| d215b5a | Chris Miller | 08 April 2014, 21:25:43 UTC | making sample-names a required input | 08 April 2014, 21:25:43 UTC |
| c635076 | APipe Tester | 08 April 2014, 20:18:48 UTC | updated graphite submodule to fe06c16 | 08 April 2014, 20:18:48 UTC |
| 1667b04 | Adam Coffman | 08 April 2014, 18:18:26 UTC | update doc to indicate that IDs or Names are now accepted | 08 April 2014, 18:18:26 UTC |
| c5bf0d1 | Adam Coffman | 08 April 2014, 18:16:24 UTC | make SomVal AnP pairing importer support sample names as well as ids | 08 April 2014, 18:16:24 UTC |
| aba0df7 | Avinash Ramu | 08 April 2014, 14:49:25 UTC | update clinseq blessed updated BWA metrics from LIMS | 08 April 2014, 14:49:25 UTC |
| 8b8fbd6 | APipe Tester | 08 April 2014, 12:20:28 UTC | Updated `gmt` tab completion. | 08 April 2014, 12:20:28 UTC |
| a39bd2b | APipe Tester | 08 April 2014, 12:19:42 UTC | Updated `genome` tab completion. | 08 April 2014, 12:19:42 UTC |
| fab5051 | dmorton | 07 April 2014, 21:48:20 UTC | Make gmt bed convert into an abstract class It was already, this just makes it formal | 07 April 2014, 21:48:20 UTC |
| 8fc5533 | dmorton | 07 April 2014, 21:47:41 UTC | Add ability to convert to one-based bed files. | 07 April 2014, 21:47:41 UTC |
| 47cf0bc | Nathaniel Nutter | 07 April 2014, 20:34:30 UTC | diable usage logging in test env | 07 April 2014, 20:34:30 UTC |
| 5091ef6 | Nathaniel Nutter | 07 April 2014, 20:33:38 UTC | add feature toggle for usage logging | 07 April 2014, 20:33:38 UTC |
| abda919 | APipe Tester | 06 April 2014, 12:18:37 UTC | Updated `gmt` tab completion. | 06 April 2014, 12:18:37 UTC |
| ba47815 | APipe Tester | 06 April 2014, 12:17:56 UTC | Updated `genome` tab completion. | 06 April 2014, 12:17:56 UTC |
| 04981dd | apregier | 05 April 2014, 16:42:46 UTC | Merge branch 'fix' into gb_master | 05 April 2014, 16:42:46 UTC |
| f88902d | apregier | 05 April 2014, 16:42:17 UTC | For some reason the png file was slightly different in my build | 05 April 2014, 16:42:17 UTC |
| 707a2a4 | apregier | 05 April 2014, 15:21:31 UTC | Merge branch 'fix' into gb_master | 05 April 2014, 15:21:31 UTC |
| 11bb048 | apregier | 05 April 2014, 15:19:51 UTC | Bless builds with new bed files and slightly changed vcf from joinx bug fix | 05 April 2014, 15:20:18 UTC |
| e291a78 | apregier | 03 April 2014, 14:13:46 UTC | Bump default joinx version to 1.8 | 05 April 2014, 15:20:18 UTC |
| b4ebab1 | apregier | 17 February 2014, 19:56:35 UTC | Extract aligned_reads_sample (not control) for conversion to bed | 05 April 2014, 15:20:17 UTC |
| 09cc8aa | apregier | 17 February 2014, 19:16:30 UTC | Add an option to select a sample for vcf2bed conversion | 05 April 2014, 15:20:16 UTC |
| cf92d5e | apregier | 17 February 2014, 18:53:54 UTC | Look up sample index based on sample name | 05 April 2014, 15:20:16 UTC |
| 5f62040 | apregier | 23 January 2014, 22:56:27 UTC | Add the step to create a bed file from the vcf file | 05 April 2014, 15:20:15 UTC |
| 5199a0e | APipe Tester | 05 April 2014, 12:17:19 UTC | Updated `genome` tab completion. | 05 April 2014, 12:17:19 UTC |
| 68c24c1 | APipe Tester | 05 April 2014, 12:15:46 UTC | Updated class browser cache. | 05 April 2014, 12:15:46 UTC |
| 5bf5070 | Eddie Belter | 04 April 2014, 21:52:23 UTC | AnP: command to update config to current | 04 April 2014, 21:52:23 UTC |
| 6f030cb | Eddie Belter | 04 April 2014, 21:51:48 UTC | AnP: rename config profile item _is_concrete() to is_concrete() | 04 April 2014, 21:51:48 UTC |
| 9451ded | APipe Tester | 04 April 2014, 12:18:18 UTC | Updated `gmt` tab completion. | 04 April 2014, 12:18:18 UTC |
| 2866917 | APipe Tester | 04 April 2014, 12:17:38 UTC | Updated `genome` tab completion. | 04 April 2014, 12:17:38 UTC |
| 2f4444a | APipe Tester | 04 April 2014, 12:16:12 UTC | Updated class browser cache. | 04 April 2014, 12:16:12 UTC |
| 868d09a | Thomas Mooney | 03 April 2014, 22:36:49 UTC | Update expected output to match synopsis changes. | 03 April 2014, 22:36:49 UTC |
| 2c755e4 | Thomas Mooney | 03 April 2014, 22:29:12 UTC | Remove reference to /gscuser/. The FASTA doesn't need to be in one's homedir, anyway. | 03 April 2014, 22:29:12 UTC |
| dba6418 | Avinash Ramu | 03 April 2014, 20:38:58 UTC | Add some detail to bamrc wrapper help | 03 April 2014, 20:39:37 UTC |
| d894969 | Tiandao Li | 03 April 2014, 20:36:59 UTC | add Concordance. | 03 April 2014, 20:36:59 UTC |
| ded8fad | Michael J. Kiwala | 03 April 2014, 20:17:09 UTC | Update the test plan | 03 April 2014, 20:17:09 UTC |
| 74f3460 | Michael J. Kiwala | 03 April 2014, 20:09:05 UTC | Do not check for updates while running cufflinks On sGMS, when not connected to an external network, cufflinks hangs indefinitely while attempting to check for updates over the network. | 03 April 2014, 20:11:12 UTC |
| e3b0a69 | Avinash Ramu | 03 April 2014, 19:40:27 UTC | move back to older test data | 03 April 2014, 19:41:06 UTC |
| 0b12cfc | Avinash Ramu | 03 April 2014, 19:27:58 UTC | update clinseq blessed build | 03 April 2014, 19:41:05 UTC |
| 7b031b7 | Avinash Ramu | 03 April 2014, 19:27:30 UTC | switch back to DNAcopy seg algorithm but use fixed seed | 03 April 2014, 19:41:05 UTC |
| b538d08 | Eddie Belter | 03 April 2014, 18:24:06 UTC | CQID: wrap assign inst data cmd executes in eval because they may die. | 03 April 2014, 18:26:19 UTC |
| ba7cef2 | apregier | 03 April 2014, 18:26:01 UTC | Merge branch 'updated' into gb_master | 03 April 2014, 18:26:01 UTC |
| 384ef98 | apregier | 03 April 2014, 18:24:49 UTC | Don't transfer refcov result metrics to build | 03 April 2014, 18:24:49 UTC |
| faf3a19 | apregier | 03 April 2014, 15:13:56 UTC | Fix how metric value is found - it won't always be a class property | 03 April 2014, 15:14:09 UTC |
| e0c514f | APipe Tester | 03 April 2014, 12:17:37 UTC | Updated `gmt` tab completion. | 03 April 2014, 12:17:37 UTC |
| da05341 | APipe Tester | 03 April 2014, 12:16:56 UTC | Updated `genome` tab completion. | 03 April 2014, 12:16:56 UTC |
| 366d0a5 | APipe Tester | 03 April 2014, 12:15:31 UTC | Updated class browser cache. | 03 April 2014, 12:15:31 UTC |
| d4e906a | Avinash Ramu | 03 April 2014, 05:59:18 UTC | update clinseq blessed build | 03 April 2014, 05:59:18 UTC |
| 0174643 | Avinash Ramu | 03 April 2014, 05:56:06 UTC | switch to a deterministic segmentation algorithm | 03 April 2014, 05:56:06 UTC |
| 827a8f5 | Avinash Ramu | 03 April 2014, 02:54:05 UTC | update blessed build to one with exome-cnv | 03 April 2014, 02:54:40 UTC |
| 33a48b5 | Avinash Ramu | 02 April 2014, 22:01:54 UTC | update clinseq to use cnmops | 03 April 2014, 02:54:39 UTC |
| 6c75d80 | Thomas Mooney | 02 April 2014, 21:38:57 UTC | Explicitly declare our inputs and outputs. | 02 April 2014, 21:38:57 UTC |
| 0ac3c7f | Avinash Ramu | 02 April 2014, 16:45:27 UTC | enable cnmops test The previous expected-results for this test were generated using a more recent version of the cn.mops package(v1.9.5) and this caused the diffs from Jenkins which has v1.8.9. The expected-results has now been updated to one generated by v1.8.9. | 02 April 2014, 16:47:02 UTC |
| 095c12c | apregier | 02 April 2014, 16:23:00 UTC | Merge branch 'updated' into gb_master | 02 April 2014, 16:23:00 UTC |
| b1a3444 | apregier | 02 April 2014, 16:19:27 UTC | Add tests for WithMode command and clarify behavior for instances where only one sample is available | 02 April 2014, 16:21:51 UTC |
| a0f0004 | Adam Coffman | 02 April 2014, 15:50:21 UTC | improve documentation for somval import command | 02 April 2014, 15:50:21 UTC |
| 8cba870 | Avinash Ramu | 02 April 2014, 15:39:51 UTC | continue to skip this test until the package dependencies are verified | 02 April 2014, 15:39:51 UTC |
| dc88904 | Avinash Ramu | 02 April 2014, 15:32:21 UTC | remove snow and Runit libraries which are not used right now | 02 April 2014, 15:32:21 UTC |
| e6dc4e6 | Avinash Ramu | 02 April 2014, 15:02:20 UTC | cnmops has now been added to genome-snapshot-deps | 02 April 2014, 15:03:23 UTC |
| 0b530aa | apregier | 02 April 2014, 14:57:42 UTC | Merge branch 'updated' into gb_master | 02 April 2014, 14:57:42 UTC |
| b343d5e | apregier | 01 April 2014, 21:19:20 UTC | Rename GenotypeVcf | 02 April 2014, 14:55:05 UTC |
| 715f3d0 | apregier | 28 March 2014, 15:36:17 UTC | Update doc to include new filter type | 02 April 2014, 14:55:04 UTC |
| 624b165 | apregier | 28 March 2014, 15:33:51 UTC | Pass in object directly as input rather than id | 02 April 2014, 14:55:04 UTC |
| 5b0a3fc | apregier | 27 March 2014, 20:44:47 UTC | Make sample names in bam and vcf match in test data | 02 April 2014, 14:55:03 UTC |
| fed6500 | apregier | 27 March 2014, 19:49:58 UTC | Make add_metrics more generic | 02 April 2014, 14:55:02 UTC |
| 8c08bae | apregier | 27 March 2014, 19:46:28 UTC | Add metrics from verifyBamId to build | 02 April 2014, 14:55:02 UTC |
| 1302546 | apregier | 27 March 2014, 19:36:01 UTC | Add metrics to verifyBamId result | 02 April 2014, 14:55:01 UTC |
| 1e7a3a4 | apregier | 27 March 2014, 18:48:31 UTC | Move genotype vcf result creation so it doesn't happen during shortcut | 02 April 2014, 14:55:01 UTC |
| 91ccbee | apregier | 27 March 2014, 16:47:57 UTC | Add test for genotype vcf result | 02 April 2014, 14:55:00 UTC |
| 6d62703 | apregier | 27 March 2014, 16:47:27 UTC | Fix filter config | 02 April 2014, 14:54:59 UTC |
| 269c8b3 | apregier | 27 March 2014, 16:46:48 UTC | Remove unnecessary line | 02 April 2014, 14:54:59 UTC |
| fd0b473 | apregier | 27 March 2014, 16:46:28 UTC | Fix filter | 02 April 2014, 14:54:58 UTC |
| 14f342d | apregier | 27 March 2014, 16:05:36 UTC | Add a test for the build step | 02 April 2014, 14:54:57 UTC |
| f774129 | apregier | 27 March 2014, 16:05:18 UTC | Fix parameters | 02 April 2014, 14:54:57 UTC |
| 7e3774d | apregier | 27 March 2014, 16:04:40 UTC | Fix error message | 02 April 2014, 14:54:56 UTC |
| eb716d2 | apregier | 27 March 2014, 16:04:06 UTC | Create directory for links if it doesn't exist already | 02 April 2014, 14:54:56 UTC |
| bfba6cc | apregier | 27 March 2014, 16:03:37 UTC | Add verify_bam_id_version to the processing profile | 02 April 2014, 14:54:55 UTC |
| 6b5fb2b | apregier | 27 March 2014, 16:02:53 UTC | Make GenotypeVcf a stageable result | 02 April 2014, 14:54:54 UTC |
| 93fd5d6 | apregier | 26 March 2014, 22:33:30 UTC | reference instead of reference_sequence_build | 02 April 2014, 14:54:54 UTC |
| 85c9316 | apregier | 26 March 2014, 22:32:49 UTC | Don't check region_of_interest on the base class | 02 April 2014, 14:54:53 UTC |
| 5bec724 | apregier | 26 March 2014, 22:00:42 UTC | VerifyBam command is WithMode | 02 April 2014, 14:54:53 UTC |
| d2f2143 | apregier | 26 March 2014, 20:34:04 UTC | Update test data | 02 April 2014, 14:54:52 UTC |
| 28db1ab | apregier | 26 March 2014, 20:33:44 UTC | Additional model is created in test factory | 02 April 2014, 14:54:51 UTC |
| ae8ffde | apregier | 26 March 2014, 20:22:00 UTC | Ignore all diffs for files ending with *.stderr | 02 April 2014, 14:54:51 UTC |
| e927903 | apregier | 26 March 2014, 19:13:06 UTC | Update define docs | 02 April 2014, 14:54:50 UTC |
| a7a4c59 | apregier | 26 March 2014, 16:34:58 UTC | Run verifyBam in tumor and normal modes | 02 April 2014, 14:54:49 UTC |
| 200196f | apregier | 26 March 2014, 16:07:40 UTC | Extract parent class SomaticValidation::Command::WithMode allows commands to run in tumor or normal mode. | 02 April 2014, 14:54:49 UTC |
| 5043b51 | apregier | 26 March 2014, 15:21:29 UTC | Check to see whether genotype data is available | 02 April 2014, 14:54:48 UTC |
| 1fbc546 | apregier | 26 March 2014, 15:07:50 UTC | Add verify-bam to somatic validation workflow | 02 April 2014, 14:54:48 UTC |
| 1bacfba | apregier | 26 March 2014, 14:53:35 UTC | Add a build step for verifyBamId | 02 April 2014, 14:54:47 UTC |
| 5c89e5e | apregier | 26 March 2014, 14:53:06 UTC | Make a software result for the vcf version of the genotype file | 02 April 2014, 14:54:46 UTC |
| b4c0729 | apregier | 24 March 2014, 21:38:51 UTC | Make verifyBamIdResult better -Takes an aligned bam input instead of instrument data -Get the allosomes from the reference sequence -Use a method that will always get a vcf file so it works for older builds as well | 02 April 2014, 14:54:46 UTC |
| 0eb0fbf | apregier | 24 March 2014, 21:30:07 UTC | Reference build has allosome_names | 02 April 2014, 14:54:45 UTC |
| 893cb56 | apregier | 24 March 2014, 21:29:43 UTC | Add a by-chromosome filter | 02 April 2014, 14:54:44 UTC |
| f15a76a | apregier | 21 March 2014, 22:09:38 UTC | Add a test factory for merged alignment results | 02 April 2014, 14:54:43 UTC |
| 9efbb2a | apregier | 21 March 2014, 22:09:00 UTC | Put a reference sequence on the imported variation list | 02 April 2014, 14:54:42 UTC |
| 0d26b85 | Nathaniel Nutter | 02 April 2014, 13:57:28 UTC | add some dv2 instrumentation | 02 April 2014, 13:57:43 UTC |
| 6b46308 | Thomas Mooney | 02 April 2014, 13:54:22 UTC | Remove commented-out references to no-longer-extant datasets. | 02 April 2014, 13:54:22 UTC |
| bea07ab | Thomas Mooney | 02 April 2014, 13:49:59 UTC | Remove old `gmt analysis detect-recurrence`. | 02 April 2014, 13:49:59 UTC |
| 429f9cd | Thomas Mooney | 02 April 2014, 13:45:30 UTC | Remove more references to "/gscuser/". | 02 April 2014, 13:45:30 UTC |
| 9285ef1 | Thomas Mooney | 02 April 2014, 13:35:08 UTC | Remove old `gmt copy-number graph` and `gmt copy-number u-test`. These modules are a mess but are disused, so just remove them. | 02 April 2014, 13:35:08 UTC |
| 032d172 | Thomas Mooney | 02 April 2014, 13:29:03 UTC | Remove reference to /gscuser/ | 02 April 2014, 13:29:03 UTC |
