| 940328e | APipe Tester | 02 July 2013, 19:05:27 UTC | Updated `genome` tab completion. | 02 July 2013, 19:05:27 UTC |
| 87d10b5 | APipe Tester | 02 July 2013, 19:03:45 UTC | Updated class browser cache. | 02 July 2013, 19:03:45 UTC |
| 5fbb77f | Scott Smith | 02 July 2013, 18:53:06 UTC | updated somatic-variation compare variants comments | 02 July 2013, 18:53:06 UTC |
| 27d4625 | Scott Smith | 02 July 2013, 18:47:43 UTC | Genome::Command::Tester from the old clinseq tester module. This module exports the run_and_diff() function. Now updated to get test the class name matching the test name by default. In this case, or when a class name is specified instead of a full command, it runs the help_synopsis(), replacing /tmp/output_dir with the desired output directory. | 02 July 2013, 18:47:43 UTC |
| 877d58f | Scott Smith | 02 July 2013, 18:36:02 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 02 July 2013, 18:36:02 UTC |
| 9cbcf8b | Scott Smith | 02 July 2013, 18:34:08 UTC | initial build comparison module for somatic variants | 02 July 2013, 18:34:08 UTC |
| 2a927be | APipe Tester | 02 July 2013, 17:15:42 UTC | Updated `genome` tab completion. | 02 July 2013, 17:15:42 UTC |
| 187cbbc | APipe Tester | 02 July 2013, 17:13:22 UTC | Updated class browser cache. | 02 July 2013, 17:13:22 UTC |
| bcc97c4 | Scott Smith | 02 July 2013, 15:42:09 UTC | add "builds" relationship for software results | 02 July 2013, 15:42:09 UTC |
| 54e2433 | Scott Smith | 02 July 2013, 15:41:26 UTC | preliminary COSMIC import | 02 July 2013, 15:41:26 UTC |
| d9e10ad | Eddie Belter | 01 July 2013, 22:51:06 UTC | SomVal: fix known sites in align rreads command | 01 July 2013, 22:52:31 UTC |
| 3a24b9e | Eddie Belter | 01 July 2013, 22:38:02 UTC | InstData GATK: fix metho name in base recalibrator | 01 July 2013, 22:48:36 UTC |
| 68ef14b | Eddie Belter | 26 June 2013, 18:17:04 UTC | InstData Gatk: base recalibrator results use version given | 01 July 2013, 22:48:35 UTC |
| 2386f91 | Eddie Belter | 26 June 2013, 18:16:05 UTC | InstData Gatk: base recalibrator bam result implemented | 01 July 2013, 22:48:35 UTC |
| eed0af9 | Eddie Belter | 26 June 2013, 18:13:53 UTC | InstData Gatk: base recalibrator result adjust kilobytes requested | 01 July 2013, 22:48:34 UTC |
| 4db76a7 | Eddie Belter | 26 June 2013, 17:54:04 UTC | InstData Gatk: base recalibrator result implemented | 01 July 2013, 22:48:34 UTC |
| 492d649 | Eddie Belter | 26 June 2013, 17:42:56 UTC | InstData Gatk: base recalibrator rresult for the output of only the base recalibrator | 01 July 2013, 22:48:33 UTC |
| 534f650 | Eddie Belter | 26 June 2013, 17:41:21 UTC | InstData Gatk: rename base reclibrator result to base recalibrator bam result | 01 July 2013, 22:48:32 UTC |
| 93ac216 | Malachi Griffith | 01 July 2013, 22:16:00 UTC | ClinSeq - update to latest version of cosmic for mutation-diagram plots | 01 July 2013, 22:16:00 UTC |
| 556806b | Thomas Mooney | 01 July 2013, 20:02:18 UTC | Update bacterial blessed build. | 01 July 2013, 20:03:02 UTC |
| 948c14f | Travis Abbott | 01 July 2013, 18:05:56 UTC | bless build 139877037 for somatic variation | 01 July 2013, 18:05:56 UTC |
| 200b089 | Thomas Mooney | 29 June 2013, 23:34:13 UTC | Make sure we operate on the class name and not an object. | 29 June 2013, 23:34:13 UTC |
| f25da58 | apregier | 28 June 2013, 22:23:58 UTC | Update blessed build for gene prediction | 28 June 2013, 22:23:58 UTC |
| 744a4c3 | APipe Tester | 28 June 2013, 22:09:47 UTC | Updated `gmt` tab completion. | 28 June 2013, 22:09:59 UTC |
| e876b81 | APipe Tester | 28 June 2013, 22:08:55 UTC | Updated `genome` tab completion. | 28 June 2013, 22:09:59 UTC |
| 9084033 | APipe Tester | 28 June 2013, 22:07:17 UTC | Updated class browser cache. | 28 June 2013, 22:09:59 UTC |
| 3842b55 | Scott Smith | 28 June 2013, 22:03:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 22:03:30 UTC |
| 8bc25e6 | Scott Smith | 28 June 2013, 22:03:15 UTC | made the CosmicOmim.pm tool compatible with new genome-db-cosmic structure, containing multiple data sets besides the original gene CSV files. | 28 June 2013, 22:03:15 UTC |
| 833b408 | Adam Coffman | 28 June 2013, 21:59:59 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:59:59 UTC |
| b445043 | Adam Coffman | 28 June 2013, 21:59:40 UTC | whitespace | 28 June 2013, 21:59:40 UTC |
| d34b8d8 | Scott Smith | 28 June 2013, 21:53:10 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:53:10 UTC |
| cd5a629 | Scott Smith | 28 June 2013, 21:52:58 UTC | gmt phred-phrap has a base class, and that module also has a base class. The later was used as the tree delegator, but is being renamed in this commit, with a title befitting its absurdities. | 28 June 2013, 21:52:58 UTC |
| f4cc365 | Scott Smith | 28 June 2013, 21:45:46 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:45:46 UTC |
| 2a2c0c0 | Scott Smith | 28 June 2013, 21:44:33 UTC | bleassed new clinseq build | 28 June 2013, 21:44:33 UTC |
| 212a0d5 | Malachi Griffith | 28 June 2013, 21:35:10 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 June 2013, 21:35:10 UTC |
| e1c8fdd | Malachi Griffith | 28 June 2013, 21:34:51 UTC | Fix option to specify no file extension in abi-to-scf | 28 June 2013, 21:34:51 UTC |
| 8df557f | Adam Coffman | 28 June 2013, 21:15:31 UTC | switch explicit lister to genome command crud | 28 June 2013, 21:15:31 UTC |
| d3b9ea9 | Adam Coffman | 28 June 2013, 21:06:05 UTC | add explicit create command | 28 June 2013, 21:06:05 UTC |
| 7345416 | Adam Coffman | 28 June 2013, 20:58:49 UTC | improve cascading delete | 28 June 2013, 20:58:49 UTC |
| cfaf76f | Adam Coffman | 28 June 2013, 20:58:20 UTC | use genome command crud instead of explicit lister | 28 June 2013, 20:58:20 UTC |
| d15e641 | APipe Tester | 28 June 2013, 20:55:34 UTC | updated ur submodule to cd3861c | 28 June 2013, 20:55:34 UTC |
| 2ad85c1 | APipe Tester | 28 June 2013, 19:30:38 UTC | Updated `genome` tab completion. | 28 June 2013, 19:30:38 UTC |
| 986ccdc | APipe Tester | 28 June 2013, 19:28:26 UTC | Updated class browser cache. | 28 June 2013, 19:28:26 UTC |
| ded9691 | Mark Burnett | 28 June 2013, 19:05:27 UTC | use a less fragile test for the GSCApp-RefSeq compatibility test | 28 June 2013, 19:05:27 UTC |
| cda7b97 | Mark Burnett | 28 June 2013, 18:58:22 UTC | fix Define-docs.t expected output for amplicon assembly | 28 June 2013, 18:58:22 UTC |
| 022fde5 | Mark Burnett | 28 June 2013, 17:53:09 UTC | Merge branch 'lims-RefSeq-bug' | 28 June 2013, 17:53:09 UTC |
| 28869f5 | Mark Burnett | 28 June 2013, 17:31:52 UTC | update define docs expected output | 28 June 2013, 17:31:52 UTC |
| b553397 | Eddie Belter | 28 June 2013, 16:29:30 UTC | InstData Import: updates to import SRAs | 28 June 2013, 16:30:05 UTC |
| cd7e2a5 | Eddie Belter | 27 June 2013, 21:45:38 UTC | Sample Manager: do not test sample hash data structure | 28 June 2013, 16:30:04 UTC |
| 4ccaa9f | Eddie Belter | 27 June 2013, 21:44:34 UTC | Sample Manager: store source files as comma delimited string | 28 June 2013, 16:30:04 UTC |
| 94e0e1b | Eddie Belter | 21 June 2013, 19:50:07 UTC | Sample Import Manager: do not display status for build | 28 June 2013, 16:30:04 UTC |
| 8c4deb1 | Eddie Belter | 21 June 2013, 19:31:43 UTC | Sample Import Manager: update status output; fix adding inst data bug | 28 June 2013, 16:30:03 UTC |
| b33f2ed | Eddie Belter | 21 June 2013, 15:29:22 UTC | Sample Import Manager: set job status on sample before make progress and then again when displaying status | 28 June 2013, 16:30:03 UTC |
| 0c64dfd | Eddie Belter | 21 June 2013, 15:24:39 UTC | Sample Import Manager: request build and delete inst data uncommented | 28 June 2013, 16:30:02 UTC |
| b0558f1 | Adam Coffman | 28 June 2013, 16:00:35 UTC | Make AnalysisProject deletions cascade Deleting an analysis project will no longer leave an orphaned configuration set and corresponding allocation. | 28 June 2013, 16:00:35 UTC |
| d1682ad | Adam Coffman | 28 June 2013, 15:59:50 UTC | auto set created_by in the constructor | 28 June 2013, 15:59:50 UTC |
| e37c5cf | Scott Smith | 27 June 2013, 22:22:34 UTC | initial comparison tool examines variant calling results | 27 June 2013, 22:22:34 UTC |
| 3614e51 | Jim Weible | 27 June 2013, 17:52:15 UTC | cleanup | 27 June 2013, 17:52:26 UTC |
| 17668be | Feiyu Du | 27 June 2013, 17:04:41 UTC | approve build diff for som-val, som-var-short and ref-align | 27 June 2013, 17:04:41 UTC |
| 68d3e1f | Mark Burnett | 27 June 2013, 15:27:28 UTC | bugfix: loading RefSeq with GSCApp now works | 27 June 2013, 15:28:35 UTC |
| 3f1cbb8 | Mark Burnett | 27 June 2013, 14:25:55 UTC | refactor: move properties from M:B:ImportedRefSeq to M:B:RefSeq | 27 June 2013, 15:28:35 UTC |
| 85b32b8 | Mark Burnett | 25 June 2013, 18:59:33 UTC | refactor: move M:B:RefSeq to its own file | 27 June 2013, 15:28:34 UTC |
| 22d03e1 | Mark Burnett | 25 June 2013, 18:36:27 UTC | refactor: move G:M:B:ImportedRefSeq to its own file | 27 June 2013, 15:28:33 UTC |
| 133dd2d | Mark Burnett | 25 June 2013, 17:51:20 UTC | refactor: move M:ImportedReferenceSequence to its own file | 27 June 2013, 15:28:33 UTC |
| c48ec48 | Mark Burnett | 25 June 2013, 17:34:40 UTC | update tests to expose broken behavior the broken behavior was introduced by commit: 87727c838b45b1412613a9a5f43086c216f06e09 | 27 June 2013, 15:28:31 UTC |
| af47c0f | APipe Tester | 27 June 2013, 15:24:51 UTC | Updated `gmt` tab completion. | 27 June 2013, 15:24:51 UTC |
| 18297ce | APipe Tester | 27 June 2013, 15:22:54 UTC | Updated `genome` tab completion. | 27 June 2013, 15:22:54 UTC |
| 027f610 | APipe Tester | 27 June 2013, 15:20:30 UTC | Updated class browser cache. | 27 June 2013, 15:20:30 UTC |
| 893a78d | Jim Weible | 26 June 2013, 18:48:25 UTC | cleanup whitespace | 27 June 2013, 13:06:44 UTC |
| bc819d3 | Jim Weible | 26 June 2013, 15:23:27 UTC | cleanup | 27 June 2013, 13:06:43 UTC |
| 7f93350 | Jim Weible | 25 June 2013, 20:00:46 UTC | basic tool to match varscan consensus calls to original vcf indels and build a new vcf file for cross sample indel calling | 27 June 2013, 13:06:42 UTC |
| ce348b9 | Scott Smith | 27 June 2013, 03:32:32 UTC | updated to dv2 BreakdancerMax | 27 June 2013, 03:32:32 UTC |
| 329c095 | Scott Smith | 27 June 2013, 03:27:12 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 27 June 2013, 03:27:12 UTC |
| a1876a1 | Scott Smith | 27 June 2013, 03:27:04 UTC | clinseq now passes the cosmic database version to the step that creates mutation diagrams | 27 June 2013, 03:27:04 UTC |
| b7dfdcb | Ben Oberkfell | 27 June 2013, 03:20:22 UTC | Put test case data where it belongs. | 27 June 2013, 03:20:22 UTC |
| cb544e9 | APipe Tester | 26 June 2013, 21:35:42 UTC | Updated `genome` tab completion. | 26 June 2013, 21:37:22 UTC |
| 830d908 | APipe Tester | 26 June 2013, 21:32:57 UTC | Updated class browser cache. | 26 June 2013, 21:37:22 UTC |
| a25ec91 | Scott Smith | 26 June 2013, 21:31:08 UTC | updated Genome/Model/ClinSeq/Command/TestGenomeCommands.t to use a new test input data set | 26 June 2013, 21:31:08 UTC |
| fbcf1da | Scott Smith | 26 June 2013, 21:24:45 UTC | update the clinseq model define docs to include new inputs | 26 June 2013, 21:24:45 UTC |
| 1e03c7d | Scott Smith | 26 June 2013, 20:49:06 UTC | Add cancer_annotation_db misc_annotation_db and cosmic_annotation_db to ClinSeq input lists, with current hard-coded values as defaults. No code actually uses these inputs yet. | 26 June 2013, 20:49:06 UTC |
| 4a3eaf0 | Scott Smith | 26 June 2013, 20:03:15 UTC | updated to handle import_iteration "0" | 26 June 2013, 20:03:15 UTC |
| 4781469 | Scott Smith | 26 June 2013, 18:54:05 UTC | fixed typos in new DV2 BreakdancerMax module | 26 June 2013, 18:54:05 UTC |
| a2c6885 | Mark Burnett | 26 June 2013, 16:21:34 UTC | M:T:Anno:TranscriptVar:V3 make temporary parameter variable optional | 26 June 2013, 17:57:47 UTC |
| 9316486 | Travis Abbott | 26 June 2013, 17:43:54 UTC | bless build diffs for indels the previously blessed results were very wrong. | 26 June 2013, 17:43:54 UTC |
| 52326b1 | Eddie Belter | 26 June 2013, 17:22:41 UTC | InstData GATK: add status msgs to show inputs | 26 June 2013, 17:25:45 UTC |
| 5fd36a1 | Eddie Belter | 26 June 2013, 17:19:25 UTC | InstData GATK: was getting indel result twice in known sites | 26 June 2013, 17:25:45 UTC |
| ec45bc5 | Eddie Belter | 18 June 2013, 17:45:24 UTC | InstData Gatk: add known sites snv vcfs to base with knowns; use only known sites indel vcf in indel realigner | 26 June 2013, 17:25:44 UTC |
| f4232c7 | Eddie Belter | 17 June 2013, 15:21:03 UTC | InstData GATK: realloc allocation | 26 June 2013, 17:25:44 UTC |
| a4cd5b1 | Feiyu Du | 26 June 2013, 16:06:47 UTC | fix the broken unit test | 26 June 2013, 16:06:47 UTC |
| 8047c3f | Feiyu Du | 26 June 2013, 15:15:10 UTC | change null gt from . to ./. | 26 June 2013, 15:16:43 UTC |
| e872b2c | Feiyu Du | 20 June 2013, 19:43:05 UTC | change not-available GT from . to ./. | 26 June 2013, 15:16:42 UTC |
| 5934562 | APipe Tester | 26 June 2013, 15:06:12 UTC | Updated `gmt` tab completion. | 26 June 2013, 15:06:12 UTC |
| 3280565 | APipe Tester | 26 June 2013, 15:05:27 UTC | Updated `genome` tab completion. | 26 June 2013, 15:05:27 UTC |
| 5e9f63e | APipe Tester | 26 June 2013, 15:03:55 UTC | Updated class browser cache. | 26 June 2013, 15:03:55 UTC |
| 42eb947 | Jasreet Hundal | 26 June 2013, 14:54:39 UTC | Tools to parse NetMHC3.4 online | 26 June 2013, 14:54:39 UTC |
| 9399c8c | Gabriel Sanderson | 25 June 2013, 23:45:35 UTC | Merge branch 'master' into gb_master | 25 June 2013, 23:45:35 UTC |
| 7192dee | Gabriel Sanderson | 25 June 2013, 23:36:29 UTC | Fixed bug that caused the REF to be included in ALT | 25 June 2013, 23:43:36 UTC |
| 50888ac | Travis Abbott | 25 June 2013, 23:02:47 UTC | bump vcf version, update test data this has to do with making sure gmt joinx normalize-indels uses natural vs numeric sorting | 25 June 2013, 23:02:47 UTC |
| a0d4444 | Travis Abbott | 25 June 2013, 22:24:04 UTC | use joinx sort instead of vcf-sort in indel normalization vcf-sort was sorting numerically (1,10,11,...) | 25 June 2013, 22:24:04 UTC |
| f76d311 | APipe Tester | 25 June 2013, 19:05:10 UTC | Updated `gmt` tab completion. | 25 June 2013, 19:05:10 UTC |
