| 75b1575 | Eddie Belter | 27 April 2015, 23:12:40 UTC | Merge pull request #657 from ebelter/cghub GMT CG Hub - Add command to help TCGA imports | 27 April 2015, 23:12:40 UTC |
| 6fe7125 | Eddie Belter | 27 April 2015, 22:02:39 UTC | GMT CG Hub: spell check | 27 April 2015, 22:02:39 UTC |
| 5dfcaa0 | Eddie Belter | 27 April 2015, 22:00:41 UTC | Cg Hub Metadata: use isa => __PACKAGE__ when validating params | 27 April 2015, 22:00:41 UTC |
| f262582 | Eddie Belter | 27 April 2015, 21:57:23 UTC | CG Hub: just return the result value | 27 April 2015, 21:57:23 UTC |
| a90d85a | Feiyu Du | 27 April 2015, 20:08:05 UTC | Merge pull request #692 from dufeiyu/bam_size Set bam_size regardless of _use_alignment_summary_cpp | 27 April 2015, 20:08:05 UTC |
| 1630762 | APipe Tester | 25 April 2015, 21:18:31 UTC | updated ur submodule to 1cd191b | 25 April 2015, 21:18:31 UTC |
| fdfd83c | David Morton | 25 April 2015, 19:53:19 UTC | Merge pull request #689 from davidlmorton/fix_encoding Encode/Decode workflow inputs and outputs when using PTero | 25 April 2015, 19:53:19 UTC |
| b763b2e | Nathaniel Nutter | 25 April 2015, 05:40:56 UTC | Merge pull request #693 from iferguson90/picard-simple-fix Stop picking up single jar versions of Picard. | 25 April 2015, 05:40:56 UTC |
| a679b33 | Ian Ferguson | 24 April 2015, 21:00:36 UTC | Stop picking up single jar versions of Picard. Prior to version 1.124, Picard was made up as a set of jars, one for each tool, installed under /usr/share/java/picard-toolsV.VVV/. Additionally, a support jar would be installed as /usr/share/java/picard-V.VVV.jar. Picard versions 1.124 and later use a single jar, installed as /usr/share/java/picard-V.VVV.jar, to provide all tools. The Picard GMT was picking up both single- and multi-jar versions of Picard, even though it could only handle the older multi-jar versions. This commit should prevent the Picard GMT from picking up the single-jar versions of Picard (1.124 and later) until single-jar support can be added. | 24 April 2015, 21:00:36 UTC |
| 7f3a9f3 | Nathaniel Nutter | 24 April 2015, 19:24:00 UTC | Merge pull request #691 from gatoravi/update_clinseq_blessed update clinseq blessed | 24 April 2015, 19:24:00 UTC |
| b5e3b29 | Avinash Ramu | 24 April 2015, 19:18:34 UTC | update clinseq blessed This is related to a new source - GuideToPharmacologyInteractions that was added to DGIdb. | 24 April 2015, 19:18:34 UTC |
| d8328ff | Nathaniel Nutter | 24 April 2015, 19:09:24 UTC | Merge pull request #690 from nnutter/clin-seq updated expected results for Genome/Model/ClinSeq/Command/AnnotateGenesByDgidb.t | 24 April 2015, 19:09:24 UTC |
| 2b3d831 | Feiyu Du | 24 April 2015, 18:51:15 UTC | set bam_size regardless of _use_alignment_summary_cpp | 24 April 2015, 18:51:15 UTC |
| 8b12655 | Nathaniel Nutter | 24 April 2015, 18:36:27 UTC | update expected results | 24 April 2015, 18:36:27 UTC |
| b4411a5 | Nathaniel Nutter | 24 April 2015, 18:35:47 UTC | fix warnings that occur when one file is longer than the other | 24 April 2015, 18:35:47 UTC |
| dfcb1ee | Feiyu Du | 24 April 2015, 17:12:54 UTC | Merge pull request #687 from dufeiyu/unlock Use Scope::Guard to ensure unlocking | 24 April 2015, 17:12:54 UTC |
| 9da822e | dmorton | 24 April 2015, 15:43:00 UTC | Encode/Decode workflow inputs and outputs We were already doing this for steps within a workflow, but some workflows take objects as inputs and return objects as outputs. This allows that to work. | 24 April 2015, 15:43:00 UTC |
| f1d2cba | APipe Tester | 24 April 2015, 12:24:59 UTC | Updated `gmt` tab completion. | 24 April 2015, 12:24:59 UTC |
| fd17962 | APipe Tester | 24 April 2015, 12:24:15 UTC | Updated `genome` tab completion. | 24 April 2015, 12:24:15 UTC |
| c6c4d05 | APipe Tester | 24 April 2015, 12:22:21 UTC | Updated class browser cache. | 24 April 2015, 12:22:21 UTC |
| 476be02 | Feiyu Du | 23 April 2015, 20:53:53 UTC | use Scope::Guard to make sure unlocking | 23 April 2015, 20:53:53 UTC |
| 97b0955 | Adam Coffman | 23 April 2015, 16:59:01 UTC | Merge pull request #683 from tmooney/delete_files_in_our_directory Delete the output files, not whatever is in the current directory. | 23 April 2015, 16:59:01 UTC |
| 17ea251 | Indraniel | 23 April 2015, 16:00:30 UTC | Merge pull request #679 from indraniel/vcf-evaluate-pt2 GMT Integration of VCF Evaluation (part 2) | 23 April 2015, 16:00:30 UTC |
| 2a405b3 | Gabriel Sanderson | 23 April 2015, 15:43:10 UTC | Merge pull request #681 from gsanders/bam_header_fix Create bam headers on demand | 23 April 2015, 15:43:10 UTC |
| 66c5b32 | Gabriel Sanderson | 23 April 2015, 15:03:52 UTC | This unless is not necessary since create_bam_flagstat checks as well | 23 April 2015, 15:03:52 UTC |
| 19dea37 | David Morton | 22 April 2015, 22:35:17 UTC | Merge pull request #682 from davidlmorton/block_n_converge Support Converge Operations when using Ptero | 22 April 2015, 22:35:17 UTC |
| 871f7c8 | Gabriel Sanderson | 22 April 2015, 18:50:13 UTC | Refactor usage of create_bam_flagstat | 22 April 2015, 18:50:13 UTC |
| 9db8b02 | Thomas Mooney | 22 April 2015, 18:39:41 UTC | Delete the output files, not whatever is in the current dir! | 22 April 2015, 18:39:41 UTC |
| a008dba | Susanna Siebert | 22 April 2015, 17:31:54 UTC | Merge pull request #678 from susannasiebert/variant_reporting_vep Don't fail optional expert parameters as required during validation | 22 April 2015, 17:31:54 UTC |
| 7ea629a | Indraniel Das | 22 April 2015, 17:24:42 UTC | + apply @acoffman 's 3rd suggestion - use the TSV reader that's already in Genome::Utility | 22 April 2015, 17:24:42 UTC |
| 2dd0d15 | Indraniel Das | 22 April 2015, 17:01:32 UTC | + apply @tmooney 's 7th suggestion - ensure there's a space between the status message sentences when creating the output directory. | 22 April 2015, 17:01:32 UTC |
| 6c87f71 | Indraniel Das | 22 April 2015, 16:59:45 UTC | + apply @tmooney 's 6th suggestion - dynamically call the stat methods instead of explicitly. This makes the code shorter. | 22 April 2015, 16:59:45 UTC |
| ad6011c | dmorton | 22 April 2015, 15:46:46 UTC | Only get the first element of `output_properties` Legacy Converge operations would only supply outputs to the first specified output_property of the operation, even if multiple outputs were specified. | 22 April 2015, 15:46:46 UTC |
| e2337f7 | Susanna Siebert | 22 April 2015, 15:42:33 UTC | Move conversion to Set::Scalar into the subroutines | 22 April 2015, 15:42:33 UTC |
| cadb299 | Susanna Siebert | 21 April 2015, 19:45:50 UTC | Remove unused subroutine | 22 April 2015, 15:38:35 UTC |
| 6b0f861 | Avinash Ramu | 22 April 2015, 14:17:34 UTC | Merge pull request #680 from gatoravi/update_build_emailaddress use ENV variables to configure build email | 22 April 2015, 14:17:34 UTC |
| 8d1623e | APipe Tester | 22 April 2015, 12:16:34 UTC | Updated `genome` tab completion. | 22 April 2015, 12:16:34 UTC |
| cf655e2 | APipe Tester | 22 April 2015, 10:27:35 UTC | updated ur submodule to 4fffe07 | 22 April 2015, 10:27:35 UTC |
| f6ff664 | dmorton | 22 April 2015, 00:59:58 UTC | Add more error checking | 22 April 2015, 00:59:58 UTC |
| c72dc9c | dmorton | 22 April 2015, 00:59:32 UTC | Ptero now supports Converge operations | 22 April 2015, 00:59:32 UTC |
| 1344407 | Indraniel Das | 21 April 2015, 23:09:22 UTC | + apply @tmooney 's & @acoffman 's 5th suggestion - refer to EvaluateVcf for the versions from EvaluateVcfs (this suggestion was recommended during an in person conversation with @tmooney and @acoffman .) | 21 April 2015, 23:18:53 UTC |
| 0a48e3e | Indraniel Das | 21 April 2015, 23:07:58 UTC | + apply @acoffman 's 2nd suggestion - actually use the bedtools, joinx, and vcflib versions in the code! | 21 April 2015, 23:18:52 UTC |
| 8168364 | Indraniel Das | 21 April 2015, 23:06:17 UTC | + apply acoffman 's 1st suggestion - use the "Path" type for the inputs that represent files and directories | 21 April 2015, 23:18:51 UTC |
| 7bbffe0 | Indraniel Das | 21 April 2015, 23:17:44 UTC | + use Genome::Sys to create the tmp directory - this is more proper, and will account for LSF's automatic cleanup if something goes amiss. | 21 April 2015, 23:17:44 UTC |
| fac1c66 | Indraniel Das | 21 April 2015, 23:16:20 UTC | + apply @tmooney 's 4th suggestion - use GENOME_TEST_INPUTS for the test data location | 21 April 2015, 23:16:20 UTC |
| b7ab783 | Indraniel Das | 21 April 2015, 21:56:32 UTC | + apply @tmooney 's 3rd suggestion - documentation fixes (1) correct misspelling ('configruation' -> 'configuration') (2) refer to the command name, rather than the Perl class name | 21 April 2015, 21:59:37 UTC |
| 04ffb15 | Indraniel Das | 21 April 2015, 21:46:30 UTC | + apply @tmooney 's 2nd suggestion - add error checking when retrieving the model and build | 21 April 2015, 21:46:30 UTC |
| 12a09a6 | Indraniel Das | 21 April 2015, 21:37:37 UTC | + apply @tmooney 's 1st suggestion - remove the commented out and unused `display_all_stats` method call. | 21 April 2015, 21:37:37 UTC |
| dd28f9f | Gabriel Sanderson | 21 April 2015, 21:20:31 UTC | Use bam locking when creating a flagstat file. | 21 April 2015, 21:20:31 UTC |
| f502926 | Gabriel Sanderson | 21 April 2015, 21:16:06 UTC | Check for bam header existence before and after locking. | 21 April 2015, 21:16:06 UTC |
| 86b19ff | Thomas B. Mooney | 21 April 2015, 21:11:50 UTC | Merge pull request #677 from tmooney/AUE-427 AnP Config Add: Pluralize tag-adding option. CHANGELOG: For the `genome analysis-project add-config-file` and `genome analysis-project add-menu-item` commands, the "--tag" parameter has been renamed "--tags". It should otherwise behave identically to the old parameter. | 21 April 2015, 21:11:50 UTC |
| dd292a5 | Gabriel Sanderson | 21 April 2015, 20:48:18 UTC | Refactor Merged.pm to remove duplicate code. | 21 April 2015, 20:48:18 UTC |
| 1396459 | Avinash Ramu | 21 April 2015, 20:45:46 UTC | use ENV vars to configure email | 21 April 2015, 20:45:46 UTC |
| ab10222 | Gabriel Sanderson | 21 April 2015, 19:31:34 UTC | Flagstat and header files will be created before revivification. Add create_bam_header method, call it before revivifying. rename _create_bam_flagstat to a 'public' method. Remove redundant flagstat_path method. | 21 April 2015, 20:41:34 UTC |
| f69d604 | Susanna Siebert | 21 April 2015, 19:25:22 UTC | Add test for planned errors of experts | 21 April 2015, 19:45:28 UTC |
| 8d62717 | Indraniel Das | 21 April 2015, 19:02:42 UTC | + comment out the true_negative_size parameter - it's good to check that this parameter works, but in 99% of the cases we're not going to use it. It's usually better to calculate this number out as part of the program execution. I'll leave it commented out so that future viewers of this test may know that the parameter can be explicitly specified instead of being calculated. | 21 April 2015, 19:11:22 UTC |
| 0de0459 | Indraniel Das | 21 April 2015, 19:00:21 UTC | + don't zcat a file that isn't gzipped - the bed file that's passed into the bed_size subroutine isn't gzipped. zcat-ting a regular file errors out. | 21 April 2015, 19:11:21 UTC |
| bf71def | Indraniel Das | 21 April 2015, 18:58:48 UTC | + calculate bed_size on the correct TN BED file - this account for my failing tests | 21 April 2015, 19:11:20 UTC |
| 61ad506 | Indraniel Das | 19 April 2015, 03:22:06 UTC | + add some status messages to measure progress | 21 April 2015, 19:11:20 UTC |
| 622d380 | Indraniel Das | 19 April 2015, 03:01:58 UTC | + include first-draft documentation | 21 April 2015, 19:11:19 UTC |
| d2f6cf2 | Indraniel Das | 19 April 2015, 02:36:14 UTC | + explicitly set the true_negative_size param - setting this exactly matches the output found in BIO-1176 (not sure if this is the correct thing to do yet.) - allowing for this also test the usage of the 'true_negative_size' option in both the G::M::T::Vcf::EvaluateVcf and G::M::T::Vcf::EvaluateVcfs tools. | 21 April 2015, 19:11:19 UTC |
| 572f82b | Indraniel Das | 19 April 2015, 02:28:45 UTC | + correctly pass the true_negative_size param - Somehow this parameter didn't get correctly setup during the initial translation. | 21 April 2015, 19:11:18 UTC |
| 017e3d3 | Indraniel Das | 19 April 2015, 02:34:48 UTC | + make the basedir a lexical global - this way the test works correctly when the SKIP block is enabled, or disabled (commented out) | 21 April 2015, 19:11:18 UTC |
| fbd11ba | Indraniel Das | 19 April 2015, 02:31:10 UTC | + accentuate the stat diag messages in the output - just introducing an extra newline in the diag string argument | 21 April 2015, 19:11:17 UTC |
| e660714 | Indraniel Das | 18 April 2015, 18:44:16 UTC | + skip evaluation tests - these are long tests that need to be run inside the TGI, and are not meant to be run in the automated pipeline. | 21 April 2015, 19:11:17 UTC |
| 8a97e14 | Indraniel Das | 18 April 2015, 18:41:52 UTC | + remove DB::singles - these were used at one point for debugging | 21 April 2015, 19:11:16 UTC |
| 27ee272 | Indraniel Das | 18 April 2015, 18:40:19 UTC | + compare the generated statistic values to expected set - ensure that the generated statistics are reasonable. | 21 April 2015, 19:11:16 UTC |
| db41fdc | Indraniel Das | 18 April 2015, 18:38:07 UTC | + store that the config and raw stat parameters - ensure that the config parameters and raw statistics are being stored in the output hash | 21 April 2015, 19:11:15 UTC |
| 48a46ad | Indraniel Das | 18 April 2015, 05:38:44 UTC | + print out a "Summary" section header - it's easier to see the overall stats that way | 21 April 2015, 19:11:14 UTC |
| 81cba73 | Indraniel Das | 18 April 2015, 05:37:18 UTC | + suppress the stats printout in EvaluateVcf execution - this make the overall output more confusing | 21 April 2015, 19:11:14 UTC |
| 7116518 | Indraniel Das | 18 April 2015, 05:35:47 UTC | + correct the bed_size input calculation - need to pass in the correct true_negative bed file name | 21 April 2015, 19:11:13 UTC |
| 0fbf154 | Indraniel Das | 09 April 2015, 22:15:16 UTC | + initial stub of G::M::T::Vcf::EvaluateVcfs.pm - this a port of the evaluate_vcfs.pl script used in CLE validation | 21 April 2015, 19:11:13 UTC |
| 2fc5994 | Susanna Siebert | 21 April 2015, 18:35:50 UTC | Don't fail optional expert parameters as required during validation | 21 April 2015, 18:35:50 UTC |
| b19d08f | Thomas B. Mooney | 21 April 2015, 14:43:39 UTC | Merge pull request #668 from tmooney/allow_assumed_variant_status_in_simplify_vcf SimplifyVCF: Add option to declare all unfiltered variants as passing/failing. | 21 April 2015, 14:43:39 UTC |
| 7bd4056 | APipe Tester | 21 April 2015, 12:51:39 UTC | Updated `gmt` tab completion. | 21 April 2015, 12:51:39 UTC |
| c092d71 | APipe Tester | 21 April 2015, 12:50:54 UTC | Updated `genome` tab completion. | 21 April 2015, 12:50:54 UTC |
| 7cb08b7 | APipe Tester | 21 April 2015, 12:49:02 UTC | Updated class browser cache. | 21 April 2015, 12:49:02 UTC |
| 12a053a | Thomas Mooney | 20 April 2015, 20:06:32 UTC | Add missing "`" for symmetry. | 20 April 2015, 20:06:32 UTC |
| b13416f | Thomas Mooney | 20 April 2015, 20:05:55 UTC | Rename tag to tags. | 20 April 2015, 20:05:55 UTC |
| ebac3c4 | Thomas B. Mooney | 20 April 2015, 19:53:12 UTC | Merge pull request #671 from tmooney/update_anp_add_docs Create common base class and update docs for AnP config-adding commands | 20 April 2015, 19:53:12 UTC |
| 6120ad0 | Thomas B. Mooney | 20 April 2015, 19:38:24 UTC | Merge pull request #646 from tmooney/find_potentially_matching_references New command to find references that have the same chromosome names as a query file. | 20 April 2015, 19:38:24 UTC |
| f7c4b23 | Thomas Mooney | 09 April 2015, 13:43:04 UTC | Use new don't-create option instead of inspecting build directly. | 20 April 2015, 18:15:48 UTC |
| a6dfe97 | Thomas Mooney | 09 April 2015, 13:42:33 UTC | Use File::Spec. | 20 April 2015, 18:15:48 UTC |
| 98f8bfe | Thomas Mooney | 09 April 2015, 13:41:59 UTC | Optionally don't try to auto-create sequence dictionary. | 20 April 2015, 18:15:48 UTC |
| e016d18 | Thomas Mooney | 08 April 2015, 21:36:21 UTC | New command to find references we're not sure aren't related to a file. We can be sure some aren't related, but we cannot know if the returned references have anything to do with the file or not. | 20 April 2015, 18:10:32 UTC |
| d25ee50 | Indraniel | 20 April 2015, 16:51:30 UTC | Merge pull request #640 from indraniel/vcf-evaluate GMT Integration of VCF Evaluation (part 1) | 20 April 2015, 16:51:30 UTC |
| eb6cd75 | Avinash Ramu | 20 April 2015, 15:58:28 UTC | Merge pull request #628 from gatoravi/clinseq_add_loh Module to identify LOH regions. | 20 April 2015, 15:58:28 UTC |
| 75079f3 | Avinash Ramu | 20 April 2015, 15:35:55 UTC | glob before unlink | 20 April 2015, 15:35:55 UTC |
| 1e1cde8 | Susanna Siebert | 20 April 2015, 15:06:23 UTC | Merge pull request #672 from susannasiebert/variant_reporting_docm Add gene annotations to the DoCM report and remove the trio.t test | 20 April 2015, 15:06:23 UTC |
| 14e11ff | Susanna Siebert | 20 April 2015, 14:46:22 UTC | Reword error message | 20 April 2015, 14:46:22 UTC |
| b999029 | Thomas Mooney | 20 April 2015, 13:56:00 UTC | Double-check that the profile item wasn't there already. | 20 April 2015, 13:56:00 UTC |
| c1119ec | Thomas Mooney | 20 April 2015, 13:52:56 UTC | Add stub for _create_profile_items. | 20 April 2015, 13:52:56 UTC |
| bf93137 | Thomas B. Mooney | 20 April 2015, 13:47:57 UTC | Merge pull request #669 from tmooney/failx_isnt_a_thing ReferenceSequence Build: Fix typos and remove trailing whitespace. | 20 April 2015, 13:47:57 UTC |
| 0efe615 | Thomas B. Mooney | 20 April 2015, 13:47:26 UTC | Merge pull request #670 from tmooney/availble_quiting Fix more typos. | 20 April 2015, 13:47:26 UTC |
| 8d8f027 | APipe Tester | 20 April 2015, 12:43:32 UTC | updated workflow submodule to 2d658c9 | 20 April 2015, 12:43:32 UTC |
| 0d2d195 | APipe Tester | 18 April 2015, 12:17:05 UTC | Updated `gmt` tab completion. | 18 April 2015, 12:17:05 UTC |
| 63be564 | APipe Tester | 18 April 2015, 12:16:19 UTC | Updated `genome` tab completion. | 18 April 2015, 12:16:19 UTC |
| 3d3bbf6 | APipe Tester | 18 April 2015, 12:14:41 UTC | Updated class browser cache. | 18 April 2015, 12:14:41 UTC |
| bafc5be | Feiyu Du | 17 April 2015, 22:05:59 UTC | Merge pull request #675 from dufeiyu/bug_fix Bug fix: bam_file, not get_bam_file | 17 April 2015, 22:05:59 UTC |
| 017a98f | Feiyu Du | 17 April 2015, 20:07:22 UTC | bug fix get_bam_file -> bam_file | 17 April 2015, 20:07:22 UTC |
