| 3ce1ad8 | kmeltzst | 13 August 2014, 20:58:15 UTC | changed requirement for anno/refbuild | 13 August 2014, 20:58:15 UTC |
| 9a90e77 | kmeltzst | 01 August 2014, 19:26:35 UTC | simplified syntax | 01 August 2014, 19:26:35 UTC |
| 6703ce8 | kmeltzst | 01 August 2014, 18:26:19 UTC | chr sep by space not comma | 01 August 2014, 18:26:19 UTC |
| 82b7df9 | Gabriel Sanderson | 01 August 2014, 18:23:06 UTC | Comma delimit chromosomes | 01 August 2014, 18:23:06 UTC |
| d4b06e8 | kmeltzst | 01 August 2014, 18:09:12 UTC | updates | 01 August 2014, 18:09:12 UTC |
| dc3bf5c | kmeltzst | 01 August 2014, 17:55:35 UTC | cleaned up | 01 August 2014, 17:55:35 UTC |
| 6e6ef8e | kmeltzst | 01 August 2014, 17:42:26 UTC | made covariates optional | 01 August 2014, 17:42:26 UTC |
| f99323e | kmeltzst | 01 August 2014, 16:47:27 UTC | updated epacts options | 01 August 2014, 16:47:27 UTC |
| ffa2225 | kmeltzst | 31 July 2014, 20:17:53 UTC | added epacts options to append to command | 31 July 2014, 20:17:53 UTC |
| 273091b | kmeltzst | 31 July 2014, 19:23:19 UTC | changes to epacts functionality | 31 July 2014, 19:23:19 UTC |
| 086eede | Gabriel Sanderson | 15 July 2014, 20:03:29 UTC | Merge branch 'master' into gotcloud | 15 July 2014, 20:03:29 UTC |
| 1ed4813 | Nathaniel Nutter | 15 July 2014, 19:40:21 UTC | add CQID status to ConfigForInstrumentData | 15 July 2014, 19:43:00 UTC |
| f5596e7 | Nathaniel Nutter | 15 July 2014, 19:21:20 UTC | fix warning when status is undefined | 15 July 2014, 19:42:59 UTC |
| ac27daf | Nathaniel Nutter | 14 July 2014, 22:02:33 UTC | remove eval | 15 July 2014, 19:42:58 UTC |
| cbe5d88 | Nathaniel Nutter | 14 July 2014, 22:02:04 UTC | deduplicate search queue before processing | 15 July 2014, 19:42:58 UTC |
| 410b4b2 | Nathaniel Nutter | 14 July 2014, 22:01:22 UTC | fix old typo | 15 July 2014, 19:42:56 UTC |
| 06955e1 | Ian Ferguson | 14 July 2014, 18:23:27 UTC | Add bwa-0.7.10 to GMT/Bwa.pm | 14 July 2014, 18:23:27 UTC |
| 1683cfa | Nathaniel Nutter | 14 July 2014, 14:37:18 UTC | add counter intstrumentation for modify_index success and failure | 14 July 2014, 14:38:38 UTC |
| 8f0caf8 | Nathaniel Nutter | 14 July 2014, 14:36:10 UTC | add timer instrumentation around modify_index | 14 July 2014, 14:36:10 UTC |
| 153c366 | Nathaniel Nutter | 14 July 2014, 14:25:51 UTC | set the (forked) process name Set the (forked) process name so we can know what's being worked on and so it's acknowledged that it's a fork and not a duplicate daemon. | 14 July 2014, 14:25:51 UTC |
| d6727b3 | APipe Tester | 12 July 2014, 12:16:40 UTC | Updated `genome` tab completion. | 12 July 2014, 12:16:40 UTC |
| 83ba091 | APipe Tester | 12 July 2014, 12:15:20 UTC | Updated class browser cache. | 12 July 2014, 12:15:20 UTC |
| 875626f | Susanna Siebert | 11 July 2014, 20:16:22 UTC | fixed incorrect test for retrieval of seg dup feature list | 11 July 2014, 20:16:22 UTC |
| 6d8cd33 | Susanna Siebert | 11 July 2014, 19:35:31 UTC | add example resource files for cle testing | 11 July 2014, 19:51:08 UTC |
| 97fe15c | Susanna Siebert | 11 July 2014, 18:10:07 UTC | removed breakpoint | 11 July 2014, 19:51:07 UTC |
| 21207d3 | Susanna Siebert | 11 July 2014, 18:09:09 UTC | fixed bug in the hash creation for unknown readcounts | 11 July 2014, 19:51:07 UTC |
| 90be793 | Susanna Siebert | 11 July 2014, 18:08:39 UTC | fixed typo for segmental duplications | 11 July 2014, 19:51:07 UTC |
| ade4035 | Jason Walker | 11 July 2014, 18:07:50 UTC | initial revision of alignment summary command for Somatic Validation models. | 11 July 2014, 18:07:50 UTC |
| 7c2bf2f | Todd Hepler | 11 July 2014, 16:55:06 UTC | change LSF queue for downloads https://jira.gsc.wustl.edu/browse/LS-1222 | 11 July 2014, 16:55:06 UTC |
| 06399a6 | APipe Tester | 11 July 2014, 12:16:36 UTC | Updated `genome` tab completion. | 11 July 2014, 12:16:36 UTC |
| 8af723d | APipe Tester | 11 July 2014, 12:15:08 UTC | Updated class browser cache. | 11 July 2014, 12:15:08 UTC |
| 1b331eb | apregier | 09 July 2014, 22:00:07 UTC | Use sort -V to order chromosomes appropriately | 10 July 2014, 22:33:40 UTC |
| 700da9f | Gabriel Sanderson | 07 July 2014, 23:13:47 UTC | Added a command to combine snv and indel reports | 10 July 2014, 22:33:40 UTC |
| 92c2872 | dmorton | 10 July 2014, 22:03:41 UTC | Update plan_files for file-based changes | 10 July 2014, 22:03:41 UTC |
| 38451bc | dmorton | 10 July 2014, 22:02:31 UTC | Change HASH to Text (json encoded) Since you cannot shortcut on a HASH type input, we json encode all such inputs (in the input_hash method) and then decode it in the Result object. | 10 July 2014, 22:02:31 UTC |
| 876ab49 | dmorton | 10 July 2014, 22:00:34 UTC | Remove environment-variables from command It turns out that you cannot do it this way. By the time the environment variables are changed they've already been checked. If we want to set these for real we might have to shell out and run another command with these environment variables set. | 10 July 2014, 22:00:34 UTC |
| 6644136 | dmorton | 10 July 2014, 21:07:29 UTC | use Genome::Sys->rsync_directory properly | 10 July 2014, 21:09:39 UTC |
| b9dbb54 | apregier | 10 July 2014, 20:55:57 UTC | Merge branch 'fireteam' into gb_master | 10 July 2014, 20:55:57 UTC |
| 42ced24 | apregier | 10 July 2014, 20:48:11 UTC | Use test components instead of production SimpleReporter components | 10 July 2014, 20:54:28 UTC |
| 0c97c20 | APipe Tester | 10 July 2014, 19:06:45 UTC | updated ur submodule to 759485b | 10 July 2014, 20:47:42 UTC |
| 563cbfd | dmorton | 10 July 2014, 20:25:53 UTC | Ensure that test-data is not on an allocation when tests are run | 10 July 2014, 20:25:53 UTC |
| 6f57c57 | dmorton | 09 July 2014, 19:46:38 UTC | Experts now 'provides_annotations' Filters and Interpreters can now 'requires_annotations'. This allows for combination Experts that provide multiple kinds of annotations. It also allows filters and interpreters to be satisfied by any of a number of potentially compatible experts. | 10 July 2014, 19:00:33 UTC |
| 4ad4892 | dmorton | 09 July 2014, 18:10:36 UTC | Move base reporter into Framework directory | 10 July 2014, 19:00:32 UTC |
| dcdc0b7 | dmorton | 09 July 2014, 04:39:46 UTC | bump version of test data for vep expert We're not ready to allow custom_annotation_tags just yet | 10 July 2014, 19:00:32 UTC |
| b049bb6 | dmorton | 08 July 2014, 21:34:14 UTC | Add new command 'CreateReport' | 10 July 2014, 19:00:32 UTC |
| 895a2e1 | dmorton | 09 July 2014, 03:58:08 UTC | add missing import | 10 July 2014, 19:00:32 UTC |
| 96e67bf | dmorton | 09 July 2014, 03:56:12 UTC | Add Framework/Test These packages will allow us to test without referencing our production experts/interpreters/filters/reporters. | 10 July 2014, 19:00:32 UTC |
| 6f7554b | dmorton | 09 July 2014, 03:54:10 UTC | Add test_expert_is_registered to test_helpers | 10 July 2014, 19:00:32 UTC |
| f310973 | dmorton | 08 July 2014, 20:30:14 UTC | rename annotation_vcf to dbsnp_vcf | 10 July 2014, 19:00:32 UTC |
| 03c6568 | dmorton | 08 July 2014, 20:26:55 UTC | Attempt to lookup allocation before md5sum'ing files | 10 July 2014, 19:00:32 UTC |
| f455953 | dmorton | 07 July 2014, 23:21:25 UTC | Rename test from Plan.t to MasterPlan.t | 10 July 2014, 19:00:31 UTC |
| ed63c61 | dmorton | 07 July 2014, 23:08:02 UTC | Dbsnp expert takes annotation_vcf instead of ImportedVariation build | 10 July 2014, 19:00:31 UTC |
| dc50ef4 | dmorton | 07 July 2014, 21:45:20 UTC | MasterPlan can now validate a ResourceProvider | 10 July 2014, 19:00:31 UTC |
| 18165b9 | dmorton | 07 July 2014, 21:44:32 UTC | Allow ResourceProviders to be read from and written to files (yaml) | 10 July 2014, 19:00:31 UTC |
| cc18203 | dmorton | 06 July 2014, 20:43:24 UTC | Add test for Expert Command's lookup_hash function | 10 July 2014, 19:00:31 UTC |
| 819b1b4 | dmorton | 06 July 2014, 20:40:56 UTC | MasterPlan can now determine resources_required The Expert's Adaptor Class specifies outputs as 'is_provided'. All Experts in the plan are then queried and the names of all such outputs are collected. | 10 July 2014, 19:00:31 UTC |
| eb7f991 | dmorton | 05 July 2014, 20:06:47 UTC | VariantReporting Expert Commands shortcut properly Properties that are considered 'paths' are hashed with the md5 algorithm and that value is used to shortcut/produce software-results. | 10 July 2014, 19:00:31 UTC |
| 0dad66a | dmorton | 05 July 2014, 20:06:27 UTC | remove wait statement from test | 10 July 2014, 19:00:31 UTC |
| b1aba87 | dmorton | 02 July 2014, 17:21:59 UTC | VariantReporting subsystem works on files not just builds The ResourceProvider replaces the build, at least conceptually. Running on a build will consist of generating a ResourceProvider first, and then running the subsystem. This commit is a regression in that sense, because running on a build has been disabled for now. The ReportGeneratorWrapper goes away entirely, since translations can be provided by the ResourceProvider. Expert commands accept files instead of objects for the most part, and when they need objects from the ResourceProvider, they are given ids only. | 10 July 2014, 19:00:30 UTC |
| 00891bc | apregier | 10 July 2014, 18:36:56 UTC | Merge branch 'fireteam' into gb_master | 10 July 2014, 18:36:56 UTC |
| da1fcad | apregier | 10 July 2014, 18:35:15 UTC | library preparation reference is called library_preparation | 10 July 2014, 18:35:15 UTC |
| 4bc1eed | Anthony Brummett | 10 July 2014, 16:05:41 UTC | distinguish between the file not existing, and having 0 size | 10 July 2014, 16:05:41 UTC |
| 303852c | Anthony Brummett | 10 July 2014, 15:56:10 UTC | add errno to the die message so we can se why it failed | 10 July 2014, 15:56:10 UTC |
| 7fe9163 | Susanna Siebert | 10 July 2014, 14:35:59 UTC | add correct handling of nonexisting readcount entry, vaf of 0. Add test coverage | 10 July 2014, 15:07:17 UTC |
| 117d11b | Susanna Siebert | 10 July 2014, 14:14:55 UTC | keep positions with readcount and/or coverage of 0 | 10 July 2014, 14:16:06 UTC |
| 52450d7 | Susanna Siebert | 09 July 2014, 21:51:23 UTC | make default value an array ref for consistency, add test coverage | 09 July 2014, 21:59:07 UTC |
| b600381 | Susanna Siebert | 09 July 2014, 21:32:13 UTC | add missing passed_alt_allele param to interpret_entry subroutines | 09 July 2014, 21:59:03 UTC |
| 37a15ae | Susanna Siebert | 09 July 2014, 18:09:52 UTC | only interpret ft string for alt alleles that were called in the sample | 09 July 2014, 21:59:01 UTC |
| 25e2f6e | Susanna Siebert | 09 July 2014, 18:03:26 UTC | we should set the VAF to 0 if the coverage is 0, irregardless of readcount | 09 July 2014, 21:59:00 UTC |
| 9987d05 | Susanna Siebert | 09 July 2014, 18:02:40 UTC | pass alleles with VAF of 0 | 09 July 2014, 21:58:58 UTC |
| d0f59ba | Susanna Siebert | 09 July 2014, 18:00:47 UTC | refactor for clarity | 09 July 2014, 21:58:57 UTC |
| f898895 | Susanna Siebert | 09 July 2014, 17:57:53 UTC | make sure the NCallersFilter handles valid_callers that aren't in the VCF | 09 July 2014, 21:58:56 UTC |
| d36c182 | Susanna Siebert | 09 July 2014, 15:25:29 UTC | set filter to pass if we do not have a bam readcount entry for the sample | 09 July 2014, 21:58:54 UTC |
| 2289c3b | Susanna Siebert | 09 July 2014, 15:23:13 UTC | make FTKeepFilter sample specific | 09 July 2014, 21:58:53 UTC |
| aa72f5d | APipe Tester | 09 July 2014, 12:16:27 UTC | Updated `genome` tab completion. | 09 July 2014, 12:16:27 UTC |
| 1508cbf | APipe Tester | 09 July 2014, 12:15:06 UTC | Updated class browser cache. | 09 July 2014, 12:15:06 UTC |
| 2352c93 | Anthony Brummett | 08 July 2014, 21:49:58 UTC | Convert base chars to upper-case before comparing Model 5babb2f1f9474861abcb2f2ef93948fa died while processing because $reference was a lower-case c and one of the $genotype_alleles was upper-case | 08 July 2014, 23:53:03 UTC |
| 7c44523 | APipe Tester | 08 July 2014, 21:10:51 UTC | updated workflow submodule to 541917f | 08 July 2014, 21:10:51 UTC |
| d8a6cde | Gabriel Sanderson | 08 July 2014, 21:01:03 UTC | Skip assigning instrument data that has already been assigned | 08 July 2014, 21:09:12 UTC |
| 547fdf6 | apregier | 08 July 2014, 19:49:30 UTC | Merge branch 'fireteam' into gb_master | 08 July 2014, 19:49:30 UTC |
| 2b32db3 | apregier | 08 July 2014, 18:47:02 UTC | Add Target file URL field to sdrf | 08 July 2014, 19:46:26 UTC |
| 029ebeb | apregier | 08 July 2014, 18:20:21 UTC | Allow builds without target_region_set_name (WGS) | 08 July 2014, 19:46:23 UTC |
| 76fa2d9 | Susanna Siebert | 08 July 2014, 18:56:54 UTC | bump test versions for Genome::VariantReporting::Framework::Command::AnnotateBuild | 08 July 2014, 18:58:49 UTC |
| 84b0296 | Gabriel Sanderson | 08 July 2014, 18:45:03 UTC | Updated plan to work with simple report changes | 08 July 2014, 18:45:03 UTC |
| 08f4050 | Susanna Siebert | 08 July 2014, 18:21:33 UTC | bump test data version | 08 July 2014, 18:21:33 UTC |
| 803c552 | Susanna Siebert | 08 July 2014, 18:07:30 UTC | add lsf resource parameter to Vep because it regularly runs out of memory for indel files | 08 July 2014, 18:08:21 UTC |
| aa174f7 | Susanna Siebert | 08 July 2014, 18:06:49 UTC | handle entries with no bam readcount information | 08 July 2014, 18:08:20 UTC |
| 7a48a44 | Susanna Siebert | 08 July 2014, 18:06:20 UTC | handle bam readcount and coverage of 0 | 08 July 2014, 18:08:19 UTC |
| c8fef1b | Susanna Siebert | 08 July 2014, 15:24:37 UTC | updated simple reporter and plan files for CLE testing | 08 July 2014, 18:08:19 UTC |
| 0a3578b | Susanna Siebert | 08 July 2014, 15:03:17 UTC | new interpreter to output info tags of an entry | 08 July 2014, 18:08:18 UTC |
| 66b74f3 | Susanna Siebert | 08 July 2014, 15:02:21 UTC | new interpreter to output whether variant is homozygous or heterozygous | 08 July 2014, 18:08:17 UTC |
| 0838fec | Jason Walker | 08 July 2014, 17:28:41 UTC | When deciding which FPKM value to report for duplicate gene_ids, handle na values to avoid numeric errors. | 08 July 2014, 17:28:41 UTC |
| d885468 | Jason Walker | 08 July 2014, 16:02:51 UTC | initial commit of CoverageStatsSummary. This command will be used to summarize the coverage metrics for all somatic valiation models given. | 08 July 2014, 16:02:51 UTC |
| 060bd9f | Feiyu Du | 08 July 2014, 14:27:34 UTC | add paired_end check to make sure the paired_end status | 08 July 2014, 14:27:34 UTC |
| 2792e25 | APipe Tester | 07 July 2014, 23:21:15 UTC | updated graphite submodule to 4370771 | 07 July 2014, 23:21:15 UTC |
| 07cac17 | APipe Tester | 07 July 2014, 22:42:46 UTC | updated graphite submodule to 8bf345a | 07 July 2014, 22:42:46 UTC |
| 4342634 | Travis Abbott | 01 July 2014, 17:44:59 UTC | remove unused params | 07 July 2014, 19:42:46 UTC |
| 43a7090 | Travis Abbott | 23 June 2014, 16:26:48 UTC | add itx processing to breakdancer-to-bed | 07 July 2014, 19:42:46 UTC |
| 347c969 | dmorton | 07 July 2014, 02:25:22 UTC | File::Vcf::Differ can return HeaderDiff objects | 07 July 2014, 02:53:57 UTC |
| 5abc0f5 | dmorton | 07 July 2014, 02:41:24 UTC | Revert "VariantReporting subsystem works on files not just builds" This reverts commit 8b86f4b7be8e3bf9407af93651f2f365ee54ba37. | 07 July 2014, 02:41:24 UTC |
