| 98084e4 | Avi Ramu | 22 March 2016, 20:26:17 UTC | Merge pull request #1318 from gatoravi/hg38-clinseq-fixes clinseq fixes for hg38 | 22 March 2016, 20:26:17 UTC |
| 3f80ed3 | Thomas B. Mooney | 21 March 2016, 20:15:58 UTC | Merge pull request #1319 from tmooney/duplication_handling_in_dispatcher_is_optional Duplication Handling in the Alignment Dispatcher Is Optional. | 21 March 2016, 20:15:58 UTC |
| 225e278 | Thomas Mooney | 21 March 2016, 17:50:30 UTC | Duplication handling is optional. | 21 March 2016, 17:50:30 UTC |
| aff1024 | Avinash Ramu | 21 March 2016, 15:48:14 UTC | Use fatal_message() | 21 March 2016, 15:48:14 UTC |
| e3c687d | Avinash Ramu | 21 March 2016, 15:47:24 UTC | Declare variable once | 21 March 2016, 15:47:24 UTC |
| 529f07e | Avinash Ramu | 21 March 2016, 15:46:53 UTC | Avoid warning from autoloader | 21 March 2016, 15:46:53 UTC |
| f01ba54 | Avinash Ramu | 21 March 2016, 15:42:26 UTC | Make folder naming consistent. | 21 March 2016, 15:42:26 UTC |
| 7cd616c | Avinash Ramu | 21 March 2016, 15:38:14 UTC | Use fatal_message() | 21 March 2016, 15:38:14 UTC |
| 3cdc454 | Avinash Ramu | 21 March 2016, 15:37:42 UTC | Add 38 to error message | 21 March 2016, 15:37:42 UTC |
| a2cda9d | Avinash Ramu | 21 March 2016, 15:36:04 UTC | Remove code-remains | 21 March 2016, 15:36:04 UTC |
| c28d308 | Avinash Ramu | 21 March 2016, 15:35:08 UTC | Use fatal_message() | 21 March 2016, 15:35:08 UTC |
| 594cf72 | Avinash Ramu | 21 March 2016, 15:30:34 UTC | Avoid warning from autoloader. | 21 March 2016, 15:30:34 UTC |
| 55a88e8 | Thomas B. Mooney | 17 March 2016, 22:57:40 UTC | Merge pull request #1315 from tmooney/align_and_merge_dags_have_unique_names Support Multiple Merge Groups for AlignAndMerge in the AlignmentDispatcher | 17 March 2016, 22:57:40 UTC |
| de8e25b | Avinash Ramu | 17 March 2016, 22:30:37 UTC | Incorporate suggestions from #1292 | 17 March 2016, 22:30:37 UTC |
| 4684f4c | Avinash Ramu | 17 March 2016, 22:23:17 UTC | Incorporate suggestions from #1292 | 17 March 2016, 22:23:17 UTC |
| 88ccc65 | Thomas B. Mooney | 17 March 2016, 19:29:16 UTC | Merge pull request #1311 from tmooney/replace_no_lsf_with_inline_backend Replace NO_LSF with "inline" Backend | 17 March 2016, 19:29:16 UTC |
| 4e9281e | Avi Ramu | 17 March 2016, 17:17:57 UTC | Merge pull request #1314 from gatoravi/mutation-spectrum-fix Skip mutation spectrum on empty input | 17 March 2016, 17:17:57 UTC |
| ef92111 | Thomas B. Mooney | 16 March 2016, 21:34:49 UTC | Merge pull request #1310 from tmooney/remove_old_refcov_result Remove old RefCov result. | 16 March 2016, 21:34:49 UTC |
| 8df1ad3 | Thomas Mooney | 16 March 2016, 21:06:20 UTC | AlignAndMerge can now be run multiple times within the same dispatcher. AlignAndMerge was claiming global input names, which leads to conflicts if the instrument data do not all come from the same merge group. (The new testcase demonstrates this situation and passes with this change.) | 16 March 2016, 21:06:20 UTC |
| 53a5f78 | Thomas Mooney | 16 March 2016, 20:44:44 UTC | Fix determination of reference and instrument_data for AlignAndMerge. * The reference selection coincidentally worked by convention since we usually use the same input name in the strategy. * The instrument data happened to work because we've heretofore wanted to align *all* the data when using AlignAndMerge, but we can't assume that's true. | 16 March 2016, 20:44:44 UTC |
| 8a47b69 | Avinash Ramu | 16 March 2016, 20:20:55 UTC | Skip mutation spectrum on empty input Currently this step attempts to run mutation spectrum sequence context on an empty input which causes the downstream R module to die unpredictably. We'd like to skip running this analysis when the tier1 variant file is empty. | 16 March 2016, 20:20:55 UTC |
| 526e5cc | Ben Ainscough | 15 March 2016, 19:29:55 UTC | Merge pull request #1309 from bainscou/master added check to see existence of wgs or exome | 15 March 2016, 19:29:55 UTC |
| e762cd7 | Ben Ainscough | 15 March 2016, 19:16:30 UTC | Remove tumor_model and normal_model call | 15 March 2016, 19:16:30 UTC |
| f7fb340 | Ben Ainscough | 15 March 2016, 16:06:15 UTC | Change ordering of check to look at exome first | 15 March 2016, 16:06:15 UTC |
| 03f60b3 | Jason Walker | 15 March 2016, 15:49:29 UTC | Merge pull request #1308 from jasonwalker80/make_tiering_bed_grch38 Tiering for GRCh38 | 15 March 2016, 15:49:29 UTC |
| 3e201ae | Avi Ramu | 15 March 2016, 14:29:27 UTC | Merge pull request #1307 from gatoravi/loh_empty_files Make FilterFalsePositives not die on empty input. | 15 March 2016, 14:29:27 UTC |
| 508ec01 | Thomas Mooney | 14 March 2016, 22:41:43 UTC | Remove NO_LSF environment variable from tests not running workflows. This should have no effect on these tests. | 15 March 2016, 13:01:05 UTC |
| d7ab52c | Thomas Mooney | 14 March 2016, 20:47:49 UTC | Replace NO_LSF=1 with inline workflow_builder_backend. | 15 March 2016, 13:01:05 UTC |
| 06fec11 | Thomas Mooney | 14 March 2016, 21:06:02 UTC | Remove old RefCov result. This appears to be unused--there are no rows in the DB for this result. | 14 March 2016, 21:11:44 UTC |
| 25cc09e | Ben Ainscough | 14 March 2016, 20:05:41 UTC | added check to see existence of wgs or exome | 14 March 2016, 20:05:41 UTC |
| 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 |
| bd86e22 | Jason Walker | 14 March 2016, 15:02:09 UTC | organize if/else as a hash of IDs to directories. | 14 March 2016, 15:02:09 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 |
| ba98a03 | Avinash Ramu | 11 March 2016, 22:55:56 UTC | Don't die on empty input. This step is run as a part of the LOH pipeline. Currently if the variant file that is passed to this module is empty, the workflow crashes with an error message(bam-readcount is invoked with an empty file which causes it to die). Instead I think we'd like this module to spit out a warning and not attempt to filter if the input is empty. | 11 March 2016, 22:55:56 UTC |
| 5ee49ca | Avinash Ramu | 11 March 2016, 21:59:05 UTC | Add ideogram for hg38 | 11 March 2016, 21:59:05 UTC |
| cfddf2f | Avinash Ramu | 11 March 2016, 21:57:48 UTC | Ignore case while checking reference base. The new reference is soft-masked, this means that regions of low complexity are in lower-case [A,C,G,T,N]. This check should pass in those regions. | 11 March 2016, 21:57:48 UTC |
| cdef72f | Avinash Ramu | 11 March 2016, 21:57:24 UTC | Remove unused variable $reference_build_ncbi_n | 11 March 2016, 21:57:24 UTC |
| d92ad82 | Avinash Ramu | 11 March 2016, 21:56:17 UTC | Skip KI contigs | 11 March 2016, 21:56:17 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 |
| f4e8b8c | Jason Walker | 10 March 2016, 17:03:37 UTC | Add a UCSC tiering directory for GRCh38 reference sequence build. | 10 March 2016, 17:03:37 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 |
| 4ec9d0b | Malachi Griffith | 04 March 2016, 19:38:50 UTC | update igv session commands to work with the build38 used by cancer genomics | 04 March 2016, 19:38:50 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 |
