| dde1f5f | Malachi Griffith | 06 February 2014, 03:53:02 UTC | fix documentation and other minor details related to installation of file based dbs from github | 06 February 2014, 03:53:02 UTC |
| 7c2a5ad | Chris Miller | 06 February 2014, 02:52:10 UTC | added code to prevent negative numbers for minimum insert size | 06 February 2014, 02:52:31 UTC |
| 8685bdd | Malachi Griffith | 06 February 2014, 01:52:16 UTC | add modules so that cancer-gene-list can be accessed via Genome::Db | 06 February 2014, 01:52:16 UTC |
| 59c1385 | Eddie Belter | 06 February 2014, 00:29:33 UTC | Alignment Result: add class for aligners having intermediate results | 06 February 2014, 00:30:10 UTC |
| 8c66ca6 | Eddie Belter | 05 February 2014, 20:35:52 UTC | AR: store iar id to test removal | 06 February 2014, 00:30:09 UTC |
| 6b56ceb | Eddie Belter | 05 February 2014, 20:35:21 UTC | AR: rm dumper statement | 06 February 2014, 00:30:09 UTC |
| 2c09aac | Eddie Belter | 05 February 2014, 20:34:34 UTC | BWA IAR: rm redundant command | 06 February 2014, 00:30:08 UTC |
| fa7ef99 | Eddie Belter | 05 February 2014, 19:50:07 UTC | BWA AR: use intermediate class directly instead of command class | 06 February 2014, 00:30:07 UTC |
| 5aa9d34 | Eddie Belter | 05 February 2014, 19:41:46 UTC | BWA AR: update messages | 06 February 2014, 00:30:07 UTC |
| b64992d | Eddie Belter | 05 February 2014, 19:30:34 UTC | BWA AR: move intermediate params outside of each pass | 06 February 2014, 00:30:06 UTC |
| 0ab0281 | Eddie Belter | 05 February 2014, 19:26:04 UTC | BWA AR: add user to intermedaite result right after creating | 06 February 2014, 00:30:05 UTC |
| 0d3901e | Eddie Belter | 05 February 2014, 19:24:37 UTC | BWA AR: check that intermediate results are removed | 06 February 2014, 00:30:05 UTC |
| 229ebd5 | Eddie Belter | 05 February 2014, 19:23:36 UTC | Alignment Result: removes underlying intermediate results | 06 February 2014, 00:30:04 UTC |
| 8fef958 | Ben Ainscough | 05 February 2014, 23:15:12 UTC | changed hardcoded cancer_annotation_db | 05 February 2014, 23:15:12 UTC |
| 9d5ce45 | Jim Weible | 05 February 2014, 20:48:37 UTC | Remove useless temp files Remove the last output temp files these tests were creating. Inability to remove them because of file permissions was breaking tests. | 05 February 2014, 20:48:37 UTC |
| 38613de | Jim Weible | 04 February 2014, 14:28:28 UTC | change warning to debug message for AUE-19 | 05 February 2014, 15:35:11 UTC |
| b786f94 | Jim Weible | 29 January 2014, 16:27:00 UTC | change noisy status messages to debug_messages | 05 February 2014, 15:35:11 UTC |
| 30b1058 | Thomas Mooney | 05 February 2014, 15:18:11 UTC | Test whether the boolean is true, not whether self is true! | 05 February 2014, 15:18:11 UTC |
| 80bc696 | Eddie Belter | 04 February 2014, 23:49:49 UTC | BWA AR: modernize and simplify test | 04 February 2014, 23:49:49 UTC |
| 37005b6 | Eddie Belter | 04 February 2014, 21:30:26 UTC | BWA AR: get or create aligner index | 04 February 2014, 21:30:26 UTC |
| ddc8509 | Eddie Belter | 04 February 2014, 21:28:24 UTC | Revert "BWA AR: remove indexing ref in test" This reverts commit 26f6cda8d7e07fea66423888fa6c08201484126c. | 04 February 2014, 21:28:24 UTC |
| 26f6cda | Eddie Belter | 04 February 2014, 21:19:40 UTC | BWA AR: remove indexing ref in test | 04 February 2014, 21:19:40 UTC |
| 583f745 | Malachi Griffith | 04 February 2014, 16:39:42 UTC | clin-seq - snv-indel-report - add gene labeling and variant tracking over time to plots | 04 February 2014, 16:39:42 UTC |
| dc7cac2 | Thomas Mooney | 04 February 2014, 15:04:47 UTC | Still run the child query when testing allocations. | 04 February 2014, 15:04:47 UTC |
| 06352ad | APipe Tester | 04 February 2014, 13:17:30 UTC | Updated `genome` tab completion. | 04 February 2014, 13:17:30 UTC |
| 8cd6b87 | APipe Tester | 04 February 2014, 13:15:49 UTC | Updated class browser cache. | 04 February 2014, 13:15:49 UTC |
| 3151ea1 | APipe Tester | 03 February 2014, 22:35:34 UTC | updated graphite submodule to 00ac7bb | 03 February 2014, 22:35:34 UTC |
| 252b7ed | Anthony Brummett | 03 February 2014, 22:28:38 UTC | Update blessed build for rnaseq test model Jason Walker changed some metadata for its instrument data which lead to different tophat args related to inner insert size | 03 February 2014, 22:32:37 UTC |
| 4f924c0 | Mark Burnett | 03 February 2014, 22:06:29 UTC | don't check for child allocations during testing | 03 February 2014, 22:06:29 UTC |
| d5a007b | Malachi Griffith | 03 February 2014, 20:52:45 UTC | clin-seq: further tweaks to snv-indel report graphics | 03 February 2014, 20:52:45 UTC |
| b9ba593 | Jim Weible | 03 February 2014, 19:44:47 UTC | remove all the database stuff from these, since it no longer matters | 03 February 2014, 19:47:51 UTC |
| 75adf64 | Jim Weible | 03 February 2014, 19:31:03 UTC | remove unused cruft | 03 February 2014, 19:47:49 UTC |
| abe5dd8 | APipe Tester | 03 February 2014, 19:40:07 UTC | updated jenkins submodule to ad9380d | 03 February 2014, 19:40:07 UTC |
| 646ed11 | apregier | 03 February 2014, 18:51:54 UTC | Merge branch 'updated' into gb_master | 03 February 2014, 18:51:54 UTC |
| e71ecca | apregier | 03 February 2014, 18:50:41 UTC | Add error message for duplicate annotations | 03 February 2014, 18:50:59 UTC |
| ee8b272 | apregier | 03 February 2014, 18:32:54 UTC | rsids are optional and don't cause warnings if not there | 03 February 2014, 18:50:58 UTC |
| 68ffca0 | Jim Weible | 29 January 2014, 15:10:12 UTC | move fastq files to temp_staging_directory to avoid filling up temp. also, cleanup afterwards | 03 February 2014, 18:48:29 UTC |
| 17f0da0 | Jim Weible | 27 January 2014, 16:44:36 UTC | clean up our temp space after we use it so we do not run out | 03 February 2014, 18:48:28 UTC |
| 93840be | APipe Tester | 01 February 2014, 13:18:05 UTC | Updated `gmt` tab completion. | 01 February 2014, 13:18:05 UTC |
| 589693d | APipe Tester | 01 February 2014, 13:17:19 UTC | Updated `genome` tab completion. | 01 February 2014, 13:17:19 UTC |
| 1bb350e | APipe Tester | 01 February 2014, 13:15:42 UTC | Updated class browser cache. | 01 February 2014, 13:15:42 UTC |
| 01d1708 | Gabriel Sanderson | 31 January 2014, 22:24:15 UTC | Fixed |= -> ||= , we were doing a bitwise or when we did not mean to be | 31 January 2014, 22:24:47 UTC |
| 77e03be | Dave Larson | 31 January 2014, 22:07:28 UTC | partially finished script for adding menu items to existing projects | 31 January 2014, 22:07:44 UTC |
| 17661ff | Malachi Griffith | 31 January 2014, 21:04:23 UTC | various fixes to snv-indel-report to cover edge cases encountered with small test variant lists | 31 January 2014, 21:04:23 UTC |
| 7d66cb2 | apregier | 31 January 2014, 18:52:43 UTC | Merge branch 'updated' into gb_master | 31 January 2014, 18:52:43 UTC |
| 2c714eb | apregier | 31 January 2014, 18:51:26 UTC | Update status messages so they reflect what is happening. | 31 January 2014, 18:51:26 UTC |
| 1bf6c7f | Avinash Ramu | 31 January 2014, 16:42:28 UTC | new somatic variation build used in clinseq couple of things - new somatic variation build has different variants, changes to bam read counts by chris miller and changes to the DV2 filter might be causing the diffs with the previous blessed build. | 31 January 2014, 16:42:28 UTC |
| cb3cbac | APipe Tester | 31 January 2014, 13:19:30 UTC | Updated `genome` tab completion. | 31 January 2014, 13:19:30 UTC |
| dd19898 | Malachi Griffith | 31 January 2014, 00:08:50 UTC | further fixes and improvements to clin-seq snv-indel reporting | 31 January 2014, 00:08:50 UTC |
| b9576ec | Thomas Mooney | 30 January 2014, 18:51:15 UTC | Blithely update expected cases since a new build was run. | 30 January 2014, 18:51:15 UTC |
| a421b6e | Thomas Mooney | 30 January 2014, 15:46:45 UTC | Ignore new microarray_cnv directory when finding the cnvs.hq file. | 30 January 2014, 15:46:45 UTC |
| 3316ee4 | Mark Burnett | 30 January 2014, 13:37:18 UTC | use select 1 in disk allocation child query | 30 January 2014, 13:45:42 UTC |
| 4f09d75 | APipe Tester | 29 January 2014, 23:59:45 UTC | updated graphite submodule to 9fc8b86 | 29 January 2014, 23:59:45 UTC |
| bb73e98 | Chris Miller | 29 January 2014, 20:36:52 UTC | fixing small indel bug | 29 January 2014, 20:37:01 UTC |
| df1c08f | Mark Burnett | 29 January 2014, 20:30:50 UTC | child & parent allocations generate error_messages | 29 January 2014, 20:31:25 UTC |
| aa2dcde | Ian Ferguson | 29 January 2014, 19:41:18 UTC | Update aligner index debug message in Bwamem/Bwasw | 29 January 2014, 19:41:18 UTC |
| d622cce | Mark Burnett | 29 January 2014, 19:18:14 UTC | have child query only look at allocation_path | 29 January 2014, 19:19:00 UTC |
| 1b00cb6 | Anthony Brummett | 28 January 2014, 22:38:21 UTC | remove hardcoded paths to these scripts | 29 January 2014, 16:27:07 UTC |
| 70931c0 | Anthony Brummett | 28 January 2014, 22:17:24 UTC | Properly report failure to run the MergedAssembledCallsets script If that script isn't executable, report that failure to this script's STDERR rather than the MergedAssembledCallsets's stderr. | 29 January 2014, 16:27:06 UTC |
| 741976d | Dave Larson | 29 January 2014, 03:49:36 UTC | if the variant frequency has been set to NA explicitly then do NOT filter and pass through for printing | 29 January 2014, 03:49:36 UTC |
| 3aea5d4 | APipe Tester | 29 January 2014, 02:21:58 UTC | updated workflow submodule to c6ef789 | 29 January 2014, 02:21:58 UTC |
| a2dbfaf | Nathaniel Nutter | 28 January 2014, 22:21:19 UTC | update workflow submodule to point to apipe-review | 28 January 2014, 22:22:13 UTC |
| d6b42ac | dmorton | 28 January 2014, 20:43:28 UTC | Remove Joinx VcfNormalizeIndels from the workflow | 28 January 2014, 20:43:28 UTC |
| b43d4ce | APipe Tester | 28 January 2014, 19:35:34 UTC | updated workflow submodule to a839497 | 28 January 2014, 19:35:34 UTC |
| 4133e9d | APipe Tester | 28 January 2014, 19:24:55 UTC | updated workflow submodule to c5e1ca5 | 28 January 2014, 19:24:55 UTC |
| c596b6d | APipe Tester | 28 January 2014, 19:22:37 UTC | updated ur submodule to ff96e98 | 28 January 2014, 19:22:37 UTC |
| 6e5a4bd | APipe Tester | 28 January 2014, 19:15:03 UTC | updated graphite submodule to 9248d50 | 28 January 2014, 19:15:03 UTC |
| a3ee09b | APipe Tester | 28 January 2014, 19:10:43 UTC | updated ur submodule to bf62261 | 28 January 2014, 19:10:43 UTC |
| 38526cd | Feiyu Du | 28 January 2014, 17:13:50 UTC | only opened when needed | 28 January 2014, 17:13:50 UTC |
| b20bc93 | APipe Tester | 28 January 2014, 13:17:27 UTC | Updated `genome` tab completion. | 28 January 2014, 13:17:27 UTC |
| 1e8e4bf | Adam Coffman | 27 January 2014, 23:35:40 UTC | Revert "Refactor ModelGroup#assign_models to be more performant" This reverts commit 29156f04a3fdb4822c5f018deed3e6d0d8260ad7. While this passed tests, we discovered a potential UR bug that kept this from working correctly. Reverting pending bugfix. | 27 January 2014, 23:35:40 UTC |
| 29156f0 | Adam Coffman | 27 January 2014, 23:14:23 UTC | Refactor ModelGroup#assign_models to be more performant The sub no longer loads all model objects in a model group. In the case where a user called assign_models() a bunch of times individually with a single model, it will be slightly slower (more DB overhead). In the general case however, it should be substantially faster. | 27 January 2014, 23:14:23 UTC |
| b9070d1 | Adam Coffman | 27 January 2014, 22:02:54 UTC | CQID: only update projects once per run | 27 January 2014, 22:02:54 UTC |
| ec14e9a | Adam Coffman | 27 January 2014, 22:02:28 UTC | skip instead of return | 27 January 2014, 22:02:28 UTC |
| 7c9a61a | Adam Coffman | 27 January 2014, 20:02:13 UTC | Add CLIA support to analysis projects. This updates analysis projects to contain an is_clia field as well as a run_as field and makes the surrounding classes aware of them. | 27 January 2014, 20:02:13 UTC |
| 56224d6 | Adam Coffman | 27 January 2014, 16:08:45 UTC | Auto-increment names for LaneQC models. We'll now auto-increment names for LaneQC models like we do other models. This is expected to have a few side effects, but we'll address them as they come up. We have a situation where a piece of instrument data could have multiple valid LaneQC models from being used in multiple analysis projects which is something that hasn't occured previously. | 27 January 2014, 16:08:45 UTC |
| 6815964 | Thomas Mooney | 27 January 2014, 15:26:53 UTC | Try to determine what error caused a build to fail. The message "Can't convert workflow errors to build errors." will no longer be displayed. If an error can't be determined, "[Unable to automatically determine error.]" will appear instead. | 27 January 2014, 15:30:11 UTC |
| f597701 | Thomas Mooney | 27 January 2014, 15:21:50 UTC | Allow the failure type to be provided. This way the error can be determined after a build is Abandoned or while it is still Running (if it is known to have a failed step). | 27 January 2014, 15:30:10 UTC |
| 1a54220 | Thomas Mooney | 27 January 2014, 15:20:46 UTC | Split out formatting and printing of the determined error. | 27 January 2014, 15:30:09 UTC |
| 9ffcce6 | Jim Weible | 10 January 2014, 14:19:11 UTC | Change status_message to debug message to remove output noise | 27 January 2014, 15:18:53 UTC |
| 6689c89 | APipe Tester | 25 January 2014, 13:18:00 UTC | Updated `gmt` tab completion. | 25 January 2014, 13:18:00 UTC |
| 37c0179 | APipe Tester | 25 January 2014, 13:17:12 UTC | Updated `genome` tab completion. | 25 January 2014, 13:17:12 UTC |
| f691d01 | APipe Tester | 25 January 2014, 13:15:29 UTC | Updated class browser cache. | 25 January 2014, 13:15:29 UTC |
| ec394ec | APipe Tester | 24 January 2014, 23:36:53 UTC | updated workflow submodule to 1824055 | 24 January 2014, 23:36:53 UTC |
| 6c81205 | APipe Tester | 24 January 2014, 23:25:42 UTC | updated ur submodule to 3570450 | 24 January 2014, 23:25:42 UTC |
| c7ded24 | Obi Griffith | 24 January 2014, 22:58:16 UTC | removed hard coding of cancer annotation db | 24 January 2014, 22:58:16 UTC |
| 9f1135a | Malachi Griffith | 24 January 2014, 22:14:00 UTC | clinseq - tolerate failure of wget for url caching | 24 January 2014, 22:14:00 UTC |
| 3128597 | Gabriel Sanderson | 24 January 2014, 21:59:42 UTC | Merge branch 'filtern' into gb_master | 24 January 2014, 21:59:42 UTC |
| 617a165 | Gabriel Sanderson | 13 January 2014, 23:42:16 UTC | CHANGELOG: Jira AT-249: Made gmt vcf FilterNonCalls to remove vcf lines with ALT = N or '.'. Added this to all create-cross-sample-vcf workflows. This should reduce the number of useless calls made by this pipeline. | 24 January 2014, 21:50:31 UTC |
| 916b91a | APipe Tester | 24 January 2014, 20:27:49 UTC | updated workflow submodule to 69ba6b1 | 24 January 2014, 20:27:49 UTC |
| 18476cf | Avinash Ramu | 24 January 2014, 18:00:42 UTC | remove unwanted variable | 24 January 2014, 18:01:02 UTC |
| a499a88 | APipe Tester | 24 January 2014, 16:33:40 UTC | updated jenkins submodule to 2ec0b5d | 24 January 2014, 16:33:40 UTC |
| 0d53c3f | APipe Tester | 24 January 2014, 16:27:45 UTC | updated jenkins submodule to c94ebc2 | 24 January 2014, 16:27:45 UTC |
| d5cf821 | APipe Tester | 24 January 2014, 16:23:17 UTC | updated jenkins submodule to a96f2e3 | 24 January 2014, 16:23:17 UTC |
| 96fb648 | APipe Tester | 24 January 2014, 16:20:48 UTC | Updated `gmt` tab completion. | 24 January 2014, 16:20:48 UTC |
| abcd244 | APipe Tester | 24 January 2014, 16:19:59 UTC | Updated `genome` tab completion. | 24 January 2014, 16:19:59 UTC |
| b77f799 | APipe Tester | 24 January 2014, 16:18:27 UTC | Updated class browser cache. | 24 January 2014, 16:18:27 UTC |
| 201b4f4 | Dave Larson | 24 January 2014, 05:44:00 UTC | revert back to regular versioning | 24 January 2014, 05:44:32 UTC |
| 6096713 | Dave Larson | 21 January 2014, 22:40:09 UTC | fix logic error on start positions | 24 January 2014, 05:44:31 UTC |
| e3598c5 | Dave Larson | 18 January 2014, 03:12:30 UTC | fix mistake where libraries not reported by bam-readcount weren't being reported. fix poort handling of NA field generations | 24 January 2014, 05:44:30 UTC |
