| 2df4013 | Eddie Belter | 29 March 2013, 20:05:33 UTC | InstData Import: move flagstat into separate method | 08 April 2013, 21:42:46 UTC |
| a2562c9 | Eddie Belter | 29 March 2013, 18:11:02 UTC | InstData Import: remove moved fail and bam tests from fastq | 08 April 2013, 21:42:46 UTC |
| 2f9619c | Eddie Belter | 29 March 2013, 18:09:33 UTC | InstData Import: mv fail tests from fastq into separate file | 08 April 2013, 21:42:46 UTC |
| c45f462 | Eddie Belter | 29 March 2013, 18:03:26 UTC | InstData Import: mv bam test from fastq into separate file | 08 April 2013, 21:42:45 UTC |
| 58e6b87 | Eddie Belter | 29 March 2013, 17:58:01 UTC | InstData Import: rename basic test | 08 April 2013, 21:42:45 UTC |
| fc317e4 | Eddie Belter | 29 March 2013, 17:49:49 UTC | InstData Import Basic: convert format into original_format and import_format | 08 April 2013, 21:42:43 UTC |
| c94d40b | APipe Tester | 08 April 2013, 21:30:13 UTC | updated jenkins submodule to bad136a | 08 April 2013, 21:30:13 UTC |
| 89cf28e | APipe Tester | 08 April 2013, 20:43:34 UTC | updated jenkins submodule to 6fdbd47 | 08 April 2013, 20:43:34 UTC |
| 5b9814a | APipe Tester | 08 April 2013, 20:43:27 UTC | updated ur submodule to 318fcdc | 08 April 2013, 20:43:27 UTC |
| 1da947a | nnutter | 08 April 2013, 17:17:53 UTC | restore default_values This tool is using defaults to find compatible models or creating new models if needed (which would then validate their inputs as well). So I think it may be an exception to the "no defaults" rule. That commit did not convert several defaults which possibly should have been converted (if this is ever unreverted). This reverts commit 935b04397f9b925fac4b80aacbdcbcf79d70dea8. | 08 April 2013, 17:33:25 UTC |
| fb75798 | Feiyu Du | 08 April 2013, 16:14:49 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 08 April 2013, 16:14:49 UTC |
| 0d04edb | nnutter | 08 April 2013, 15:57:48 UTC | updated expected data Updated several files expected outputs: genome-instrument-data-list2.out genome-model-clinseq-list1.out genome-model-clinseq-list3.out genome-model-rnaseq-list2.out genome-instrument-data-list2.out was because insert size information was added to the instrument data. The other three are all related to rebuilding of dependent builds due to some issue with the alignments (tmooney handled that). | 08 April 2013, 16:02:04 UTC |
| f5f07e2 | Feiyu Du | 08 April 2013, 15:57:50 UTC | bug fix get_default_alignment_results method | 08 April 2013, 15:58:25 UTC |
| cd7849a | Dave Larson | 08 April 2013, 15:40:23 UTC | rename method for grabbing blessed build and remove use above | 08 April 2013, 15:40:23 UTC |
| db48199 | nnutter | 08 April 2013, 15:02:40 UTC | output changed because default value was made to an example value | 08 April 2013, 15:02:40 UTC |
| af0a8ec | Dave Larson | 08 April 2013, 14:18:12 UTC | added test for DiffBlessed refactor | 08 April 2013, 14:18:12 UTC |
| 026b382 | Scott Smith | 06 April 2013, 20:55:32 UTC | Revamp Genome::Model::ReferenceSequence. * Updated to use newer input handling. * Legacy "*Imported*" modules still are in place but are empty. * Genome::Model::Build::ReferenceSequence exists but is smaller. | 06 April 2013, 21:02:13 UTC |
| 0d9b7ea | Anthony Brummett | 05 April 2013, 22:07:57 UTC | Avoid uninitialized value warnings | 05 April 2013, 22:31:41 UTC |
| 334847f | Anthony Brummett | 05 April 2013, 21:46:46 UTC | command_execute_ok doesn't work with this kind of command | 05 April 2013, 22:31:41 UTC |
| e6a023b | Anthony Brummett | 05 April 2013, 21:28:15 UTC | make tests less chatty | 05 April 2013, 22:31:40 UTC |
| 45573e9 | Anthony Brummett | 05 April 2013, 21:27:14 UTC | Forgot to use Sub::Install | 05 April 2013, 22:31:40 UTC |
| 4b0db30 | Anthony Brummett | 05 April 2013, 18:51:44 UTC | Add test command_execute_fail_ok() that passes if the command execution returns false | 05 April 2013, 22:31:40 UTC |
| 1283565 | Anthony Brummett | 05 April 2013, 18:11:23 UTC | Make the output from vep go to /dev/null in the test | 05 April 2013, 22:31:39 UTC |
| 0b55d56 | APipe Tester | 05 April 2013, 22:10:26 UTC | updated ur submodule to ffdf52f | 05 April 2013, 22:10:26 UTC |
| cd4d2ef | Dave Larson | 05 April 2013, 21:44:14 UTC | add some file accessors to clinseq | 05 April 2013, 21:55:18 UTC |
| 314eff7 | Dave Larson | 05 April 2013, 21:33:27 UTC | refactored to have methods | 05 April 2013, 21:55:17 UTC |
| 23f272e | Dave Larson | 05 April 2013, 21:32:42 UTC | remove accessors from tool (moved to ClinSeq) | 05 April 2013, 21:55:17 UTC |
| e607fd4 | Malachi Griffith | 05 April 2013, 21:03:12 UTC | ClinSeq - Extra input file checking in converge all-events | 05 April 2013, 21:03:12 UTC |
| 0ac2520 | Gabriel Sanderson | 05 April 2013, 20:47:31 UTC | Merge branch 'default' into gb_master | 05 April 2013, 20:47:31 UTC |
| 85eb548 | Gabriel Sanderson | 05 April 2013, 20:47:16 UTC | Remove default parameters. Remove unused CeuYri module. | 05 April 2013, 20:47:26 UTC |
| 2eee6b7 | nnutter | 05 April 2013, 20:23:56 UTC | add runtime check for ambiguous property definitions | 05 April 2013, 20:45:00 UTC |
| 035674a | Jason Walker | 05 April 2013, 20:44:47 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 April 2013, 20:44:47 UTC |
| 5ec0475 | Jason Walker | 05 April 2013, 20:44:40 UTC | Get or create the to model-group. | 05 April 2013, 20:44:40 UTC |
| 3cd1671 | Ben Oberkfell | 05 April 2013, 20:44:09 UTC | actually capture this in a closure | 05 April 2013, 20:44:09 UTC |
| af219a8 | Gabriel Sanderson | 05 April 2013, 20:38:44 UTC | Merge branch 'default' into gb_master | 05 April 2013, 20:38:44 UTC |
| 935b043 | Gabriel Sanderson | 05 April 2013, 20:25:38 UTC | remove default values | 05 April 2013, 20:38:40 UTC |
| 8bbb520 | APipe Tester | 05 April 2013, 20:32:48 UTC | updated ur submodule to a12ce7f | 05 April 2013, 20:32:48 UTC |
| 5b2fc40 | Gabriel Sanderson | 05 April 2013, 20:19:10 UTC | Merge branch 'default' into gb_master | 05 April 2013, 20:19:10 UTC |
| e031351 | Gabriel Sanderson | 05 April 2013, 20:16:39 UTC | remove default values | 05 April 2013, 20:16:39 UTC |
| cdb0224 | Gabriel Sanderson | 05 April 2013, 20:09:53 UTC | Merge branch 'default' into gb_master | 05 April 2013, 20:09:53 UTC |
| 98df15b | Gabriel Sanderson | 05 April 2013, 20:08:38 UTC | eliminate default values | 05 April 2013, 20:08:38 UTC |
| 301fc93 | Gabriel Sanderson | 05 April 2013, 20:03:45 UTC | Merge branch 'default' into gb_master | 05 April 2013, 20:03:45 UTC |
| 54e92af | Gabriel Sanderson | 05 April 2013, 20:03:18 UTC | remove default values | 05 April 2013, 20:03:18 UTC |
| 552408b | Gabriel Sanderson | 05 April 2013, 19:09:46 UTC | Merge branch 'default' into gb_master | 05 April 2013, 19:09:46 UTC |
| ddd8618 | Jason Walker | 05 April 2013, 19:07:35 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 April 2013, 19:07:35 UTC |
| 3b64e6b | Gabriel Sanderson | 05 April 2013, 18:55:43 UTC | removed default values | 05 April 2013, 18:55:43 UTC |
| 34369dd | Gabriel Sanderson | 05 April 2013, 18:49:38 UTC | Merge branch 'default' into gb_master | 05 April 2013, 18:49:38 UTC |
| 55e2a00 | Gabriel Sanderson | 05 April 2013, 18:45:13 UTC | remove default values | 05 April 2013, 18:49:28 UTC |
| d420a07 | Gabriel Sanderson | 05 April 2013, 18:41:11 UTC | Merge branch 'default' into gb_master | 05 April 2013, 18:41:11 UTC |
| def2737 | Gabriel Sanderson | 05 April 2013, 18:38:26 UTC | remove default values | 05 April 2013, 18:38:26 UTC |
| 75502c0 | Gabriel Sanderson | 05 April 2013, 18:34:35 UTC | Merge branch 'default' into gb_master | 05 April 2013, 18:34:35 UTC |
| 4a16edf | Gabriel Sanderson | 05 April 2013, 18:33:03 UTC | eliminate default values | 05 April 2013, 18:33:03 UTC |
| eea6596 | Gabriel Sanderson | 05 April 2013, 18:30:25 UTC | Merge branch 'default' into gb_master | 05 April 2013, 18:30:25 UTC |
| 8ca25e0 | Gabriel Sanderson | 05 April 2013, 18:29:16 UTC | remove default values | 05 April 2013, 18:29:16 UTC |
| 1a858f1 | Gabriel Sanderson | 05 April 2013, 18:25:49 UTC | Merge branch 'default' into gb_master | 05 April 2013, 18:25:49 UTC |
| 87369b3 | Gabriel Sanderson | 05 April 2013, 18:24:46 UTC | Eliminate default values | 05 April 2013, 18:24:46 UTC |
| 622f225 | Scott Smith | 05 April 2013, 15:22:13 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 April 2013, 15:22:13 UTC |
| 872d00e | Scott Smith | 05 April 2013, 15:22:02 UTC | remove debug code | 05 April 2013, 15:22:02 UTC |
| 1cc4c36 | Malachi Griffith | 05 April 2013, 15:13:47 UTC | clin-seq ignore R files in test case diff | 05 April 2013, 15:13:47 UTC |
| e5f05dc | Scott Smith | 05 April 2013, 15:03:08 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 April 2013, 15:03:08 UTC |
| 2c3157f | Scott Smith | 05 April 2013, 15:02:48 UTC | Builds now get properties from the model even if a build module with some code exists. | 05 April 2013, 15:03:01 UTC |
| a699233 | nnutter | 05 April 2013, 14:14:21 UTC | Revert recent changes to GenomeDiskAllocationTest.pm. This reverts commit e99d713b7e74df8b1987827f3e9b2977c5231952 and commit 7975508dc7dc593b6e1add408c18d8f39c1b10ea. | 05 April 2013, 15:03:00 UTC |
| 98baa44 | nnutter | 05 April 2013, 14:15:33 UTC | delete funky test, will move concept to runtime check | 05 April 2013, 15:03:00 UTC |
| 9bb4d83 | Malachi Griffith | 05 April 2013, 05:10:53 UTC | ClinSeq - generate clonality plots test now takes ~60s instead of ~1400s to run, other minor fixes | 05 April 2013, 15:02:59 UTC |
| 8ff1cbe | Ian Ferguson | 04 April 2013, 22:41:58 UTC | Cleaned up and removed defaults from GMT/Varscan/* Removed default reference sequence parameters from GMT/Varscan/CopyNumberParallel, CopySegmentParallel, QuickReadcounts, Readcounts, Somatic, SomaticParallel, SomaticParallelFilter, and SomaticParallelMerge. If the reference sequence was marked as is_optional => 1 in those classes, it is now marked as is_optional => 0. Changed the reference sequence parameters to is_optional => 0 in Consensus, NormalizeCopySegments, and SomaticMt (they had recently had their default reference sequence removed). Also reformatted class definitions for all modules under GMT/Varscan (added line breaks and fixed indentation for better consistency and readability). | 05 April 2013, 15:02:59 UTC |
| c11ace8 | APipe Tester | 04 April 2013, 22:43:22 UTC | updated workflow submodule to 192ebaa | 05 April 2013, 15:02:59 UTC |
| ace4978 | APipe Tester | 04 April 2013, 22:43:18 UTC | updated ur submodule to 1babdee | 05 April 2013, 15:02:58 UTC |
| 29f1abc | Anthony Brummett | 04 April 2013, 22:34:48 UTC | Remove another skip_all to get the module to compile/run | 05 April 2013, 15:02:58 UTC |
| e8b765d | Anthony Brummett | 04 April 2013, 22:18:34 UTC | Moved the test 'skip_all' from GenomeDiskAllocationTest.pm to the individual tests Another test (SoftwareResult_ambiguous_property_definitions.t) was failing because it does a 'ur show subclasses', which internally loads everything that looks like a .pm file. As GenomeDiskAllocationTest.pm loaded, the 'skip_all' told the test harness that SoftwareResult_ambiguous_property_definitions.t should skip. | 05 April 2013, 15:02:58 UTC |
| 64ae776 | Scott Smith | 04 April 2013, 21:25:27 UTC | switch to looking at just the first 2000 rows for htseq test | 05 April 2013, 15:02:57 UTC |
| 9470b22 | Anthony Brummett | 04 April 2013, 20:52:43 UTC | Fix the number of tests | 05 April 2013, 15:02:57 UTC |
| 3767b0c | Anthony Brummett | 04 April 2013, 20:26:49 UTC | Make the test less chatty | 05 April 2013, 15:02:57 UTC |
| baea2c2 | Anthony Brummett | 04 April 2013, 20:26:04 UTC | Don't warn about the removal if we're running in a test | 05 April 2013, 15:02:56 UTC |
| 48954a6 | Anthony Brummett | 04 April 2013, 20:12:28 UTC | diags about differences are now 1-based instead of 0-based makes it easier for people to read | 05 April 2013, 15:02:56 UTC |
| 1d62112 | Anthony Brummett | 04 April 2013, 19:44:39 UTC | Add command_execute_ok() test function | 05 April 2013, 15:02:56 UTC |
| bbaa167 | Anthony Brummett | 03 April 2013, 16:30:03 UTC | remove text_is() and text_like() from Genome::Utility::Text and replace with remove_ansi() | 05 April 2013, 15:02:55 UTC |
| 8f65479 | Gabriel Sanderson | 04 April 2013, 20:45:53 UTC | Fixed a broken error message. class_name->class | 05 April 2013, 15:02:55 UTC |
| ef17db3 | Ian Ferguson | 04 April 2013, 20:21:14 UTC | Remove b36 defaults from GMT/Somatic/LaunchPindel | 05 April 2013, 15:02:55 UTC |
| f23a794 | nnutter | 04 April 2013, 20:16:26 UTC | disable tests because they require special permissions to function well | 05 April 2013, 15:02:54 UTC |
| 03231a0 | nnutter | 05 April 2013, 14:14:21 UTC | Revert recent changes to GenomeDiskAllocationTest.pm. This reverts commit e99d713b7e74df8b1987827f3e9b2977c5231952 and commit 7975508dc7dc593b6e1add408c18d8f39c1b10ea. | 05 April 2013, 14:17:47 UTC |
| 4b29f38 | nnutter | 05 April 2013, 14:15:33 UTC | delete funky test, will move concept to runtime check | 05 April 2013, 14:17:46 UTC |
| 179f33b | Malachi Griffith | 05 April 2013, 05:10:53 UTC | ClinSeq - generate clonality plots test now takes ~60s instead of ~1400s to run, other minor fixes | 05 April 2013, 05:10:53 UTC |
| cf6a655 | Ian Ferguson | 04 April 2013, 22:41:58 UTC | Cleaned up and removed defaults from GMT/Varscan/* Removed default reference sequence parameters from GMT/Varscan/CopyNumberParallel, CopySegmentParallel, QuickReadcounts, Readcounts, Somatic, SomaticParallel, SomaticParallelFilter, and SomaticParallelMerge. If the reference sequence was marked as is_optional => 1 in those classes, it is now marked as is_optional => 0. Changed the reference sequence parameters to is_optional => 0 in Consensus, NormalizeCopySegments, and SomaticMt (they had recently had their default reference sequence removed). Also reformatted class definitions for all modules under GMT/Varscan (added line breaks and fixed indentation for better consistency and readability). | 04 April 2013, 22:48:28 UTC |
| 9451b2c | APipe Tester | 04 April 2013, 22:43:22 UTC | updated workflow submodule to 192ebaa | 04 April 2013, 22:43:22 UTC |
| e4ea3e7 | APipe Tester | 04 April 2013, 22:43:18 UTC | updated ur submodule to 1babdee | 04 April 2013, 22:43:18 UTC |
| e99d713 | Anthony Brummett | 04 April 2013, 22:34:48 UTC | Remove another skip_all to get the module to compile/run | 04 April 2013, 22:34:48 UTC |
| 0dac76d | Anthony Brummett | 04 April 2013, 22:20:45 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 April 2013, 22:20:45 UTC |
| 7975508 | Anthony Brummett | 04 April 2013, 22:18:34 UTC | Moved the test 'skip_all' from GenomeDiskAllocationTest.pm to the individual tests Another test (SoftwareResult_ambiguous_property_definitions.t) was failing because it does a 'ur show subclasses', which internally loads everything that looks like a .pm file. As GenomeDiskAllocationTest.pm loaded, the 'skip_all' told the test harness that SoftwareResult_ambiguous_property_definitions.t should skip. | 04 April 2013, 22:18:34 UTC |
| 8092f13 | Scott Smith | 04 April 2013, 21:25:27 UTC | switch to looking at just the first 2000 rows for htseq test | 04 April 2013, 21:25:27 UTC |
| 0eb8b72 | Anthony Brummett | 04 April 2013, 20:52:43 UTC | Fix the number of tests | 04 April 2013, 20:53:25 UTC |
| 1740a67 | Anthony Brummett | 04 April 2013, 20:26:49 UTC | Make the test less chatty | 04 April 2013, 20:53:24 UTC |
| 2a810c1 | Anthony Brummett | 04 April 2013, 20:26:04 UTC | Don't warn about the removal if we're running in a test | 04 April 2013, 20:53:24 UTC |
| 3515b98 | Anthony Brummett | 04 April 2013, 20:12:28 UTC | diags about differences are now 1-based instead of 0-based makes it easier for people to read | 04 April 2013, 20:53:23 UTC |
| eca3e16 | Anthony Brummett | 04 April 2013, 19:44:39 UTC | Add command_execute_ok() test function | 04 April 2013, 20:53:23 UTC |
| 2b3a8f4 | Anthony Brummett | 03 April 2013, 16:30:03 UTC | remove text_is() and text_like() from Genome::Utility::Text and replace with remove_ansi() | 04 April 2013, 20:53:22 UTC |
| 81837ed | Gabriel Sanderson | 04 April 2013, 20:46:11 UTC | Merge branch 'ccsvcf' into gb_master | 04 April 2013, 20:46:11 UTC |
| e00daba | Gabriel Sanderson | 04 April 2013, 20:45:53 UTC | Fixed a broken error message. class_name->class | 04 April 2013, 20:46:00 UTC |
| 0f7d0f1 | Ian Ferguson | 04 April 2013, 20:21:14 UTC | Remove b36 defaults from GMT/Somatic/LaunchPindel | 04 April 2013, 20:22:44 UTC |
| 36032b3 | nnutter | 04 April 2013, 20:16:26 UTC | disable tests because they require special permissions to function well | 04 April 2013, 20:17:31 UTC |
| 93008bc | Scott Smith | 04 April 2013, 19:18:25 UTC | add "genome processing-profile diff A B" | 04 April 2013, 19:18:25 UTC |
