5081d6fa39e/https://sourceforge.net/p/harfang/code/ci/a65fb74a2daf7b6d881926ac903e5574dbe0f925/Stopped gff3_rename.py from clobbering CDS IDsIan ReidMon, 06 Jul 2020 16:31:27 -0000https://sourceforge.net/p/harfang/code/ci/a65fb74a2daf7b6d881926ac903e5574dbe0f925/https://sourceforge.net/p/harfang/code/ci/566036436a1fbf6780fbe9e680731af3038bf9a9/Refactored gff32predictedTranscriptsAndProteins.pyIan ReidMon, 06 Jul 2020 16:31:27 -0000https://sourceforge.net/p/harfang/code/ci/566036436a1fbf6780fbe9e680731af3038bf9a9/https://sourceforge.net/p/harfang/code/ci/69bd6f157570ab8c8788fa26c995d0c33dc21161/Added hash and comparison functions to ClassifiedSplice classIan ReidFri, 03 Jul 2020 14:58:30 -0000https://sourceforge.net/p/harfang/code/ci/69bd6f157570ab8c8788fa26c995d0c33dc21161/https://sourceforge.net/p/harfang/code/ci/4291439d6cfdb84b2edebcd80caddcaf9ddae99d/Added check for duplicate splice junctions to avoid spurious retained intron errors in score_models.pyIan ReidFri, 03 Jul 2020 14:58:30 -0000https://sourceforge.net/p/harfang/code/ci/4291439d6cfdb84b2edebcd80caddcaf9ddae99d/https://sourceforge.net/p/harfang/code/ci/6b44a07c045caab8570128cb4fceb4015242ad5d/Corrected sub-version check in HarfangIan ReidThu, 02 Jul 2020 14:03:53 -0000https://sourceforge.net/p/harfang/code/ci/6b44a07c045caab8570128cb4fceb4015242ad5d/https://sourceforge.net/p/harfang/code/ci/45f7b4311ba147afedb31ab65190b67daee44ec7/added trim_to_exons method to GFF3mRNAIan ReidThu, 02 Jul 2020 13:46:03 -0000https://sourceforge.net/p/harfang/code/ci/45f7b4311ba147afedb31ab65190b67daee44ec7/https://sourceforge.net/p/harfang/code/ci/6b8325ce81b001964246041e826399a27eb12e4f/Fixes to ensure that all GFF3 files comply with SO specIan ReidMon, 29 Jun 2020 21:29:28 -0000https://sourceforge.net/p/harfang/code/ci/6b8325ce81b001964246041e826399a27eb12e4f/https://sourceforge.net/p/harfang/code/ci/1f6a513998b455cbaddac831e652280b3c18e0ed/Added Unknown to status_precedence dictionary in group_transcripts.pyIan ReidSun, 28 Jun 2020 01:53:25 -0000https://sourceforge.net/p/harfang/code/ci/1f6a513998b455cbaddac831e652280b3c18e0ed/https://sourceforge.net/p/harfang/code/ci/3bb39ce69410bef074ac55656a05910fa31129c3/Doubled { and } in task_Complete_Score_ModelsIan ReidSun, 28 Jun 2020 01:37:57 -0000https://sourceforge.net/p/harfang/code/ci/3bb39ce69410bef074ac55656a05910fa31129c3/https://sourceforge.net/p/harfang/code/ci/baf9db345b92f36264f0c89819203648097841c2/Try doubling % in task_make_BAM_hints for compatibility with CmdAction.expand_actionIan ReidSun, 28 Jun 2020 00:52:08 -0000https://sourceforge.net/p/harfang/code/ci/baf9db345b92f36264f0c89819203648097841c2/https://sourceforge.net/p/harfang/code/ci/22562777f98a154cf887b3a8f807ee731ef90726/modified task_make_BAM_hints to yield dictionary literalIan ReidSun, 28 Jun 2020 00:14:37 -0000https://sourceforge.net/p/harfang/code/ci/22562777f98a154cf887b3a8f807ee731ef90726/https://sourceforge.net/p/harfang/code/ci/e33bbf1ee62b4e1136282b4c17b91abfbda16358/modified task_make_BAM_hints to avoid string formatting error by doit task parserIan ReidSat, 27 Jun 2020 16:13:07 -0000https://sourceforge.net/p/harfang/code/ci/e33bbf1ee62b4e1136282b4c17b91abfbda16358/https://sourceforge.net/p/harfang/code/ci/79b2bba7ea71b3e1b9d4a38ca1fbb83c9c594c87/Corrected spelling of coverage.wig.gzIan ReidFri, 26 Jun 2020 19:44:15 -0000https://sourceforge.net/p/harfang/code/ci/79b2bba7ea71b3e1b9d4a38ca1fbb83c9c594c87/https://sourceforge.net/p/harfang/code/ci/bc0ae264e6794ebfdbb01d1fe80065bc58350f8c/Implemented split_models_at_coverage_gaps.pyIan ReidFri, 26 Jun 2020 18:23:02 -0000https://sourceforge.net/p/harfang/code/ci/bc0ae264e6794ebfdbb01d1fe80065bc58350f8c/https://sourceforge.net/p/harfang/code/ci/8af8b063a358d2c764de1d777e6292c4b76476a2/Added bin/src/depth2wig.pyIan ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/8af8b063a358d2c764de1d777e6292c4b76476a2/https://sourceforge.net/p/harfang/code/ci/561e7fee43d0f31bbf3936d03a67243c65f47b4f/Updated README.txtIan ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/561e7fee43d0f31bbf3936d03a67243c65f47b4f/https://sourceforge.net/p/harfang/code/ci/8f4d1337067fad9fdc3930a927da90366d277b3a/Reolaced gff3Iterator.py and gff3Record.py with latest version from transcriptomicsIan ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/8f4d1337067fad9fdc3930a927da90366d277b3a/https://sourceforge.net/p/harfang/code/ci/d3017e0a1fad0e9fb3906a8f699197c752c04505/Replaced gtftogff3.py with gtf2gff3.py from transcriptomicsIan ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/d3017e0a1fad0e9fb3906a8f699197c752c04505/https://sourceforge.net/p/harfang/code/ci/beea178f076384fc7e4a751f21fb191f15ea4491/Changed run_Harfang.py run() function to accept either cd-hit or cdhit as the executable name (Bug 290)Ian ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/beea178f076384fc7e4a751f21fb191f15ea4491/https://sourceforge.net/p/harfang/code/ci/5f48438373ff17246ad3408dcaea483f1d52bca4/Changed run_Harfang.py run() function to ensure that configured values for ProjectDir, Genome, MappedReads, MaskedGenome, and ExternalPredictions are absolute paths (Bug 291)Ian ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/5f48438373ff17246ad3408dcaea483f1d52bca4/https://sourceforge.net/p/harfang/code/ci/adb125d102e49cdbff68c90875a650cfa9e23408/Changed run_Harfang.py run() function to ensure that configured values for ProjectDir, Genome, MappedReads, MaskedGenome, and ExternalPredictions are absolute paths (Bug 291)Ian ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/adb125d102e49cdbff68c90875a650cfa9e23408/https://sourceforge.net/p/harfang/code/ci/3eb06e568c3c56835383b5dc51b2acf1c06b3d0f/Modified mRNA __eq__() to ignore regular exons if CDS records are present (Bug 316)Ian ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/3eb06e568c3c56835383b5dc51b2acf1c06b3d0f/https://sourceforge.net/p/harfang/code/ci/fab75df0208dbc74c8b0b18d988fc33971f66e70/Added logging to task_Pool_Augustus_Models for debuggingIan ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/fab75df0208dbc74c8b0b18d988fc33971f66e70/https://sourceforge.net/p/harfang/code/ci/2a519d0f067dfc45fa151e8449493fe4e84fd985/Fixed score testing in group_transcripts.pyIan ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/2a519d0f067dfc45fa151e8449493fe4e84fd985/https://sourceforge.net/p/harfang/code/ci/c98ce721635e6fdf7bf9c0ed23e5ced4ca7dc122/Fixed gene model generation in gff3IteratorIan ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/c98ce721635e6fdf7bf9c0ed23e5ced4ca7dc122/https://sourceforge.net/p/harfang/code/ci/796012b64d454220ec60f916099c2c236453578a/Modified src/score_models.check_splice_compatibility to allow exon status to append multiple valuesIanMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/796012b64d454220ec60f916099c2c236453578a/https://sourceforge.net/p/harfang/code/ci/4dd1de3e235bb1e6cf8f95af5dbb8ec411ceb1e3/Modified src/score_models.check_splice_compatibility to allow exon status to append multiple valuesIanMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/4dd1de3e235bb1e6cf8f95af5dbb8ec411ceb1e3/https://sourceforge.net/p/harfang/code/ci/9b40e0e01cdcb228d641dd33a7b1ecd86b8690a8/Modified src/score_models.check_splice_compatibility to allow exon status to append multiple valuesIanMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/9b40e0e01cdcb228d641dd33a7b1ecd86b8690a8/https://sourceforge.net/p/harfang/code/ci/6a44f7c7435d557facf3d21a59edc6b57b6e0297/Modified src/score_models.check_splice_compatibility to allow exon status to append multiple valuesIanMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/6a44f7c7435d557facf3d21a59edc6b57b6e0297/https://sourceforge.net/p/harfang/code/ci/88437e4f525b4c1e090bbba6f1ca51a0ada4daf5/MergedIan ReidMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/88437e4f525b4c1e090bbba6f1ca51a0ada4daf5/https://sourceforge.net/p/harfang/code/ci/bab7c95dbd14a84d2e8508ebb41b494ef749b210/Added test to testScore_models.pyIanMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/bab7c95dbd14a84d2e8508ebb41b494ef749b210/https://sourceforge.net/p/harfang/code/ci/fddf697866df50c7e20754efadb8521f9a35d263/Updated islands2genes.pyIanMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/fddf697866df50c7e20754efadb8521f9a35d263/https://sourceforge.net/p/harfang/code/ci/5d670409552f2766aa6f85cd24e73491fe429b9f/Modified bin/src/gff3Iterator.py to handle null parentsIanMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/5d670409552f2766aa6f85cd24e73491fe429b9f/https://sourceforge.net/p/harfang/code/ci/73b8d6c1791b3011f4a8f76e66d6b7620903d3e1/Modified bin/src/gff3Record.py to handle null parentsIanMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/73b8d6c1791b3011f4a8f76e66d6b7620903d3e1/https://sourceforge.net/p/harfang/code/ci/b517a2130ddaea3e87a0472202a594e1331badac/Modified bin/src/gff3Record.py to handle null parentsIanMon, 22 Jun 2020 15:45:56 -0000https://sourceforge.net/p/harfang/code/ci/b517a2130ddaea3e87a0472202a594e1331badac/