| 3bdcbfc | Jason Walker | 14 March 2016, 16:44:57 UTC | Merge pull request #1305 from jasonwalker80/allow_empty_variants Zero size variants in CreateReport | 14 March 2016, 16:44:57 UTC |
| 8b6f1ee | Jason Walker | 14 March 2016, 15:46:59 UTC | Make an empty clean BED file. | 14 March 2016, 15:46:59 UTC |
| 36b0658 | Jason Walker | 14 March 2016, 14:56:32 UTC | Create empty files rather than skipping steps. | 14 March 2016, 14:56:32 UTC |
| 43123a5 | Thomas B. Mooney | 14 March 2016, 13:15:13 UTC | Merge pull request #1298 from tmooney/production_uses_new_prodbuilder_user Production No Longer Hardcoded to "apipe-builder". | 14 March 2016, 13:15:13 UTC |
| 8a73537 | Thomas B. Mooney | 14 March 2016, 13:13:49 UTC | Merge pull request #1295 from tmooney/get_email_from_user_object Get E-Mail Address from User Object | 14 March 2016, 13:13:49 UTC |
| d8ed15b | Thomas B. Mooney | 14 March 2016, 13:13:13 UTC | Merge pull request #1289 from tmooney/migrate_refalign_pp_to_model Migrate ReferenceAlignment Parameter Specification to the Model Class | 14 March 2016, 13:13:13 UTC |
| 6f698af | APipe Tester | 12 March 2016, 13:15:46 UTC | Updated `genome` tab completion. | 12 March 2016, 13:15:46 UTC |
| f41f4bd | Eddie Belter | 11 March 2016, 19:02:06 UTC | Merge pull request #1301 from ebelter/instdata-import-singletons InstData Import: Split by read into paireds, read1s and read2s | 11 March 2016, 19:02:06 UTC |
| 8e6e79c | Jason Walker | 11 March 2016, 16:15:28 UTC | Merge pull request #1304 from jasonwalker80/refseq_convert_by_md5 New chr_md5 reference converter | 11 March 2016, 16:15:28 UTC |
| 99153f1 | Jason Walker | 10 March 2016, 22:14:41 UTC | The original logic produced an indel file with trailing tabs instead or dbsnp rsid. Remove the test for an indels VCF since it is never produced and the original code only checked for the presence of a snvs VCF. | 10 March 2016, 22:14:41 UTC |
| 25d1b4b | Thomas B. Mooney | 10 March 2016, 22:12:47 UTC | Merge pull request #1286 from tmooney/consolidate_gmt_test_helpers Consolidate GMT TestHelpers into Genome::Utility::Test. | 10 March 2016, 22:12:47 UTC |
| 30b5fd3 | Jason Walker | 10 March 2016, 21:16:36 UTC | A few parameterized warnings and subroutine fixes. | 10 March 2016, 21:16:36 UTC |
| e14d1a0 | Jason Walker | 10 March 2016, 19:17:08 UTC | Allow for zero size variant files. | 10 March 2016, 19:17:08 UTC |
| 831f8ff | Jason Walker | 10 March 2016, 16:55:45 UTC | Add additional fields to more mock seqdict. | 10 March 2016, 16:55:45 UTC |
| 27c4458 | Jason Walker | 10 March 2016, 15:03:30 UTC | Add additional expected seqdict fields to mock seqdict. | 10 March 2016, 15:03:30 UTC |
| 4895353 | Jason Walker | 09 March 2016, 23:33:38 UTC | Define a set of keys, names and positions for fields in sequence dictionary. Move redundant parsing of each field to its own subroutine. | 09 March 2016, 23:33:38 UTC |
| d75baff | Jason Walker | 09 March 2016, 23:31:58 UTC | Use List::MoreUtils::each_array rather than sentinel counter loop | 09 March 2016, 23:31:58 UTC |
| b31b8a8 | Jason Walker | 09 March 2016, 22:46:45 UTC | Define a new chr_md5 converter algorithm. Use the seqdict md5 to convert chromosome names between builds. | 09 March 2016, 22:46:45 UTC |
| 1408043 | Jason Walker | 09 March 2016, 22:45:45 UTC | Parse additional fields of the seqdict including md5. | 09 March 2016, 22:45:45 UTC |
| 4b5353e | Eddie Belter | 09 March 2016, 18:41:03 UTC | Move determining read type into sub | 09 March 2016, 18:41:03 UTC |
| 96e8579 | Eddie Belter | 09 March 2016, 18:40:37 UTC | Test print cleanup | 09 March 2016, 18:40:37 UTC |
| 521fa00 | Thomas B. Mooney | 09 March 2016, 16:56:44 UTC | Merge pull request #1302 from tmooney/bamqc_works_on_non_laneqc_builds BamQC should only check instrument data for the result it will run on. | 09 March 2016, 16:56:44 UTC |
| 3aa60bc | Thomas Mooney | 09 March 2016, 13:51:43 UTC | BamQC should only check instrument data for the result it will run on. | 09 March 2016, 13:51:43 UTC |
| f5f801a | APipe Tester | 09 March 2016, 13:16:49 UTC | Updated `genome` tab completion. | 09 March 2016, 13:16:49 UTC |
| 3cf1098 | APipe Tester | 09 March 2016, 13:15:13 UTC | Updated class browser cache. | 09 March 2016, 13:15:13 UTC |
| c63dfc6 | Eddie Belter | 09 March 2016, 00:09:42 UTC | InstData Import: split into paired reads, read1 singletons and reaed2 singletons | 09 March 2016, 00:09:42 UTC |
| 6d80cbd | Thomas B. Mooney | 08 March 2016, 21:27:57 UTC | Merge pull request #1299 from tmooney/one_bam_to_rule_them_all ReferenceAlignment makes one BAM regardless of mixed sample assignment. | 08 March 2016, 21:27:57 UTC |
| c518931 | Thomas B. Mooney | 08 March 2016, 19:48:15 UTC | Merge pull request #1296 from tmooney/base_of_ssg_command_tree Add a base for the SSG command tree. | 08 March 2016, 19:48:15 UTC |
| 407bad4 | Thomas Mooney | 08 March 2016, 15:09:49 UTC | Use new Genome::Sys->user_has_role() to decide if production. | 08 March 2016, 15:09:49 UTC |
| 0e9e4be | Thomas Mooney | 08 March 2016, 15:03:57 UTC | Class method to check if a user belongs to a role. | 08 March 2016, 15:03:57 UTC |
| db6aeba | Thomas Mooney | 08 March 2016, 13:57:26 UTC | ReferenceAlignment makes one BAM regardless of mixed sample assignment. | 08 March 2016, 13:57:26 UTC |
| 84575d4 | APipe Tester | 08 March 2016, 13:16:36 UTC | Updated `genome` tab completion. | 08 March 2016, 13:16:36 UTC |
| 7dc29ee | APipe Tester | 08 March 2016, 13:14:59 UTC | Updated class browser cache. | 08 March 2016, 13:14:59 UTC |
| c77894f | Thomas B. Mooney | 07 March 2016, 23:58:27 UTC | Merge pull request #1297 from tmooney/add_scheduled_as_build_status Add Scheduled as valid build status. | 07 March 2016, 23:58:27 UTC |
| cbd4fbd | Thomas Mooney | 07 March 2016, 23:53:31 UTC | Use production role to decide when to take prod-ish actions. | 07 March 2016, 23:53:31 UTC |
| b7671cf | Thomas Mooney | 07 March 2016, 23:38:42 UTC | Apply higher cap to all production users. | 07 March 2016, 23:48:33 UTC |
| c757f7d | Thomas Mooney | 07 March 2016, 23:36:40 UTC | Check all production users for failures. * Consider production models regardless of who ran the build. * Disregard non-production models even if we did run the build. | 07 March 2016, 23:48:12 UTC |
| 584ea76 | Thomas Mooney | 07 March 2016, 23:34:32 UTC | Production models now set run_as to "prod-builder". | 07 March 2016, 23:34:32 UTC |
| 8ec12ca | Thomas Mooney | 07 March 2016, 23:12:13 UTC | Add Scheduled as valid build status. | 07 March 2016, 23:12:13 UTC |
| df80edc | Thomas Mooney | 07 March 2016, 22:13:36 UTC | Don't really create the object (so non-admins can run test!) | 07 March 2016, 22:13:36 UTC |
| 0d9ca0c | Thomas Mooney | 07 March 2016, 19:54:56 UTC | Add a base for the SSG command tree. This should fix tab-completion and the commands showing up in `genome model --help`. | 07 March 2016, 19:56:09 UTC |
| 9abd497 | Thomas Mooney | 07 March 2016, 16:55:19 UTC | Update GMTs to lookup e-mail addresses from the User object. | 07 March 2016, 16:55:19 UTC |
| d2f08f7 | Anthony Brummett | 07 March 2016, 16:11:45 UTC | Merge pull request #1283 from brummett/build-volume-command2 Build volume lister command | 07 March 2016, 16:11:45 UTC |
| 32599e2 | Jason Walker | 07 March 2016, 15:03:45 UTC | Merge pull request #1285 from jasonwalker80/qc_build_metric_report Qc build metric report | 07 March 2016, 15:03:45 UTC |
| b122913 | Thomas Mooney | 07 March 2016, 14:19:43 UTC | Look up the e-mail from the User object. Now we support users across multiple domains. | 07 March 2016, 14:19:43 UTC |
| 478c87b | Jason Walker | 07 March 2016, 14:13:20 UTC | Merge pull request #1293 from jasonwalker80/somatic_subject_subroutines Common somatic interface to the tumor/normal samples. | 07 March 2016, 14:13:20 UTC |
| f3fae09 | Jason Walker | 04 March 2016, 21:50:00 UTC | Common somatic interface to the tumor/normal samples. | 04 March 2016, 21:50:00 UTC |
| 71d2957 | Eddie Belter | 04 March 2016, 20:37:31 UTC | Merge pull request #1269 from ebelter/anp-replace-model-uses-profile AnP Replace Model Uses Config Profile | 04 March 2016, 20:37:31 UTC |
| eb660fa | Jason Walker | 04 March 2016, 19:02:31 UTC | For exome, use the metric headers in a loop since the hash key is the same but uppercase. | 04 March 2016, 19:02:31 UTC |
| 14f9f4d | APipe Tester | 04 March 2016, 13:15:58 UTC | Updated `genome` tab completion. | 04 March 2016, 13:15:58 UTC |
| b61cda8 | APipe Tester | 04 March 2016, 13:14:18 UTC | Updated class browser cache. | 04 March 2016, 13:14:18 UTC |
| 3410fc2 | Thomas B. Mooney | 03 March 2016, 14:07:11 UTC | Merge pull request #1280 from tmooney/remove_remnants_of_old_druggablegene Remove Remnants of old Perl-based DruggableGene. | 03 March 2016, 14:07:11 UTC |
| 21da6b9 | Thomas Mooney | 02 March 2016, 17:56:13 UTC | Migrate RefAlign PP to the model class definition. | 03 March 2016, 14:04:53 UTC |
| 5a3d52f | APipe Tester | 03 March 2016, 13:17:22 UTC | Updated `gmt` tab completion. | 03 March 2016, 13:17:22 UTC |
| 2374259 | APipe Tester | 03 March 2016, 13:16:39 UTC | Updated `genome` tab completion. | 03 March 2016, 13:16:39 UTC |
| c5dba6f | APipe Tester | 03 March 2016, 13:15:06 UTC | Updated class browser cache. | 03 March 2016, 13:15:06 UTC |
| be853cb | Thomas B. Mooney | 02 March 2016, 20:10:33 UTC | Merge pull request #1275 from tmooney/remove_liftovermultiplecolumns_gmt Remove "LiftOverMultipleColumns" GMT. | 02 March 2016, 20:10:33 UTC |
| c34b289 | Thomas Mooney | 02 March 2016, 17:55:03 UTC | Move subject down with other non-processing profile params. | 02 March 2016, 17:55:03 UTC |
| a3e6442 | Thomas B. Mooney | 02 March 2016, 17:43:06 UTC | Merge pull request #1245 from tmooney/remove_refalign_pp_subclasses_part_two Complete the removal of RefAlign PP subclasses. | 02 March 2016, 17:43:06 UTC |
| 4d5bc61 | Thomas B. Mooney | 02 March 2016, 15:53:43 UTC | Merge pull request #1270 from tmooney/refalign_doesnt_use_stages ReferenceAlignment No Longer Uses a Staged ProcessingProfile. | 02 March 2016, 15:53:43 UTC |
| 0e105eb | APipe Tester | 01 March 2016, 13:17:22 UTC | Updated `gmt` tab completion. | 01 March 2016, 13:17:22 UTC |
| da8c1d5 | APipe Tester | 01 March 2016, 13:16:40 UTC | Updated `genome` tab completion. | 01 March 2016, 13:16:40 UTC |
| 9421777 | APipe Tester | 01 March 2016, 13:15:10 UTC | Updated class browser cache. | 01 March 2016, 13:15:10 UTC |
| c62b391 | Thomas Mooney | 29 February 2016, 23:07:34 UTC | Remove now unused GMT::TestHelpers::General. | 29 February 2016, 23:07:34 UTC |
| afbcfdc | Thomas Mooney | 29 February 2016, 23:07:10 UTC | Dindel TestHelpers use Genome::Utility::Test for data_dir. | 29 February 2016, 23:07:10 UTC |
| ee41d85 | Thomas Mooney | 29 February 2016, 23:04:17 UTC | Move blessed-file checking into Genome::Utility::Test. | 29 February 2016, 23:04:17 UTC |
| eafffa8 | Thomas Mooney | 29 February 2016, 22:57:39 UTC | Escape matching side of s///. | 29 February 2016, 22:57:39 UTC |
| 31d15d8 | Thomas Mooney | 29 February 2016, 22:56:11 UTC | Remove unused import. | 29 February 2016, 22:56:11 UTC |
| b61ad48 | Thomas Mooney | 29 February 2016, 22:45:11 UTC | Incorporate GMT TestHelpers::Data into Genome::Utility::Test. | 29 February 2016, 22:45:11 UTC |
| cea3aaa | Thomas Mooney | 29 February 2016, 21:10:26 UTC | Use Genome::Utility::Test to get data_dir. | 29 February 2016, 21:10:26 UTC |
| a33737c | Anthony Brummett | 29 February 2016, 20:54:09 UTC | avoid "redefined" warnings | 29 February 2016, 20:54:09 UTC |
| fe8e5c1 | Thomas Mooney | 29 February 2016, 20:47:11 UTC | Update to use Genome::Utility::Test. | 29 February 2016, 20:47:11 UTC |
| 867eab9 | Jason Walker | 29 February 2016, 20:37:49 UTC | Expect a single element array instead of scalar for verifyBamId results. | 29 February 2016, 20:37:49 UTC |
| 7abbfc2 | Jason Walker | 29 February 2016, 18:48:28 UTC | Remove VerifyBamId dedup logic since results from builds are now unique. | 29 February 2016, 18:48:28 UTC |
| 1467af5 | Susanna Kiwala | 29 February 2016, 18:13:20 UTC | Merge pull request #1284 from susannasiebert/epitope_prediction_bugfix Epitope length needs to be of Integer data type instead of Text | 29 February 2016, 18:13:20 UTC |
| b8cade6 | Jason Walker | 29 February 2016, 17:54:05 UTC | Add QC config test factory. | 29 February 2016, 17:54:05 UTC |
| aa86f95 | Jason Walker | 29 February 2016, 17:43:32 UTC | Add PF_READS. Resolve the qc config type rather than defining a profile as user input. | 29 February 2016, 17:43:32 UTC |
| a333a65 | Thomas B. Mooney | 29 February 2016, 14:08:14 UTC | Merge pull request #1278 from tmooney/alignmentresult_uses_alignmentsummary_gmt AlignmentResult uses the AlignmentSummary GMT. | 29 February 2016, 14:08:14 UTC |
| 6b70f20 | Thomas B. Mooney | 29 February 2016, 14:07:57 UTC | Merge pull request #1271 from tmooney/remove_seefive_gmts Remove disused "SeeFive" GMT tree. | 29 February 2016, 14:07:57 UTC |
| e28906e | Thomas B. Mooney | 29 February 2016, 14:07:48 UTC | Merge pull request #1272 from tmooney/remove_completegenomics_gmts Remove disused "CompleteGenomics" GMTs. | 29 February 2016, 14:07:48 UTC |
| 5fb69cc | Thomas B. Mooney | 29 February 2016, 14:07:35 UTC | Merge pull request #1273 from tmooney/remove_getsubdirectories_gmt Remove "GetSubDirectories" GMT. | 29 February 2016, 14:07:35 UTC |
| 150c6a0 | Thomas B. Mooney | 29 February 2016, 14:07:26 UTC | Merge pull request #1274 from tmooney/remove_wiki_gmts Remove old GMTs for updating MediaWiki and indexing in Solr. | 29 February 2016, 14:07:26 UTC |
| 0e9e58e | Thomas B. Mooney | 29 February 2016, 14:07:13 UTC | Merge pull request #1276 from tmooney/remove_sword_gmts Remove unfinished "Sword" GMTs. | 29 February 2016, 14:07:13 UTC |
| c3f8cde | Thomas B. Mooney | 29 February 2016, 14:07:00 UTC | Merge pull request #1277 from tmooney/remove_text_gmt Remove head of "Text" GMT tree. | 29 February 2016, 14:07:00 UTC |
| 87c465e | Thomas B. Mooney | 29 February 2016, 14:06:47 UTC | Merge pull request #1279 from tmooney/remove_updatehistory Remove Genome::UpdateHistory. | 29 February 2016, 14:06:47 UTC |
| 2d34c8c | Thomas B. Mooney | 29 February 2016, 14:06:34 UTC | Merge pull request #1281 from tmooney/lsf_tmpdir_is_group_accessible Configure permissions on tempdir when using LSF location. | 29 February 2016, 14:06:34 UTC |
| df78ef7 | Susanna Kiwala | 26 February 2016, 20:20:18 UTC | Epitope length needs to be of Integer data type instead of Text | 26 February 2016, 20:20:18 UTC |
| fdfa20e | Anthony Brummett | 26 February 2016, 16:56:37 UTC | forgot "use Genonme" | 26 February 2016, 16:56:37 UTC |
| 02e80af | Chris Miller | 25 February 2016, 22:17:20 UTC | Merge pull request #1282 from chrisamiller/vscn adding name to the jobs for monitoring | 25 February 2016, 22:17:20 UTC |
| 20e92bc | Chris Miller | 25 February 2016, 21:50:40 UTC | adding name to the jobs for monitoring | 25 February 2016, 21:50:40 UTC |
| 519c00c | Thomas Mooney | 25 February 2016, 21:00:28 UTC | Configure permissions on tempdir when using LSF location. This will allow for easier debugging of jobs, while still restricting access to the authorized group. | 25 February 2016, 21:00:28 UTC |
| 3f444b4 | Thomas Mooney | 25 February 2016, 19:07:06 UTC | Remove last of DruggableGene namespace. Please see genome/dgi-db for the new and better version! | 25 February 2016, 19:08:43 UTC |
| 0adbbbd | Thomas Mooney | 25 February 2016, 19:06:44 UTC | Remove old DruggableGene importers. | 25 February 2016, 19:06:44 UTC |
| c2a9f6c | Thomas Mooney | 25 February 2016, 19:05:12 UTC | Remove old DruggableGene paths from web-app. | 25 February 2016, 19:05:12 UTC |
| 785f3c5 | Thomas Mooney | 25 February 2016, 19:02:07 UTC | Remove XSLT for non-existent classes. | 25 February 2016, 19:02:07 UTC |
| 167b646 | Anthony Brummett | 25 February 2016, 18:39:21 UTC | Lister command to list allocations of builds It's a bit of a hack on the standard lister. It allows --filter to apply to builds and fetches those builds. Then creates UR sets of allocations of those builds which is faster than iterating through the allocation objects directly. Finally, it applies the --show to those allocation sets. | 25 February 2016, 18:39:21 UTC |
| 998e884 | Anthony Brummett | 12 January 2016, 20:22:15 UTC | Constrain the valid values for a build's status This is the complete list of values currently present in the DB | 25 February 2016, 18:38:08 UTC |
| 8f85868 | David Morton | 25 February 2016, 17:33:09 UTC | Merge pull request #1266 from davidlmorton/inline_workflowbuilder Inline workflowbuilder DAG execution | 25 February 2016, 17:33:09 UTC |
| 2173780 | Thomas Mooney | 25 February 2016, 16:53:31 UTC | Remove Genome::UpdateHistory. It points to a non-existent table. | 25 February 2016, 16:53:31 UTC |
| 355c40a | Thomas Mooney | 25 February 2016, 16:15:40 UTC | AlignmentResult uses the AlignmentSummary GMT. | 25 February 2016, 16:15:40 UTC |
