| d79fa7f | dmorton | 30 June 2014, 22:54:55 UTC | Move GetInitialVcfResult.pm to Framework | 01 July 2014, 14:36:39 UTC |
| c20dad3 | dmorton | 30 June 2014, 22:52:31 UTC | Move Common::Dag to Framework | 01 July 2014, 14:36:33 UTC |
| 84cbacc | dmorton | 30 June 2014, 22:50:02 UTC | Move ReportGenerator to Framework | 01 July 2014, 14:36:33 UTC |
| 0b3c063 | dmorton | 30 June 2014, 22:47:15 UTC | Move Factory to Framework | 01 July 2014, 14:36:33 UTC |
| 3d3cf85 | dmorton | 30 June 2014, 22:45:49 UTC | Move Command to Framework | 01 July 2014, 14:36:32 UTC |
| e8651cd | dmorton | 30 June 2014, 22:43:21 UTC | Move TestHelpers to Framework | 01 July 2014, 14:36:32 UTC |
| 4c40346 | dmorton | 30 June 2014, 22:30:10 UTC | Move generic interpreters to Generic namespace | 01 July 2014, 14:36:32 UTC |
| 54ebb57 | dmorton | 30 June 2014, 22:25:20 UTC | Move Interpreter::FpkmInterpreter to Fpkm | 01 July 2014, 14:36:32 UTC |
| 7301236 | dmorton | 30 June 2014, 22:23:59 UTC | Move Interpreter::GmafInterpreter to Dbsnp | 01 July 2014, 14:36:32 UTC |
| aa4f62e | dmorton | 30 June 2014, 22:22:01 UTC | Move Interpreter::DbsnpInterpreter to Dbsnp | 01 July 2014, 14:36:32 UTC |
| cac308f | dmorton | 30 June 2014, 22:20:27 UTC | Move Interpreter::VepInterpreter to Vep | 01 July 2014, 14:36:32 UTC |
| 6b13ed4 | dmorton | 30 June 2014, 22:17:35 UTC | Moved generic filters to Generic namespace | 01 July 2014, 14:36:32 UTC |
| 0e36e0d | dmorton | 30 June 2014, 22:15:17 UTC | Fix class names in ur property description Not sure how this didn't cause errors to be honest. | 01 July 2014, 14:36:31 UTC |
| 67f07df | dmorton | 30 June 2014, 22:03:38 UTC | Move Filter::MinFpkmFilter to Fpkm | 01 July 2014, 14:36:31 UTC |
| 0ebb239 | dmorton | 30 June 2014, 21:59:20 UTC | Move Filter::Tier1Filter to Vep | 01 July 2014, 14:36:31 UTC |
| 5077b67 | dmorton | 30 June 2014, 21:56:32 UTC | Move Filter::DamagingFilter to Vep | 01 July 2014, 14:36:31 UTC |
| dcd7a9d | dmorton | 30 June 2014, 21:53:38 UTC | Move Filter::MaxGmafFilter to Dbsnp | 01 July 2014, 14:36:31 UTC |
| 46c5a02 | dmorton | 30 June 2014, 21:52:10 UTC | Move Filter::MaxAfFilter to Dbsnp | 01 July 2014, 14:36:31 UTC |
| e61ab14 | dmorton | 30 June 2014, 21:26:11 UTC | Move Filter::GenotypeVafFilter to BamReadcount | 01 July 2014, 14:36:30 UTC |
| c105a91 | dmorton | 30 June 2014, 21:24:06 UTC | Move Filter/CoverageVafFilter to BamReadcount | 01 July 2014, 14:36:30 UTC |
| 019fb86 | Gabriel Sanderson | 30 June 2014, 22:56:05 UTC | Slight refactor so gene_list methods only return lists | 30 June 2014, 22:56:05 UTC |
| 1962ddc | Gabriel Sanderson | 30 June 2014, 22:45:25 UTC | Add a 'gene' filter to variant reporting that filters to a gene list. For now this filter only accepts 'acmg' as a valid list, but others could be added. | 30 June 2014, 22:45:25 UTC |
| c72ff45 | Gabriel Sanderson | 30 June 2014, 21:29:47 UTC | Remove unused lib | 30 June 2014, 21:38:08 UTC |
| fe73081 | dmorton | 30 June 2014, 20:52:44 UTC | Move Expert/Fpkm to VariantReporting/Fpkm | 30 June 2014, 20:52:44 UTC |
| 0b57438 | dmorton | 30 June 2014, 20:46:06 UTC | Move Expert/Dbsnp to VariantReporting/Dbsnp | 30 June 2014, 20:46:06 UTC |
| faa2144 | dmorton | 30 June 2014, 20:33:50 UTC | Move Expert/BamReadcount to VariantReporting/BamReadcount | 30 June 2014, 20:33:50 UTC |
| b6f8694 | Susanna Siebert | 30 June 2014, 19:55:12 UTC | make calculated property optional so it doesn't need to be specified on the command line | 30 June 2014, 19:55:29 UTC |
| 88f6e3f | Susanna Siebert | 30 June 2014, 18:44:53 UTC | updates to modules to match reorganization paths | 30 June 2014, 18:46:21 UTC |
| f53ae3a | Susanna Siebert | 30 June 2014, 18:20:04 UTC | new variant callers interpreter module and tests | 30 June 2014, 18:46:20 UTC |
| bc2c694 | Susanna Siebert | 30 June 2014, 18:19:28 UTC | add function and test for retrieval of callers in a vcf | 30 June 2014, 18:46:20 UTC |
| 323c79c | Susanna Siebert | 30 June 2014, 14:20:24 UTC | new variant type interpreter module and tests | 30 June 2014, 18:46:18 UTC |
| 7368e17 | Mark Burnett | 30 June 2014, 16:13:47 UTC | allow lower case ref bases in G:M:T:Vcf:Convert:Snv:Samtools | 30 June 2014, 16:14:48 UTC |
| d6f245a | dmorton | 29 June 2014, 22:05:22 UTC | Move Expert/Vep to VariantReporting/Vep | 30 June 2014, 14:57:08 UTC |
| 7577e3d | dmorton | 29 June 2014, 21:54:40 UTC | Move Dag to Common | 30 June 2014, 14:57:08 UTC |
| 365b94d | dmorton | 29 June 2014, 21:50:57 UTC | Move WithSampleName to Component directory | 30 June 2014, 14:57:07 UTC |
| 95038a1 | dmorton | 29 June 2014, 21:48:58 UTC | Move WithTranslatedInputs to Component directory | 30 June 2014, 14:57:07 UTC |
| 1de5196 | Dave Larson | 30 June 2014, 14:46:05 UTC | make Sniper1.0.4 available to GMS | 30 June 2014, 14:46:05 UTC |
| b61b427 | dmorton | 29 June 2014, 03:48:59 UTC | Move Interpreter/Base to Component/Interpreter | 29 June 2014, 03:48:59 UTC |
| 0e14322 | dmorton | 29 June 2014, 03:33:15 UTC | Move Filter/Base to Component/Filter | 29 June 2014, 03:44:14 UTC |
| c435d03 | dmorton | 29 June 2014, 02:54:39 UTC | Move Expert/CommandBase to Component/Expert/Command | 29 June 2014, 02:54:39 UTC |
| 04e9c24 | dmorton | 29 June 2014, 02:48:19 UTC | Move Expert/CommandBase to Component/Expert/Command | 29 June 2014, 02:48:19 UTC |
| f80988c | dmorton | 29 June 2014, 02:18:04 UTC | Move Expert/Base to Component/Expert | 29 June 2014, 02:18:04 UTC |
| 4686682 | dmorton | 29 June 2014, 00:13:37 UTC | Moved AdaptorBase to Component/Adaptor | 29 June 2014, 00:31:08 UTC |
| 76b7bce | dmorton | 28 June 2014, 23:31:51 UTC | Moved ComponentBase to Component/Base | 28 June 2014, 23:31:51 UTC |
| f73710d | dmorton | 28 June 2014, 22:49:22 UTC | Move Plan.t and Plan-validate.t into Plan directory | 28 June 2014, 22:49:22 UTC |
| 97437f1 | Susanna Siebert | 27 June 2014, 16:00:40 UTC | updated netMHC package path | 27 June 2014, 16:00:40 UTC |
| 379afef | APipe Tester | 27 June 2014, 12:17:42 UTC | Updated `genome` tab completion. | 27 June 2014, 12:17:42 UTC |
| ceea59a | APipe Tester | 26 June 2014, 22:01:22 UTC | updated getopt-complete submodule to 2dc69f2 | 26 June 2014, 22:01:22 UTC |
| 6b93616 | APipe Tester | 26 June 2014, 22:00:50 UTC | updated ur submodule to 676e05b | 26 June 2014, 22:00:50 UTC |
| 528f95d | Feiyu Du | 26 June 2014, 21:25:12 UTC | add indel to test | 26 June 2014, 21:25:12 UTC |
| 9609e72 | Nathaniel Nutter | 26 June 2014, 20:38:51 UTC | builds validate instrument data bam_path has size | 26 June 2014, 20:38:51 UTC |
| 2365575 | Nathaniel Nutter | 26 June 2014, 20:36:11 UTC | InstrumentData needs an allocation to be valid | 26 June 2014, 20:36:43 UTC |
| 69ce4e6 | Nathaniel Nutter | 26 June 2014, 00:27:48 UTC | validate instrument data bam_path has size This might be overreaching on the base Genome::Model::Build class but it's definitely needed for anything that does BWA, BWAMEM, or BWASW alignment. For those types of alignment instrument data with a bam_path but no size results in an invalid Workflow model that cannot be commited to the DB. | 26 June 2014, 20:36:42 UTC |
| 4fc0cde | Nathaniel Nutter | 26 June 2014, 00:27:40 UTC | whitespace | 26 June 2014, 20:36:40 UTC |
| 3d64f31 | Thomas Mooney | 26 June 2014, 19:57:08 UTC | Use existing implementation of camel_case_to_string. Only override to get the error behaviour we're after. | 26 June 2014, 19:57:08 UTC |
| 52b7ba1 | Thomas Mooney | 26 June 2014, 19:55:42 UTC | Use existing method to get sub-command names. The alternative implementation was defective. It would not hyphenate commands appropriately. Rather than fix this one, use the one that commands use generally. | 26 June 2014, 19:55:42 UTC |
| c12dcda | Ian Ferguson | 26 June 2014, 19:01:52 UTC | Add bwa versions 0.7.8 and 0.7.9a to GMT::Bwa | 26 June 2014, 19:01:52 UTC |
| b2d01f0 | Adam Coffman | 26 June 2014, 18:44:32 UTC | changed date_scheduled to created_at in query | 26 June 2014, 18:44:32 UTC |
| 1726e9e | Thomas Mooney | 26 June 2014, 14:22:05 UTC | Blithely update expected output again. | 26 June 2014, 14:22:05 UTC |
| a98aaf6 | apregier | 25 June 2014, 20:40:59 UTC | Merge branch 'updated' into gb_master | 25 June 2014, 20:40:59 UTC |
| 1c8623a | apregier | 25 June 2014, 17:52:07 UTC | Add sift,polyphen, and condel to tumor-only report | 25 June 2014, 20:40:19 UTC |
| fde4524 | apregier | 24 June 2014, 21:12:33 UTC | Correctly query for deletions in bam readcount entries | 25 June 2014, 20:40:18 UTC |
| 5375eb0 | apregier | 24 June 2014, 20:16:48 UTC | Correctly query bam-readcount for insertion alleles | 25 June 2014, 20:40:17 UTC |
| 0018208 | Thomas Mooney | 25 June 2014, 19:36:49 UTC | Quiet undefined warnings. | 25 June 2014, 19:36:49 UTC |
| 6fc25d6 | Thomas Mooney | 25 June 2014, 19:17:52 UTC | Don't try to re-purge purged allocations. | 25 June 2014, 19:17:52 UTC |
| 5ad5ae3 | Eddie Belter | 25 June 2014, 17:11:26 UTC | Build Cmds: uses associated_disk_allocations instaed of all_allocations | 25 June 2014, 17:32:49 UTC |
| 43baedd | Eddie Belter | 25 June 2014, 17:11:26 UTC | Build Unarchive: uses associated_disk_allocations instaed of all_allocations | 25 June 2014, 17:11:57 UTC |
| b5dfae3 | APipe Tester | 25 June 2014, 12:17:11 UTC | Updated `genome` tab completion. | 25 June 2014, 12:17:11 UTC |
| 5ee871d | APipe Tester | 25 June 2014, 12:15:35 UTC | Updated class browser cache. | 25 June 2014, 12:15:35 UTC |
| 97d44e5 | dmorton | 24 June 2014, 22:55:42 UTC | Clean up unneeded code This was implemented before the use of Memoize library but wasn't removed once Memoize was utilized | 24 June 2014, 22:56:36 UTC |
| e2c5257 | dmorton | 24 June 2014, 22:54:52 UTC | Add test that covers problem with using tmp file path as SR input | 24 June 2014, 22:56:36 UTC |
| 61f4989 | dmorton | 24 June 2014, 17:06:13 UTC | Ensure that ConvertedBedResults can shortcut They were prviously being provided with tmp file paths as an input, which would never allow them to shortcut. | 24 June 2014, 22:56:36 UTC |
| c0bf6c2 | Eddie Belter | 24 June 2014, 20:43:44 UTC | GM: reader factory unarchives instdata if archived | 24 June 2014, 21:34:16 UTC |
| 08b067d | Eddie Belter | 24 June 2014, 20:42:24 UTC | Test Factory: imported inst data uses disk alloc factory | 24 June 2014, 21:34:15 UTC |
| d65c9d4 | Eddie Belter | 24 June 2014, 20:39:44 UTC | Test Factory: disk allocation archive stores the mount path; unarchive sets the previous mount path or new temp one | 24 June 2014, 21:34:15 UTC |
| 78c7f27 | Eddie Belter | 23 June 2014, 19:12:39 UTC | Build: add _unarchive_disk_allocations method that calls unarchive command for use with objects w/ allocations | 24 June 2014, 21:34:14 UTC |
| 6c01570 | Eddie Belter | 19 June 2014, 13:39:45 UTC | GM: remove commented out lines in test module | 24 June 2014, 21:34:14 UTC |
| b364b17 | Eddie Belter | 24 June 2014, 20:58:21 UTC | Hmp: rmove unused test | 24 June 2014, 20:58:57 UTC |
| 70adc12 | Nathaniel Nutter | 24 June 2014, 20:27:40 UTC | remove unused argument As far as I could tell this argument doesn't get used and may have been a copy-paste from the Cache version. | 24 June 2014, 20:38:30 UTC |
| 68942c3 | Nathaniel Nutter | 24 June 2014, 20:27:04 UTC | move 'path' argument to PSGI env Plack::Middleware do not pass on arguments, only the PSGI env, so to be compatible with Plack::Middleware we need an alternative to arguments. I don't know if this is the correct solution but it seems to work. | 24 June 2014, 20:38:30 UTC |
| d47b024 | Nathaniel Nutter | 24 June 2014, 20:24:31 UTC | move 'ajax_refresh' argument to PSGI env Plack::Middleware do not pass on arguments, only the PSGI env, so to be compatible with Plack::Middleware we need an alternative to arguments. I don't know if this is the correct solution but it seems to work. | 24 June 2014, 20:38:29 UTC |
| cb0c34b | Eddie Belter | 24 June 2014, 20:34:26 UTC | InstData Import: mv HMP commands to Site/TGI/Hmp | 24 June 2014, 20:35:20 UTC |
| c499117 | Eddie Belter | 04 June 2014, 22:00:18 UTC | InstData: rename headers var in generate file for reimport | 24 June 2014, 20:35:18 UTC |
| 2d06de4 | Eddie Belter | 04 June 2014, 21:58:13 UTC | InstData: fix reimport class name; add reimported_from method | 24 June 2014, 20:35:17 UTC |
| ed19641 | Eddie Belter | 04 June 2014, 21:43:34 UTC | InstData: add reimport helper class; use it in generate file for reimport | 24 June 2014, 20:35:17 UTC |
| 4c470f7 | Eddie Belter | 04 June 2014, 21:33:00 UTC | InstData: mv generate source files tsv to base command dir; remove most references to source files | 24 June 2014, 20:35:16 UTC |
| 0522f6a | Eddie Belter | 04 June 2014, 21:12:06 UTC | InstData Import: command to generate tsv file to reimport | 24 June 2014, 20:35:15 UTC |
| be76916 | Thomas Mooney | 24 June 2014, 15:39:18 UTC | New command to show config (mis)matches for an instrument-data | 24 June 2014, 15:39:18 UTC |
| 9114971 | APipe Tester | 24 June 2014, 12:17:02 UTC | Updated `genome` tab completion. | 24 June 2014, 12:17:02 UTC |
| baccbc0 | Nathaniel Nutter | 23 June 2014, 22:24:24 UTC | delegate permission changes to allocation | 23 June 2014, 22:27:40 UTC |
| 82175ba | Nathaniel Nutter | 23 June 2014, 22:19:17 UTC | add set_files_read_only (as opposed to files and directories) | 23 June 2014, 22:27:39 UTC |
| 71e5381 | Nathaniel Nutter | 23 June 2014, 22:18:55 UTC | add alias for function | 23 June 2014, 22:27:38 UTC |
| dc9fda7 | Thomas Mooney | 23 June 2014, 20:46:51 UTC | Update ClinSeq to account for DGIdb changes. | 23 June 2014, 20:46:51 UTC |
| 1a890a9 | Nathaniel Nutter | 23 June 2014, 20:12:22 UTC | add --unstartable-ok option In BQM unstartable "failures" do not need to result in an error since they are monitored downstream. Using this option will keep BQM from turning red when there are unstartable builds. | 23 June 2014, 20:12:22 UTC |
| 3cca138 | Thomas Mooney | 23 June 2014, 18:14:32 UTC | Merge the keys of the response hash instead of overwriting them | 23 June 2014, 18:14:32 UTC |
| 7a6de6e | Jim Weible | 23 June 2014, 15:22:59 UTC | allow 0 sized output files | 23 June 2014, 15:22:59 UTC |
| fe60d05 | Steve Wilkerson | 20 June 2014, 21:41:41 UTC | Added additional fields for report | 20 June 2014, 21:42:48 UTC |
| 57953aa | Nathaniel Nutter | 20 June 2014, 14:25:11 UTC | fix not telling Perl that string was an octal number | 20 June 2014, 14:25:39 UTC |
| a7791f6 | APipe Tester | 20 June 2014, 12:17:59 UTC | Updated `gmt` tab completion. | 20 June 2014, 12:17:59 UTC |
| fc3889e | APipe Tester | 20 June 2014, 12:17:16 UTC | Updated `genome` tab completion. | 20 June 2014, 12:17:16 UTC |
