| daff515 | Eddie Belter | 02 October 2015, 22:11:08 UTC | InstData Import: create instdata test use new bams with updated read groups | 08 October 2015, 21:45:35 UTC |
| 702db34 | Eddie Belter | 02 October 2015, 21:39:32 UTC | InstData Import: use File::Spec in create instdata test | 08 October 2015, 21:45:35 UTC |
| 7f14f1e | Eddie Belter | 02 October 2015, 21:26:31 UTC | InstData Import: spell check | 08 October 2015, 21:45:34 UTC |
| 5ebd2d1 | Eddie Belter | 02 October 2015, 21:09:15 UTC | InstData Import: rename write reads to process reads | 08 October 2015, 21:45:33 UTC |
| e6051d9 | Eddie Belter | 02 October 2015, 21:08:35 UTC | InstData Import: remove unused read group ids var and property | 08 October 2015, 21:45:32 UTC |
| 78d6a40 | Eddie Belter | 02 October 2015, 21:06:15 UTC | InstData Import: split out getting rg_id and updating to new rg_id | 08 October 2015, 21:45:32 UTC |
| fbbca35 | Eddie Belter | 02 October 2015, 20:59:57 UTC | InstData Import: add writing of reads to method of getting fh to write to | 08 October 2015, 21:45:31 UTC |
| a3e4c3d | Eddie Belter | 02 October 2015, 20:31:50 UTC | InstData Import: separate hash for old to new rg id mapping | 08 October 2015, 21:45:30 UTC |
| 333abe5 | Eddie Belter | 01 October 2015, 22:54:50 UTC | InstData Import: split by rg converts rg ids to instdata ids | 08 October 2015, 21:45:29 UTC |
| ff27187 | Eddie Belter | 01 October 2015, 22:19:06 UTC | InstData Import: add unknown read group during setting of read groups | 08 October 2015, 21:45:28 UTC |
| 9128756 | Eddie Belter | 01 October 2015, 22:13:41 UTC | InstData Import: split by rg uses rg tags | 08 October 2015, 21:45:28 UTC |
| ddc7b34 | Eddie Belter | 01 October 2015, 22:13:11 UTC | InstData Import: more stringent test for split by rg | 08 October 2015, 21:45:26 UTC |
| c65dd94 | Eddie Belter | 01 October 2015, 21:05:05 UTC | InstData Import: return RG tags instead of line from read_groups_and_tags_from_headers | 08 October 2015, 21:45:25 UTC |
| 68e9ab8 | Eddie Belter | 01 October 2015, 20:55:02 UTC | InstData Import: use throws_ok instead of eval | 08 October 2015, 21:45:24 UTC |
| bffa712 | Eddie Belter | 30 September 2015, 22:54:45 UTC | InstData Import: print/store split token instead of lines | 08 October 2015, 21:45:24 UTC |
| 71b4a91 | Eddie Belter | 30 September 2015, 22:29:50 UTC | InstData Import: remove unused removed_reads_cnt | 08 October 2015, 21:45:23 UTC |
| e15618a | Eddie Belter | 29 September 2015, 22:35:08 UTC | InstData Import: use autogen id for read group id in fastq to bam | 08 October 2015, 21:45:22 UTC |
| 43101e7 | Thomas B. Mooney | 07 October 2015, 15:25:56 UTC | Merge pull request #1035 from tmooney/add_delay_in_wait_for_lsf_jobs Wait 10s before checking status of LSF jobs again. | 07 October 2015, 15:25:56 UTC |
| a5d0895 | APipe Tester | 07 October 2015, 12:18:25 UTC | Updated `genome` tab completion. | 07 October 2015, 12:18:25 UTC |
| 48d0801 | Thomas B. Mooney | 06 October 2015, 20:27:29 UTC | Merge pull request #1036 from tmooney/build_start_unit_test_doesnt_launch_builds Don't really start builds in this test. | 06 October 2015, 20:27:29 UTC |
| 6b546ab | Thomas Mooney | 06 October 2015, 19:40:23 UTC | Don't really start builds in this test. The integration (model) tests will try running a build all the way through. This just needs to make sure Start works. (This was testing the "inline" build process, anyway, which is not how builds are usually run in production.) | 06 October 2015, 19:40:23 UTC |
| 2928efc | Thomas Mooney | 06 October 2015, 17:46:03 UTC | Wait 10s before checking status of jobs again. | 06 October 2015, 17:46:03 UTC |
| 5a6cb76 | Thomas B. Mooney | 06 October 2015, 17:39:44 UTC | Merge pull request #1033 from tmooney/better_alignment_user_handling Better User Handling with IntermediateAlignmentResults | 06 October 2015, 17:39:44 UTC |
| 2020e77 | Anthony Brummett | 06 October 2015, 16:23:26 UTC | Merge pull request #1034 from brummett/search-queue-test-fix Fix the Search Queue test | 06 October 2015, 16:23:26 UTC |
| f16b248 | Jason Walker | 06 October 2015, 14:52:16 UTC | Merge pull request #1006 from jasonwalker80/remove_picard_path Remove picard path | 06 October 2015, 14:52:16 UTC |
| 135b9ba | Thomas B. Mooney | 06 October 2015, 14:47:24 UTC | Merge pull request #1025 from tmooney/archive_command_accepts_paths Disk Allocation Archive command accepts paths | 06 October 2015, 14:47:24 UTC |
| 7b24f6a | Anthony Brummett | 05 October 2015, 22:53:58 UTC | Fix the Search Queue test This test uses a nonsensical pattern: * create a software transaction * commit the lowest-level Context (inside the dedup functionality) * roll back the software transaction Since the guts of Genome::Search::Queue::dedup() make a low-level commit, the whole test needs to operate on that level. An impending UR PR will make the old behavior throw an exception | 05 October 2015, 22:53:58 UTC |
| 613b07f | Thomas B. Mooney | 05 October 2015, 20:07:50 UTC | Merge pull request #1029 from tmooney/remove_last_use_of_alignment_prod Use generic config variable for alignment queue. | 05 October 2015, 20:07:50 UTC |
| eb8c761 | Jason Walker | 05 October 2015, 18:44:20 UTC | Add proper picard path to new tests that did not exist until merge. | 05 October 2015, 18:44:20 UTC |
| 6cac08e | Jason Walker | 05 October 2015, 17:43:50 UTC | Merge with master to resolve conflicts. | 05 October 2015, 17:43:50 UTC |
| d441a59 | Jason Walker | 05 October 2015, 16:01:10 UTC | Merge pull request #1023 from jasonwalker80/qc_build_metrics Qc build metrics | 05 October 2015, 16:01:10 UTC |
| e34da5c | Thomas Mooney | 05 October 2015, 13:43:58 UTC | More accurate debug message. (The alignments should already be done.) | 05 October 2015, 13:43:58 UTC |
| cfeca00 | Thomas Mooney | 05 October 2015, 13:42:26 UTC | The users don't get added until just before commit--can't check here. | 05 October 2015, 13:42:26 UTC |
| ae84244 | Thomas Mooney | 05 October 2015, 13:40:58 UTC | Don't hardcode the labels for deactivating users. There may be custom users passed in the hash that we should also deactivate in order for the IAR deletion to succeed. | 05 October 2015, 13:42:07 UTC |
| 6a22285 | Jason Walker | 02 October 2015, 19:51:18 UTC | Merge pull request #1015 from jasonwalker80/deprecated_anp_status_timeline_event Deprecated AnP status Timeline event. | 02 October 2015, 19:51:18 UTC |
| 6ba6da5 | Jason Walker | 02 October 2015, 19:49:02 UTC | Explicitly list exports. Remove commented lines. | 02 October 2015, 19:49:02 UTC |
| e3807d7 | Feiyu Du | 02 October 2015, 17:58:45 UTC | Merge pull request #1026 from dufeiyu/error_msg Show more info on error message to help troubleshooting | 02 October 2015, 17:58:45 UTC |
| 6d4764f | Feiyu Du | 02 October 2015, 16:12:33 UTC | remove unnecessary sprintf | 02 October 2015, 16:12:33 UTC |
| 5c44f2d | Thomas Mooney | 01 October 2015, 20:45:36 UTC | Use generic config variable for alignment queue. | 01 October 2015, 20:45:36 UTC |
| a2539a6 | APipe Tester | 01 October 2015, 15:01:35 UTC | updated ur submodule to 5ed8164 | 01 October 2015, 15:01:35 UTC |
| 2d760e8 | APipe Tester | 30 September 2015, 21:22:48 UTC | updated graphite submodule to 488ed04 | 30 September 2015, 21:22:48 UTC |
| 7a19d4c | Feiyu Du | 30 September 2015, 18:06:28 UTC | Show more info on error message to help debugging | 30 September 2015, 18:06:28 UTC |
| fdbcc0d | Avinash Ramu | 30 September 2015, 16:31:26 UTC | Merge pull request #1024 from gatoravi/update_clinseq_circos_test Add an additional dir to ignored paths. | 30 September 2015, 16:31:26 UTC |
| 7918581 | Avinash Ramu | 30 September 2015, 15:47:52 UTC | Don't compare filenames | 30 September 2015, 15:47:52 UTC |
| 4215026 | APipe Tester | 29 September 2015, 18:46:09 UTC | updated jenkins submodule to 043c617 | 29 September 2015, 18:46:09 UTC |
| 35572c9 | Thomas Mooney | 29 September 2015, 17:38:11 UTC | Remove paths parameter from unarchive command. CHANGELOG: Commands that take allocations can now look up those allocations by paths directly in the parameter. Accordingly the "--paths" option has been removed from these commands: * genome disk allocation unarchive * genome disk allocation delay-archiving | 29 September 2015, 17:43:57 UTC |
| 0cadf27 | Thomas Mooney | 29 September 2015, 17:36:50 UTC | Update archive command to remove separate "paths" option. | 29 September 2015, 17:36:50 UTC |
| b03b1dc | Thomas Mooney | 29 September 2015, 17:29:43 UTC | Allow allocations to be resolved from paths. | 29 September 2015, 17:29:43 UTC |
| e55473f | Thomas Mooney | 29 September 2015, 13:52:16 UTC | Spelling: archiev => archive. | 29 September 2015, 13:52:16 UTC |
| fa589a5 | Thomas Mooney | 29 September 2015, 13:51:07 UTC | Add subtest for new "paths" parameter. | 29 September 2015, 13:51:07 UTC |
| d603184 | Thomas Mooney | 29 September 2015, 13:50:12 UTC | Remove extra layer of tempdirs. This way the paths are closer in structure to real allocation paths. | 29 September 2015, 13:50:12 UTC |
| cd77761 | Thomas Mooney | 29 September 2015, 13:42:42 UTC | Convert to subtests. | 29 September 2015, 13:44:11 UTC |
| 16b7533 | Thomas Mooney | 29 September 2015, 13:40:01 UTC | Extract allocation creation into a subroutine. | 29 September 2015, 13:40:01 UTC |
| d1d3e5a | Thomas Mooney | 29 September 2015, 13:39:23 UTC | Quiet warnings about variables used once. | 29 September 2015, 13:39:23 UTC |
| 12de9e3 | Thomas Mooney | 29 September 2015, 13:38:36 UTC | Allow paths to be used to look up allocations to archive. | 29 September 2015, 13:38:36 UTC |
| 3406d6e | Jason Walker | 29 September 2015, 13:25:20 UTC | Remove unused module. | 29 September 2015, 13:25:20 UTC |
| 35161ac | APipe Tester | 29 September 2015, 12:18:41 UTC | Updated `gmt` tab completion. | 29 September 2015, 12:18:41 UTC |
| cb8907c | APipe Tester | 29 September 2015, 12:17:49 UTC | Updated `genome` tab completion. | 29 September 2015, 12:17:49 UTC |
| 027d5ed | Avinash Ramu | 28 September 2015, 22:43:39 UTC | Add an additional build-dir to ignored paths | 28 September 2015, 22:43:39 UTC |
| 31c3b97 | Jason Walker | 28 September 2015, 21:06:47 UTC | Dump QC build metrics as YAML, support nested metrics hash and operate on merged QC results rather than assuming per-lane alignments. | 28 September 2015, 21:06:47 UTC |
| adc7712 | Jason Walker | 28 September 2015, 16:14:27 UTC | Updated build metrics to assume QC results are run on the merged result, not the per instrument data QC results. Also dump as YAML after recreating nesting with the unflattened metric hash. | 28 September 2015, 16:14:27 UTC |
| 678fd54 | Allison Penner Regier | 28 September 2015, 15:32:07 UTC | Merge pull request #1020 from apregier/evaluate_vcf Evaluate vcf | 28 September 2015, 15:32:07 UTC |
| 77f94bf | APipe Tester | 26 September 2015, 12:18:18 UTC | Updated `gmt` tab completion. | 26 September 2015, 12:18:18 UTC |
| a7d39ea | APipe Tester | 26 September 2015, 12:17:25 UTC | Updated `genome` tab completion. | 26 September 2015, 12:17:25 UTC |
| b6a6182 | Chris Miller | 25 September 2015, 17:15:57 UTC | Merge pull request #1014 from chrisamiller/epitope binding threshold exposed as parameter | 25 September 2015, 17:15:57 UTC |
| 46c9379 | Jason Walker | 25 September 2015, 16:49:57 UTC | Merge pull request #1019 from susannasiebert/parse_all_metrics Improvements to the flattening of QC metrics hashes | 25 September 2015, 16:49:57 UTC |
| 46bd04c | apregier | 24 September 2015, 21:23:08 UTC | Make true negative file optional If there is no true negative file, just report 'NA' for the relevant stats | 25 September 2015, 16:15:43 UTC |
| ad61902 | apregier | 23 September 2015, 21:58:07 UTC | Enable empty pass_only_expression If the pass_only_expression is an empty string, simply don't run the vcffilter command. | 25 September 2015, 16:15:43 UTC |
| 6b2a0da | Eddie Belter | 24 September 2015, 21:10:28 UTC | Merge pull request #1005 from ebelter/net-ldap Sync Users: use Net::LDAP and add tests | 24 September 2015, 21:10:28 UTC |
| c3c55e1 | Susanna Siebert | 24 September 2015, 20:10:32 UTC | Provide a get_unflattened_metrics subroutine that returns a nested hash of all the metrics for a result | 24 September 2015, 20:10:32 UTC |
| 3161887 | Susanna Siebert | 24 September 2015, 19:57:35 UTC | Have Qc::Tool::VerifyBamId use the centralized _flatten_metrics_hash subroutine | 24 September 2015, 19:57:35 UTC |
| 81f0e1b | Susanna Siebert | 24 September 2015, 19:56:53 UTC | move _flatten_metrics_hash to the Qc::Tool level | 24 September 2015, 19:56:53 UTC |
| 8acb32b | Thomas B. Mooney | 24 September 2015, 19:54:51 UTC | Merge pull request #1018 from tmooney/more_metrics_more_problems_PR998 Remove more category names from keys. | 24 September 2015, 19:54:51 UTC |
| 68944d6 | Thomas Mooney | 24 September 2015, 19:39:37 UTC | Remove more category names from keys. | 24 September 2015, 19:39:37 UTC |
| 3a76417 | Eddie Belter | 24 September 2015, 19:32:27 UTC | Sync Users: do not use dumper | 24 September 2015, 19:32:27 UTC |
| bbcea7e | Jason Walker | 24 September 2015, 17:35:06 UTC | Merge pull request #1016 from susannasiebert/parse_all_metrics Make read group accumulation level not the default at this time | 24 September 2015, 17:35:06 UTC |
| e3a4ebb | Jason Walker | 24 September 2015, 17:16:11 UTC | Use all AnP valid statuses as valid values for AnP timeline events. | 24 September 2015, 17:16:11 UTC |
| 371e75d | Chris Miller | 24 September 2015, 15:59:44 UTC | numeric -> number | 24 September 2015, 15:59:44 UTC |
| e18e5d0 | Thomas B. Mooney | 24 September 2015, 15:46:23 UTC | Merge pull request #1017 from tmooney/metric_parsing_followup_fixes_PR998 Fixes to Metric Parsing in ClinSeq SummarizeBuilds | 24 September 2015, 15:46:23 UTC |
| a631fec | APipe Tester | 24 September 2015, 12:18:19 UTC | Updated `gmt` tab completion. | 24 September 2015, 12:18:19 UTC |
| b621220 | APipe Tester | 24 September 2015, 12:17:29 UTC | Updated `genome` tab completion. | 24 September 2015, 12:17:29 UTC |
| 1ed55e3 | APipe Tester | 24 September 2015, 12:15:45 UTC | Updated class browser cache. | 24 September 2015, 12:15:45 UTC |
| 723c091 | Thomas Mooney | 23 September 2015, 22:15:05 UTC | The word "CATEGORY" is no longer included in the key name. | 23 September 2015, 22:15:05 UTC |
| 9ba8def | Thomas Mooney | 23 September 2015, 22:14:00 UTC | Add the now required _metric_header_as_key for GCBias metrics. | 23 September 2015, 22:14:00 UTC |
| dc815ce | Allison Penner Regier | 23 September 2015, 21:51:23 UTC | Merge pull request #1013 from apregier/change_evaluate_vcf evaluate-vcf takes a file rather than a build | 23 September 2015, 21:51:23 UTC |
| 2be3cfa | Susanna Siebert | 23 September 2015, 20:52:10 UTC | Also remove the sample accumulation level since sample=all reads in our BAMs | 23 September 2015, 20:52:10 UTC |
| 6b6033b | Susanna Siebert | 23 September 2015, 20:19:38 UTC | Make read group accumulation level not the default at this time | 23 September 2015, 20:19:38 UTC |
| 78ef0a0 | Susanna Kiwala | 23 September 2015, 18:09:03 UTC | Merge pull request #998 from susannasiebert/parse_all_metrics Production QC improvements | 23 September 2015, 18:09:03 UTC |
| 9200da5 | Susanna Siebert | 23 September 2015, 17:21:37 UTC | Call parse_file_into_metrics_hashref on the actual class | 23 September 2015, 17:21:37 UTC |
| fe67611 | Jason Walker | 23 September 2015, 17:11:42 UTC | Add valid_value for Deprecated AnP status. | 23 September 2015, 17:11:42 UTC |
| 9a2a958 | Chris Miller | 23 September 2015, 17:05:19 UTC | binding threshold exposed as parameter | 23 September 2015, 17:05:19 UTC |
| 8b8787b | Susanna Kiwala | 23 September 2015, 15:30:36 UTC | Merge pull request #4 from tmooney/flatten_all_metrics_PR998 Improved Metric Flattening! And passing tests. | 23 September 2015, 15:30:36 UTC |
| a8dd260 | Thomas Mooney | 23 September 2015, 15:26:08 UTC | Don't just talk about it: die if we unexpectedly found another line. | 23 September 2015, 15:26:08 UTC |
| 3f03bd9 | Thomas Mooney | 23 September 2015, 15:21:20 UTC | Whitespace. | 23 September 2015, 15:21:20 UTC |
| dfd77ce | APipe Tester | 23 September 2015, 15:16:31 UTC | updated jenkins submodule to 6b0b504 | 23 September 2015, 15:16:31 UTC |
| a5eceea | Jason Walker | 23 September 2015, 14:51:51 UTC | update the expected JAR paths in QC tests. | 23 September 2015, 14:51:51 UTC |
| 4ae904f | APipe Tester | 23 September 2015, 14:14:23 UTC | updated jenkins submodule to e51279c | 23 September 2015, 14:14:23 UTC |
| c050f31 | APipe Tester | 23 September 2015, 14:14:14 UTC | updated ur submodule to f5d4da5 | 23 September 2015, 14:14:14 UTC |
| 18f9b33 | Dave Larson | 23 September 2015, 13:21:25 UTC | Merge pull request #1010 from ernfrid/drop_contig_converter add converter to remove extra contigs | 23 September 2015, 13:21:25 UTC |
| bf46351 | apregier | 23 September 2015, 02:56:59 UTC | evaluate-vcf takes a file rather than a build This will make it easier to use the evaluation script outside of model/build paradigm | 23 September 2015, 02:56:59 UTC |
