| 87e6812 | Jason Walker | 21 November 2016, 20:56:58 UTC | Merge pull request #1621 from jasonwalker80/remove_instdata_limitation Remove imported restriction to assiging instrument data. | 21 November 2016, 20:56:58 UTC |
| 6507ebe | Thomas B. Mooney | 21 November 2016, 19:26:54 UTC | Merge pull request #1617 from tmooney/bwamem_converts_fragment_bam_to_fastq_properly BWA-MEM: Only pass parameter for paired FASTQs if "-p" flag used. | 21 November 2016, 19:26:54 UTC |
| cea8865 | Jason Walker | 21 November 2016, 19:13:53 UTC | Remove imported restriction to assiging instrument data. | 21 November 2016, 19:13:53 UTC |
| 2d48d2d | Thomas B. Mooney | 21 November 2016, 19:10:04 UTC | Merge pull request #1618 from tmooney/remove_spurious_whitespace_in_jobiterator Remove spurious whitespace in regex. | 21 November 2016, 19:10:04 UTC |
| 9214d38 | Thomas B. Mooney | 21 November 2016, 19:09:50 UTC | Merge pull request #1615 from tmooney/remove_gmt_kmer Remove old `gmt kmer` tree. | 21 November 2016, 19:09:50 UTC |
| f46646e | Thomas B. Mooney | 21 November 2016, 19:09:43 UTC | Merge pull request #1612 from tmooney/use_testdata_for_adapter_file Use test input for adapter file instead of hardcoded path. | 21 November 2016, 19:09:43 UTC |
| 4204697 | Thomas B. Mooney | 21 November 2016, 19:09:26 UTC | Merge pull request #1609 from tmooney/analysis_project_view_includes_inactive_configs Add separate flag to control display of inactive configs. | 21 November 2016, 19:09:26 UTC |
| d602fe1 | Thomas B. Mooney | 21 November 2016, 19:09:15 UTC | Merge pull request #1604 from tmooney/remove_park_beta Remove "Park" beta. | 21 November 2016, 19:09:15 UTC |
| 5058219 | Thomas B. Mooney | 17 November 2016, 18:27:57 UTC | Merge pull request #1620 from tmooney/correct_operator_precedence_in_test_builder Test::Builder: Don't return before evaluating the entire expression. | 17 November 2016, 18:27:57 UTC |
| 44e515d | Thomas B. Mooney | 17 November 2016, 18:26:56 UTC | Merge branch 'master' into remove_park_beta Conflicts: lib/perl/Genome/Model/GenePrediction/Command/Pap/Blast/BladeBlastBatcher.pm lib/perl/Genome/Model/GenePrediction/Command/Pap/KEGGScan/RunKeggScan.pm | 17 November 2016, 18:26:56 UTC |
| 3052740 | Thomas B. Mooney | 17 November 2016, 18:24:28 UTC | Merge pull request #1611 from tmooney/configurable_memory_limit_for_picard Make Java heap and permgen configurable for calling Picard. | 17 November 2016, 18:24:28 UTC |
| 5b8e1fe | Thomas B. Mooney | 17 November 2016, 18:24:01 UTC | Merge pull request #1619 from tmooney/sr_avoid_calling_each_while_inserting_into_hash Avoid using `each()` in loop where we insert into the hash. | 17 November 2016, 18:24:01 UTC |
| ff05d0a | Thomas B. Mooney | 16 November 2016, 23:42:35 UTC | Don't return before evaluating the entire expression. This module really shouldn't be in the repository to begin with... but as long as we're supporting old systems it shall remain. | 16 November 2016, 23:42:35 UTC |
| c811b39 | Thomas B. Mooney | 16 November 2016, 22:37:56 UTC | Avoid using `each()` in loop where we insert into the hash. Newer Perl's provide this warning: > Use of each() on hash after insertion without resetting hash iterator > results in undefined behavior | 16 November 2016, 22:37:56 UTC |
| 9f9c7bd | Thomas B. Mooney | 16 November 2016, 22:24:29 UTC | Remove spurious whitespace in regex. Perl 5.22 warned of an unescaped "{". Seems like it was a quantifier gone wrong. The history of this module is obscured, though. | 16 November 2016, 22:24:29 UTC |
| 7399b54 | Thomas B. Mooney | 16 November 2016, 14:30:57 UTC | Only pass parameter for paired output if "-p" flag used in bwa-mem. | 16 November 2016, 14:30:57 UTC |
| 91fd81b | Joshua McMichael | 15 November 2016, 16:11:55 UTC | Merge pull request #1593 from tmooney/bugfix_coverage_html_table_structure Coverage Report: Use a wrapping <div> for the hiding. Apply dataTables to the <table>. | 15 November 2016, 16:11:55 UTC |
| 5413417 | APipe Tester | 11 November 2016, 13:18:03 UTC | Updated `gmt` tab completion. | 11 November 2016, 13:18:03 UTC |
| 91d6132 | APipe Tester | 11 November 2016, 13:17:20 UTC | Updated `genome` tab completion. | 11 November 2016, 13:17:20 UTC |
| 8667111 | APipe Tester | 11 November 2016, 13:15:46 UTC | Updated class browser cache. | 11 November 2016, 13:15:46 UTC |
| 9418845 | Thomas B. Mooney | 10 November 2016, 22:40:36 UTC | Merge pull request #1616 from tmooney/remove_obsolete_utilities Remove various "Genome::Utility" entries that seem disused. | 10 November 2016, 22:40:36 UTC |
| 558bd96 | Thomas B. Mooney | 10 November 2016, 16:52:41 UTC | Merge pull request #1610 from tmooney/make_it_possible_to_disable_fs_caching Make it possible to disable local filesystem caching. | 10 November 2016, 16:52:41 UTC |
| 1428b3f | Thomas B. Mooney | 10 November 2016, 16:51:56 UTC | Merge pull request #1613 from tmooney/remove_gmt_analysis_indels_dbsnpconcord Remove old `gmt analysis indels dbsnp-concord` tool. | 10 November 2016, 16:51:56 UTC |
| 31f52ca | Thomas B. Mooney | 10 November 2016, 16:51:43 UTC | Merge pull request #1614 from tmooney/remove_disabled_gmt_bedtools_coverage Remove old tool that was "disabled" in 2010. | 10 November 2016, 16:51:43 UTC |
| f9dd0b3 | APipe Tester | 10 November 2016, 13:18:52 UTC | Updated `gmt` tab completion. | 10 November 2016, 13:18:52 UTC |
| fd779ee | APipe Tester | 10 November 2016, 13:18:04 UTC | Updated `genome` tab completion. | 10 November 2016, 13:18:04 UTC |
| 07f318b | APipe Tester | 10 November 2016, 13:16:24 UTC | Updated class browser cache. | 10 November 2016, 13:16:24 UTC |
| 302c831 | Thomas B. Mooney | 09 November 2016, 22:57:13 UTC | Remove Genome::Utility::BioPerl tree. | 09 November 2016, 22:57:13 UTC |
| 786e7fc | Thomas B. Mooney | 09 November 2016, 22:52:15 UTC | Remove "Editor" Utility. I heartell this idea never got put to full use. | 09 November 2016, 22:52:15 UTC |
| d22285a | Thomas B. Mooney | 09 November 2016, 22:47:23 UTC | Remove TranscriptHelper Utility. | 09 November 2016, 22:47:23 UTC |
| 8675712 | Thomas B. Mooney | 09 November 2016, 22:43:22 UTC | Remove 454TrimFile Utility and tools. | 09 November 2016, 22:43:22 UTC |
| f3fc70c | Thomas B. Mooney | 09 November 2016, 22:41:56 UTC | Remove SeqcleanReport Utility and tool. | 09 November 2016, 22:41:56 UTC |
| da92807 | Thomas B. Mooney | 09 November 2016, 22:39:44 UTC | Remove Genome::Utility::IAValidate. | 09 November 2016, 22:39:44 UTC |
| ab7bf1d | Thomas B. Mooney | 09 November 2016, 22:28:47 UTC | Remove `gmt kmer` tree. | 09 November 2016, 22:28:47 UTC |
| 6a4de1d | Thomas B. Mooney | 09 November 2016, 21:58:55 UTC | Remove old tool that was "disabled" in 2010. | 09 November 2016, 21:58:55 UTC |
| fd1e430 | Thomas B. Mooney | 09 November 2016, 21:52:22 UTC | Remove old tool with nonexistent path. | 09 November 2016, 21:52:22 UTC |
| d3f8fb0 | Thomas B. Mooney | 09 November 2016, 21:23:09 UTC | Use test input for adapter file instead of hardcoded path. | 09 November 2016, 21:28:45 UTC |
| d48cd9a | Thomas B. Mooney | 09 November 2016, 19:36:35 UTC | Merge pull request #1605 from tmooney/retire_geneprediction_bacterial_models Retire GenePrediction::Bacterial model type. | 09 November 2016, 19:36:35 UTC |
| 7ddc365 | Thomas B. Mooney | 09 November 2016, 19:36:26 UTC | Merge pull request #1607 from tmooney/reduce_gsc_references Eliminate "low-hanging" /gsc/ references. | 09 November 2016, 19:36:26 UTC |
| 82b2d77 | Thomas B. Mooney | 09 November 2016, 19:32:20 UTC | Make Java heap and permgen configurable for calling Picard. | 09 November 2016, 19:32:20 UTC |
| 82f78c3 | Thomas B. Mooney | 08 November 2016, 19:36:37 UTC | Make it possible to disable local filesystem caching. Set config to empty string or non-existent location to disable cache. (This will fall back to original location if cache is temporarily unavailable as well.) | 08 November 2016, 19:36:37 UTC |
| 2ced190 | Thomas B. Mooney | 08 November 2016, 15:33:38 UTC | Add separate flag to control display of inactive configs. Closes #1608. | 08 November 2016, 15:33:38 UTC |
| 33ec279 | APipe Tester | 03 November 2016, 12:18:04 UTC | Updated `gmt` tab completion. | 03 November 2016, 12:18:04 UTC |
| a46368f | APipe Tester | 03 November 2016, 12:17:22 UTC | Updated `genome` tab completion. | 03 November 2016, 12:17:22 UTC |
| f061473 | APipe Tester | 03 November 2016, 12:15:49 UTC | Updated class browser cache. | 03 November 2016, 12:15:49 UTC |
| c6e359c | Chris Miller | 03 November 2016, 05:15:37 UTC | Merge pull request #1601 from chrisamiller/master fixing issues with target-region filtering, header, and indels | 03 November 2016, 05:15:37 UTC |
| c5b3cca | Chris Miller | 02 November 2016, 19:24:24 UTC | sanitizing strings and using build instead of model for target region | 02 November 2016, 19:24:38 UTC |
| f3ddc7b | Chris Miller | 21 October 2016, 21:42:35 UTC | fixing header on output files | 02 November 2016, 19:24:37 UTC |
| 63cb4e0 | Chris Miller | 21 October 2016, 17:33:25 UTC | fixing several issues with target-region filtering and indels | 02 November 2016, 19:24:37 UTC |
| a4d23dd | Thomas B. Mooney | 02 November 2016, 15:37:25 UTC | Merge pull request #1606 from tmooney/reduce_gscuser_references Reduce "gscuser" references. | 02 November 2016, 15:37:25 UTC |
| d97229f | Thomas B. Mooney | 02 November 2016, 15:21:48 UTC | Merge pull request #1603 from tmooney/use_annotation_db_for_gene_targets_file_in_cnview_tests Use the annotation DB instead of a hardcoded path for targets file. | 02 November 2016, 15:21:48 UTC |
| c13a2f7 | Susanna Kiwala | 02 November 2016, 15:18:13 UTC | Merge pull request #1598 from susannasiebert/snv_indel_report Also look for the snv_indel_report_clean_unfiltered_file and snv_indel_report_clean_filtered_file by the subject's name | 02 November 2016, 15:18:13 UTC |
| 45243c6 | Susanna Kiwala | 02 November 2016, 15:17:51 UTC | Merge pull request #1588 from susannasiebert/clinseq_failure Make sure the $tumor_subject_common_name is defined before regexing it | 02 November 2016, 15:17:51 UTC |
| 9bf7b61 | Thomas B. Mooney | 01 November 2016, 21:39:10 UTC | Remove obsolete Workflow callback. | 01 November 2016, 21:39:10 UTC |
| bb6aab9 | Thomas B. Mooney | 01 November 2016, 21:36:19 UTC | Remove defunct command. | 01 November 2016, 21:36:19 UTC |
| b74ea69 | Thomas B. Mooney | 01 November 2016, 21:34:44 UTC | We already broke /gsc/bin/perl. | 01 November 2016, 21:34:44 UTC |
| 9a01f43 | Thomas B. Mooney | 01 November 2016, 21:31:37 UTC | Make default simply /var/log/. In practice we don't write to this directory anyway. | 01 November 2016, 21:31:37 UTC |
| 391fcad | Thomas B. Mooney | 01 November 2016, 21:28:42 UTC | Reduce path to just snapshot number. | 01 November 2016, 21:28:42 UTC |
| 7460de9 | Thomas B. Mooney | 01 November 2016, 21:20:52 UTC | Remove broken mpileup-for-variants tool. | 01 November 2016, 21:20:52 UTC |
| ffecb8d | Thomas B. Mooney | 01 November 2016, 21:19:49 UTC | Shorten example to just filename since example location is nonexistent. | 01 November 2016, 21:19:49 UTC |
| c2c94ed | Thomas B. Mooney | 01 November 2016, 21:18:18 UTC | Remove broken "PhaseVariants" tool. | 01 November 2016, 21:18:18 UTC |
| efe4442 | Thomas B. Mooney | 01 November 2016, 21:14:59 UTC | Remove broken "Sammy" tools. | 01 November 2016, 21:16:48 UTC |
| 62a0941 | Thomas B. Mooney | 01 November 2016, 21:13:49 UTC | Remove broken Bowtie batch commands. | 01 November 2016, 21:13:49 UTC |
| 31bcc50 | Thomas B. Mooney | 01 November 2016, 21:10:46 UTC | Remove commented-out require. | 01 November 2016, 21:10:46 UTC |
| 7da96d2 | Thomas B. Mooney | 01 November 2016, 21:10:13 UTC | Remove broken Plink tools. | 01 November 2016, 21:10:13 UTC |
| 78e2d89 | Thomas B. Mooney | 01 November 2016, 21:08:52 UTC | Remove broken "AlignToGenome" tools. | 01 November 2016, 21:08:52 UTC |
| c2a7111 | Thomas B. Mooney | 01 November 2016, 21:06:07 UTC | Remove broken test. | 01 November 2016, 21:06:07 UTC |
| 38b4b7f | Thomas B. Mooney | 01 November 2016, 20:27:15 UTC | Remove support for GenePrediction::Bacterial. Removes the BAP, GAP, and PAP namespaces. | 01 November 2016, 20:59:01 UTC |
| 037961b | Thomas B. Mooney | 01 November 2016, 20:50:31 UTC | Remove references to homedir in ModelPair test. Mostly this was in a TODO anyway, so it wasn't even used. | 01 November 2016, 20:50:31 UTC |
| cfaccd8 | Thomas B. Mooney | 01 November 2016, 19:44:13 UTC | Remove Park beta and dependent CrossSample Indel tool. | 01 November 2016, 19:44:13 UTC |
| e55fef0 | Thomas B. Mooney | 01 November 2016, 19:40:06 UTC | The name of the road is "Forest Park Avenue". | 01 November 2016, 19:40:06 UTC |
| ca4b4a2 | Thomas B. Mooney | 31 October 2016, 19:19:31 UTC | Use the annotation DB instead of a hardcoded path for targets file. | 31 October 2016, 19:19:31 UTC |
| 784dc9d | APipe Tester | 29 October 2016, 12:17:45 UTC | Updated `genome` tab completion. | 29 October 2016, 12:17:45 UTC |
| 8c1ca36 | APipe Tester | 29 October 2016, 12:16:00 UTC | Updated class browser cache. | 29 October 2016, 12:16:00 UTC |
| 098e23d | Eddie Belter | 28 October 2016, 21:13:28 UTC | Merge pull request #1600 from ebelter/export-de-novo-build Export DeNovoAssembly Builds | 28 October 2016, 21:13:28 UTC |
| 47d25af | Feiyu Du | 25 October 2016, 18:42:06 UTC | Merge pull request #1602 from dufeiyu/master Update blessed build | 25 October 2016, 18:42:06 UTC |
| e2754e2 | Feiyu Du | 25 October 2016, 15:41:54 UTC | update blessed build | 25 October 2016, 15:41:54 UTC |
| 8b4eded | APipe Tester | 25 October 2016, 12:18:36 UTC | Updated `gmt` tab completion. | 25 October 2016, 12:18:36 UTC |
| 7890ead | APipe Tester | 25 October 2016, 12:17:56 UTC | Updated `genome` tab completion. | 25 October 2016, 12:17:56 UTC |
| e4429f0 | APipe Tester | 25 October 2016, 12:16:35 UTC | Updated class browser cache. | 25 October 2016, 12:16:35 UTC |
| 59986d3 | Eddie Belter | 24 October 2016, 18:36:41 UTC | PR recommendations | 24 October 2016, 18:36:41 UTC |
| 162aab0 | Thomas B. Mooney | 24 October 2016, 17:15:35 UTC | Merge pull request #1597 from tmooney/remove_build_workflow_config Remove old build workflow configuration. | 24 October 2016, 17:15:35 UTC |
| d34fa56 | Thomas B. Mooney | 24 October 2016, 17:14:31 UTC | Merge pull request #1587 from tmooney/remove_email_pipeline_noisy Remove "email_pipeline_noisy" config. | 24 October 2016, 17:14:31 UTC |
| 3863ab3 | Thomas B. Mooney | 24 October 2016, 17:14:15 UTC | Merge pull request #1577 from tmooney/pullonetwobpindels_test_generates_fof PullOneTwoBpIndels test: Generate the FOF to pass to the tool. | 24 October 2016, 17:14:15 UTC |
| 023a89c | Thomas B. Mooney | 24 October 2016, 17:13:58 UTC | Merge pull request #1571 from tmooney/make_gatksomaticindel_input_indices_nonglobal Use object properties instead of global variables to store positions. | 24 October 2016, 17:13:58 UTC |
| 964c50b | Thomas B. Mooney | 24 October 2016, 17:13:23 UTC | Merge pull request #1569 from tmooney/remove_capture_mutationsfromgroup Remove `gmt capture mutations-from-group`. | 24 October 2016, 17:13:23 UTC |
| 70e59ed | Thomas B. Mooney | 24 October 2016, 17:13:12 UTC | Merge pull request #1568 from tmooney/remove_old_copynumber_readdepth_tools Remove old CopyNumber ReadDepth tools. | 24 October 2016, 17:13:12 UTC |
| bb9b30c | Thomas B. Mooney | 24 October 2016, 17:13:02 UTC | Merge pull request #1566 from tmooney/remove_old_varscan_copynumber_tools Remove old Varscan Copy-Number tools. | 24 October 2016, 17:13:02 UTC |
| 8c3ace6 | Thomas B. Mooney | 24 October 2016, 17:12:53 UTC | Merge pull request #1564 from tmooney/remove_bash_completion_helper Remove out-dated bash completion helper. | 24 October 2016, 17:12:53 UTC |
| 42b80e6 | Thomas B. Mooney | 24 October 2016, 17:12:44 UTC | Merge pull request #1563 from tmooney/remove_systemsnapshot_utilities Remove Genome::Utility::SystemSnapshot. | 24 October 2016, 17:12:44 UTC |
| 37e9640 | Thomas B. Mooney | 24 October 2016, 17:12:33 UTC | Merge pull request #1552 from tmooney/remove_old_log_dir_config Remove old, unused "log_dir" configuration variable. | 24 October 2016, 17:12:33 UTC |
| c113d14 | Thomas B. Mooney | 24 October 2016, 17:12:15 UTC | Merge pull request #1545 from tmooney/determine_error_has_blacklist Add a blacklist for locations from which to not report errors. | 24 October 2016, 17:12:15 UTC |
| 68fef53 | Thomas B. Mooney | 24 October 2016, 17:12:04 UTC | Merge pull request #1538 from tmooney/ccsvcf_result_command_is_optional CCSVCF Result: "command" property should be optional. | 24 October 2016, 17:12:04 UTC |
| c8f61bb | Jason Walker | 24 October 2016, 16:47:35 UTC | Merge pull request #1590 from jasonwalker80/purge_report_with_anp_name Purge Report with AnP Name | 24 October 2016, 16:47:35 UTC |
| 864afc0 | Eddie Belter | 20 October 2016, 23:32:55 UTC | Check if model is supported | 20 October 2016, 23:34:20 UTC |
| 7574d19 | Eddie Belter | 20 October 2016, 23:07:10 UTC | Clean up additioanl files for assembler | 20 October 2016, 23:34:19 UTC |
| 03d4275 | Eddie Belter | 20 October 2016, 22:48:30 UTC | move velvet fastq file function | 20 October 2016, 23:34:19 UTC |
| 8121c74 | Eddie Belter | 20 October 2016, 22:40:27 UTC | Check is assembler is supported when resolving builds | 20 October 2016, 23:34:18 UTC |
| 23e145f | Eddie Belter | 20 October 2016, 22:34:34 UTC | is_assembler_supported | 20 October 2016, 23:34:18 UTC |
| 6f0e94d | Eddie Belter | 20 October 2016, 22:12:58 UTC | Use File::Spec and _messages, general clean up | 20 October 2016, 23:34:17 UTC |
