| c05428a | Ian Ferguson | 19 June 2013, 22:14:53 UTC | Approve indel diffs in somatic-validation test | 19 June 2013, 22:15:10 UTC |
| 24deccd | Ian Ferguson | 19 June 2013, 22:14:02 UTC | Approve indel diffs in somatic-variation-short test | 19 June 2013, 22:15:08 UTC |
| 33e43c8 | Mark Burnett | 19 June 2013, 21:25:06 UTC | bugfix: M:SVar:C:Anno&UpVars -> used uninitialized variable | 19 June 2013, 21:27:57 UTC |
| 8e55b9e | Adam Coffman | 19 June 2013, 21:24:34 UTC | whitespace fix | 19 June 2013, 21:24:34 UTC |
| 3ee9fc9 | Adam Coffman | 19 June 2013, 21:18:22 UTC | loading an object shouldnt update its timestamp | 19 June 2013, 21:18:22 UTC |
| 34c86b5 | Ian Ferguson | 19 June 2013, 20:28:15 UTC | Approve indel diffs in reference-alignment test | 19 June 2013, 20:28:24 UTC |
| cfd72b7 | Todd Hepler | 19 June 2013, 20:05:39 UTC | try to download faster | 19 June 2013, 20:05:39 UTC |
| 6a7a668 | Todd Hepler | 19 June 2013, 19:48:35 UTC | preparing for GeneTorrent version 3.8.3 | 19 June 2013, 19:48:51 UTC |
| 7249884 | apregier | 19 June 2013, 19:45:30 UTC | Do not request builds for tcga-bam imports | 19 June 2013, 19:45:48 UTC |
| 4faa45e | APipe Tester | 19 June 2013, 19:43:22 UTC | updated ur submodule to 1060c84 | 19 June 2013, 19:43:22 UTC |
| d10faa4 | Nathan Nutter | 19 June 2013, 19:14:04 UTC | subset_name is not required so don't assume it is set | 19 June 2013, 19:14:26 UTC |
| 28eebb3 | Adam Coffman | 19 June 2013, 18:12:56 UTC | check in lister for analysis projects | 19 June 2013, 18:12:56 UTC |
| 29e8a1c | Adam Coffman | 19 June 2013, 18:05:47 UTC | add lister for menu items | 19 June 2013, 18:05:47 UTC |
| 8343772 | Feiyu Du | 19 June 2013, 15:32:43 UTC | bug fix | 19 June 2013, 15:32:43 UTC |
| ed5ed25 | Feiyu Du | 19 June 2013, 15:17:22 UTC | Move alignment metrics conversion to inside bamqc software result generation | 19 June 2013, 15:17:22 UTC |
| f9e9dea | Scott Smith | 19 June 2013, 14:30:29 UTC | updated Strelka wrapper module for Strelka 1.0.7 | 19 June 2013, 14:30:29 UTC |
| cfb00d9 | Scott Smith | 19 June 2013, 12:53:11 UTC | updated testdata for Genome/Model/ClinSeq/original-scripts/converge/convergeStats.t | 19 June 2013, 12:53:11 UTC |
| 2f14ceb | Scott Smith | 19 June 2013, 12:13:14 UTC | updated Command/TestGenomeCommands.t test data, and added verbosity to Command/Tester.pm output | 19 June 2013, 12:13:14 UTC |
| 461f9dc | Thomas Mooney | 18 June 2013, 23:03:57 UTC | Update expected to account for sorting change. | 18 June 2013, 23:03:57 UTC |
| 09c8cab | Thomas Mooney | 18 June 2013, 22:32:58 UTC | Sort normalized VCF. | 18 June 2013, 22:32:58 UTC |
| a43aa1c | Ben Oberkfell | 18 June 2013, 21:20:42 UTC | Merge branch 'add_allocation_archive_date' | 18 June 2013, 21:20:42 UTC |
| af00744 | APipe Tester | 18 June 2013, 18:33:10 UTC | Updated `gmt` tab completion. | 18 June 2013, 18:33:10 UTC |
| a05503a | APipe Tester | 18 June 2013, 18:32:14 UTC | Updated `genome` tab completion. | 18 June 2013, 18:32:14 UTC |
| 6197f45 | APipe Tester | 18 June 2013, 18:30:04 UTC | Updated class browser cache. | 18 June 2013, 18:30:04 UTC |
| 2a71942 | Chris Miller | 18 June 2013, 18:21:53 UTC | bug fixes, new features | 18 June 2013, 18:22:30 UTC |
| 08b4996 | Malachi Griffith | 18 June 2013, 18:19:19 UTC | ClinSeq - fix update analysis test | 18 June 2013, 18:19:19 UTC |
| c4ec385 | Adam Coffman | 18 June 2013, 15:32:16 UTC | Add explicit timestamp fields for database syncing | 18 June 2013, 15:32:16 UTC |
| 5bbfc0d | Adam Coffman | 18 June 2013, 15:25:22 UTC | add comment about timestamp database columns | 18 June 2013, 15:25:22 UTC |
| bdb408e | Adam Coffman | 18 June 2013, 14:59:00 UTC | update table name map for postgres | 18 June 2013, 14:59:00 UTC |
| 92897f1 | Obi Griffith | 18 June 2013, 14:52:43 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 June 2013, 14:52:43 UTC |
| 91c1aef | Obi Griffith | 18 June 2013, 14:52:17 UTC | added tumor_sample_type to default options for clinseq-update-analysis | 18 June 2013, 14:52:17 UTC |
| fd2ba85 | APipe Tester | 18 June 2013, 14:42:55 UTC | updated jenkins submodule to 993de09 | 18 June 2013, 14:42:55 UTC |
| c32006e | APipe Tester | 18 June 2013, 14:40:19 UTC | updated jenkins submodule to eebf076 | 18 June 2013, 14:40:19 UTC |
| 77bf6ba | Jim Weible | 18 June 2013, 13:51:51 UTC | bless Somatic Validation test model for indel normalization | 18 June 2013, 13:52:08 UTC |
| 3f45042 | Obi Griffith | 18 June 2013, 00:10:32 UTC | removed rna_features_gff_path and changed htseq-count to use gtf file instead | 18 June 2013, 00:10:32 UTC |
| 4e81553 | Obi Griffith | 17 June 2013, 23:30:01 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 17 June 2013, 23:30:01 UTC |
| b7fb58c | pbender | 17 June 2013, 22:59:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 17 June 2013, 22:59:17 UTC |
| 23573e5 | pbender | 17 June 2013, 22:59:05 UTC | properly stringified BAM | 17 June 2013, 22:59:05 UTC |
| 02d1468 | Adam Coffman | 17 June 2013, 21:40:06 UTC | Merge branch master of ssh://git/srv/git/genome | 17 June 2013, 21:40:06 UTC |
| e12ada7 | Adam Coffman | 17 June 2013, 21:38:35 UTC | temporarily modify AQID to ignore instrument data with an analysis project id | 17 June 2013, 21:38:35 UTC |
| ab9dc90 | Ben Oberkfell | 17 June 2013, 21:04:32 UTC | Bring master in. Merge branch 'master' of git:/srv/git/genome into allocation_scheduled_archive | 17 June 2013, 21:04:32 UTC |
| 64700e0 | Jim Weible | 17 June 2013, 19:41:06 UTC | approve indel normalization changes for somatic-validation short test | 17 June 2013, 19:41:22 UTC |
| d34dadf | Ian Ferguson | 17 June 2013, 19:03:07 UTC | Use bam-errorrate0.7. Start using bam-errorrate0.7, which should prevent crashes when a bam contains a CIGAR string that begins with a D. This is running out of my home directory until I can get it properly packaged. | 17 June 2013, 19:05:05 UTC |
| 4160155 | APipe Tester | 17 June 2013, 18:55:55 UTC | updated workflow submodule to 0092917 | 17 June 2013, 18:55:55 UTC |
| b7b9fba | Jim Weible | 17 June 2013, 18:47:44 UTC | approve somatic-variation-short model test for indel normalization | 17 June 2013, 18:47:58 UTC |
| e4a2a91 | APipe Tester | 17 June 2013, 18:28:38 UTC | updated ur submodule to b9cff02 | 17 June 2013, 18:28:38 UTC |
| 355f84a | Nathan Nutter | 17 June 2013, 18:21:08 UTC | Merge branch '93155' | 17 June 2013, 18:21:08 UTC |
| 0b169c4 | Nathan Nutter | 17 June 2013, 16:34:11 UTC | cleanup and changes to .gitignore | 17 June 2013, 18:19:55 UTC |
| b68e0d1 | Nathan Nutter | 17 June 2013, 14:05:59 UTC | add -h and --help options to genome-test-env | 17 June 2013, 18:19:55 UTC |
| b4a8ffd | Nathan Nutter | 14 June 2013, 14:02:32 UTC | remove comments | 17 June 2013, 18:19:54 UTC |
| ce80695 | Nathan Nutter | 14 June 2013, 14:01:19 UTC | whitespace | 17 June 2013, 18:19:54 UTC |
| cbb3fb1 | Nathan Nutter | 17 June 2013, 16:40:11 UTC | use LWP instead of curl so we can better check failures | 17 June 2013, 18:18:50 UTC |
| 606b0d4 | Anthony Brummett | 06 June 2013, 19:21:21 UTC | Only count time for the set aggregation function when computing allocated_kb Before it may have included the time to connect to the DB in many cases | 17 June 2013, 16:32:38 UTC |
| 2a240bd | APipe Tester | 17 June 2013, 15:51:49 UTC | updated jenkins submodule to 4bd4ee7 | 17 June 2013, 15:51:49 UTC |
| 0718970 | APipe Tester | 17 June 2013, 14:52:21 UTC | updated jenkins submodule to f9f4bd6 | 17 June 2013, 14:52:21 UTC |
| 55a752e | Nathan Nutter | 17 June 2013, 14:36:20 UTC | fail better Add the --fail option to curl so it will suppress error content in response. Otherwise the error content is passed on to the JSON parser which crashes with an indirect cause. | 17 June 2013, 14:36:20 UTC |
| 50e57ec | Nathan Nutter | 17 June 2013, 14:34:31 UTC | remove --insecure option from curl The TCGA website appears to have a valid SSL certificate so --insecure should not be required. | 17 June 2013, 14:34:31 UTC |
| d8aa8d1 | Nathan Nutter | 17 June 2013, 14:21:10 UTC | expand short options for easier readability | 17 June 2013, 14:21:10 UTC |
| 0cefc63 | Nathan Nutter | 17 June 2013, 14:18:30 UTC | whitespace | 17 June 2013, 14:18:30 UTC |
| d757e5c | Jim Weible | 17 June 2013, 13:33:23 UTC | make indel normalization use joinx 1.7 | 17 June 2013, 13:33:23 UTC |
| 62dc270 | Obi Griffith | 16 June 2013, 22:36:43 UTC | fixed minor typo | 16 June 2013, 22:36:43 UTC |
| 0626bea | Thomas Mooney | 16 June 2013, 01:31:43 UTC | Only pass ASSUME_SORTED if it was defined. | 16 June 2013, 01:31:43 UTC |
| 9d4563a | Feiyu Du | 14 June 2013, 22:29:12 UTC | assume_sorted only applies to picard version 1.77 and later | 14 June 2013, 22:29:12 UTC |
| 5eff0ef | Eddie Belter | 14 June 2013, 21:30:00 UTC | InstData Gatk: change allocation disk group and subdir | 14 June 2013, 21:30:12 UTC |
| 645e0f8 | Eddie Belter | 14 June 2013, 21:28:54 UTC | InstData AlignResult: inherits from software result stageable | 14 June 2013, 21:30:11 UTC |
| d84710c | Kyung Kim | 14 June 2013, 19:33:09 UTC | Update to find newbler program in either versions bin or applicationBin directories | 14 June 2013, 19:33:09 UTC |
| beb8f39 | APipe Tester | 14 June 2013, 18:31:15 UTC | Updated `genome` tab completion. | 14 June 2013, 18:31:15 UTC |
| 8b8213a | APipe Tester | 14 June 2013, 18:28:50 UTC | Updated class browser cache. | 14 June 2013, 18:28:50 UTC |
| 563b195 | Eddie Belter | 14 June 2013, 17:32:07 UTC | InstData Gatk: mv ref build and ref fasta method from gatk base to aligned bam | 14 June 2013, 17:32:07 UTC |
| d5a6c25 | Eddie Belter | 14 June 2013, 17:31:33 UTC | InstData Gatk: known_sites are inputs instead of params | 14 June 2013, 17:31:33 UTC |
| fd3aaf8 | Eddie Belter | 14 June 2013, 16:27:46 UTC | InstData Gatk: add refine reads for gatk best practices | 14 June 2013, 16:27:46 UTC |
| 78d1b97 | Eddie Belter | 14 June 2013, 16:27:20 UTC | InstData Gatk: add ref build to bam_source for test data | 14 June 2013, 16:27:20 UTC |
| 027b8ff | Eddie Belter | 14 June 2013, 01:12:23 UTC | InstData Gatk: rename known indels to known sites | 14 June 2013, 01:12:23 UTC |
| 93196df | Eddie Belter | 13 June 2013, 23:54:35 UTC | InstData add refine reads tree | 14 June 2013, 00:44:30 UTC |
| b6da1f8 | Eddie Belter | 13 June 2013, 23:25:53 UTC | Revert "InstData Gatk: remove result from names to make the commands with saved results" This reverts commit 9c1ae1cd66884d3ace377ae40f6198982f441491. | 14 June 2013, 00:44:29 UTC |
| 3fff28e | Eddie Belter | 13 June 2013, 23:25:32 UTC | Revert "InstData Gatk: remove Result from class names" This reverts commit 5d2b1d5112b4ae9f20f6dc01c4b7c71a776afae6. | 14 June 2013, 00:44:29 UTC |
| 2d8b755 | Eddie Belter | 13 June 2013, 20:40:36 UTC | InstData Gatk: remove Result from class names | 14 June 2013, 00:44:28 UTC |
| 2060727 | Eddie Belter | 13 June 2013, 20:38:36 UTC | InstData Gatk: remove result from names to make the commands with saved results | 14 June 2013, 00:44:28 UTC |
| 63b0d48 | Eddie Belter | 12 June 2013, 19:49:21 UTC | InstData Gatk: add comments to tests | 14 June 2013, 00:44:27 UTC |
| 3f07dbb | Eddie Belter | 12 June 2013, 19:46:41 UTC | GMT GATK Print Reads: rename bai to match samtools standard | 14 June 2013, 00:44:27 UTC |
| aa51417 | Eddie Belter | 12 June 2013, 19:34:00 UTC | InstData Gatk: add base recalibrator | 14 June 2013, 00:44:26 UTC |
| 8100988 | Eddie Belter | 12 June 2013, 18:48:38 UTC | InstData Gatk: indel realigner test compares intervals file and flagstat | 14 June 2013, 00:44:26 UTC |
| d1f41f6 | Eddie Belter | 12 June 2013, 18:36:07 UTC | InstData Aligned Bam: add bam_flagstat_file | 14 June 2013, 00:44:25 UTC |
| dfdcf55 | Eddie Belter | 12 June 2013, 18:14:51 UTC | InstData Gatk: indel realigner test uses known indels | 14 June 2013, 00:44:25 UTC |
| 3516b34 | Eddie Belter | 12 June 2013, 18:00:00 UTC | InstData Gatk: add version to base and indel realigner | 14 June 2013, 00:44:24 UTC |
| 1a110d8 | Eddie Belter | 11 June 2013, 20:15:04 UTC | InstData Gatk: rm prepare output dir and known indels from indel realigner and make the class inherit from base with known indels | 14 June 2013, 00:44:24 UTC |
| af7c08e | Eddie Belter | 11 June 2013, 20:13:41 UTC | InstData Gatk: mv prepare output dir to base class | 14 June 2013, 00:44:23 UTC |
| 26b0196 | Eddie Belter | 11 June 2013, 20:12:14 UTC | InstData Gatk: add base with known indels class | 14 June 2013, 00:44:23 UTC |
| 737b308 | Eddie Belter | 11 June 2013, 20:11:46 UTC | InstData Gatk: add known indels to Test.pm | 14 June 2013, 00:44:22 UTC |
| b846dcf | Eddie Belter | 10 June 2013, 19:28:09 UTC | InstData GATK: indel realigner uses test module | 14 June 2013, 00:44:22 UTC |
| 574d812 | Eddie Belter | 10 June 2013, 19:27:48 UTC | InstData GATK: add test module w/ ref and bam for testing | 14 June 2013, 00:44:21 UTC |
| c26f3df | Eddie Belter | 07 June 2013, 16:53:13 UTC | GATK Inst Data Indel Realigner Result | 14 June 2013, 00:44:21 UTC |
| 82be323 | Eddie Belter | 07 June 2013, 16:41:55 UTC | Alignment Result: is now AlignedBamResult | 14 June 2013, 00:44:20 UTC |
| 650a442 | Eddie Belter | 07 June 2013, 16:41:23 UTC | Merged Alignment Result: is now AlignedBamResult; add is_output to bam_file | 14 June 2013, 00:44:20 UTC |
| 0e353c1 | Eddie Belter | 07 June 2013, 16:37:27 UTC | Aligned Bam Result: add bam_file as output; add flagstat calculation on output bam | 14 June 2013, 00:44:19 UTC |
| 1e707c4 | Thomas Mooney | 14 June 2013, 00:02:54 UTC | Pass along known sites if we're using refinements. | 14 June 2013, 00:02:54 UTC |
| c36028f | Thomas Mooney | 13 June 2013, 23:56:53 UTC | Rename varia{nt,tion}_list to known_sites | 13 June 2013, 23:56:53 UTC |
| 9558a02 | Thomas Mooney | 13 June 2013, 23:51:47 UTC | Use the parent class of Merged results. | 13 June 2013, 23:51:47 UTC |
| 09dd292 | Thomas Mooney | 13 June 2013, 22:38:54 UTC | Add support for a "refiner" to be run at the end of the merge process. For now this happens within the same command as merging and deduplication. Eventually merge, deduplicate, and this refinment all should be made into their own workflow. | 13 June 2013, 22:38:54 UTC |
| 5233726 | Thomas Mooney | 13 June 2013, 22:15:50 UTC | Allow for variants to be supplied for refinement. | 13 June 2013, 22:15:50 UTC |
