| f5db12f | Gabriel Sanderson | 23 September 2014, 18:45:40 UTC | Always add our errors in (if any) before returning errors. | 25 September 2014, 15:33:51 UTC |
| d1f3ce1 | Gabriel Sanderson | 23 September 2014, 18:42:34 UTC | fix test output consistency | 25 September 2014, 15:33:48 UTC |
| 82efc80 | Gabriel Sanderson | 23 September 2014, 17:49:36 UTC | Find simple errors before the workflow starts. | 25 September 2014, 15:33:44 UTC |
| 9b49c7e | Gabriel Sanderson | 23 September 2014, 17:16:18 UTC | Test failure when nonexistant resource file or vcf provided | 25 September 2014, 15:33:40 UTC |
| 65c881c | Mark Burnett | 24 September 2014, 17:52:10 UTC | Merge pull request #57 from tmooney/dont_uncreate_new_owners Only reload the Allocation's owner if there's an existing object. | 24 September 2014, 17:52:10 UTC |
| 0f22266 | Jim Weible | 24 September 2014, 17:45:52 UTC | Merge pull request #36 from tmooney/tag_somval_subject_mappings Allow Tags in Subject Mapping Importer for Somatic Validation | 24 September 2014, 17:45:52 UTC |
| 646c643 | Mark Burnett | 24 September 2014, 13:05:25 UTC | Merge pull request #54 from mark-burnett/purge-archived-allocations Purge archived allocations | 24 September 2014, 13:05:25 UTC |
| 77e6fa6 | APipe Tester | 24 September 2014, 12:15:44 UTC | Updated `genome` tab completion. | 24 September 2014, 12:15:44 UTC |
| 95647db | APipe Tester | 24 September 2014, 12:14:15 UTC | Updated class browser cache. | 24 September 2014, 12:14:15 UTC |
| e609dfc | Thomas Mooney | 23 September 2014, 22:20:37 UTC | Query the context instead of inspecting object's internal hashref. | 23 September 2014, 22:20:37 UTC |
| d6eed9f | Feiyu Du | 23 September 2014, 21:54:08 UTC | Merge pull request #53 from dufeiyu/master Namespace change: G/VR/Framework/Command/ to G/VR/Command | 23 September 2014, 21:54:08 UTC |
| c3b7b1b | Thomas Mooney | 23 September 2014, 21:34:57 UTC | Only reload if there's an existing object. Otherwise the new object gets dropped instead. | 23 September 2014, 21:34:57 UTC |
| e464d84 | Eddie Belter | 23 September 2014, 21:15:43 UTC | Test Factory: improved disk allocation generate_obj | 23 September 2014, 21:15:43 UTC |
| 85a4ced | Mark Burnett | 23 September 2014, 20:03:04 UTC | D:Volume add clear error when missing trash_volume | 23 September 2014, 20:03:04 UTC |
| 893ea22 | Thomas B. Mooney | 23 September 2014, 19:40:29 UTC | Merge pull request #51 from tmooney/fix_sys_typo Spelling: spmething => something | 23 September 2014, 19:40:29 UTC |
| 61a6da7 | Feiyu Du | 23 September 2014, 18:03:58 UTC | relocate test sample_legend.tsv | 23 September 2014, 18:03:58 UTC |
| e8d2085 | Thomas B. Mooney | 23 September 2014, 17:57:48 UTC | Merge pull request #40 from tmooney/cqid_respects_tagging CQID Respects Tagging | 23 September 2014, 17:57:48 UTC |
| a87df7e | Eddie Belter | 18 September 2014, 23:16:04 UTC | InstData Import: make id first 6 chars of md5; use id as job name; display job name in status | 23 September 2014, 17:14:38 UTC |
| d2af6a1 | Eddie Belter | 18 September 2014, 20:04:25 UTC | InstData Import: added downsmaple ratio to imported instdata | 23 September 2014, 17:14:37 UTC |
| 10939be | Eddie Belter | 18 September 2014, 19:33:26 UTC | Instdata Import: add downsample option to generate file for reimport | 23 September 2014, 17:14:36 UTC |
| bb52afc | Eddie Belter | 18 September 2014, 19:32:57 UTC | InstData Import: try to get source file from bam path, then archive path when getting attrs for reimport | 23 September 2014, 17:14:36 UTC |
| a3b08b3 | Mark Burnett | 23 September 2014, 16:42:32 UTC | D:D:A:Purger expand _destination_dir() | 23 September 2014, 16:42:32 UTC |
| 34290f4 | Mark Burnett | 23 September 2014, 16:41:06 UTC | D:Allocation::_get_trash_folder returns allocation-specific dir | 23 September 2014, 16:41:06 UTC |
| 07ec8e3 | Feiyu Du | 23 September 2014, 16:30:17 UTC | Merge remote-tracking branch 'origin/master' | 23 September 2014, 16:30:17 UTC |
| ef9a20a | Mark Burnett | 23 September 2014, 16:11:00 UTC | D:Volume have database select trash volume by aggr | 23 September 2014, 16:11:00 UTC |
| 5932515 | Mark Burnett | 23 September 2014, 16:09:13 UTC | move get_trash_folder functionality to D:Volume | 23 September 2014, 16:09:13 UTC |
| 67fce4d | Feiyu Du | 23 September 2014, 15:51:21 UTC | update VR/Command mapping | 23 September 2014, 15:51:21 UTC |
| 5a3ae62 | Susanna Siebert | 23 September 2014, 14:28:52 UTC | Merge pull request #43 from susannasiebert/cle_sample_legend Write a legend file of the sample name and the label used to refer to it | 23 September 2014, 14:28:52 UTC |
| 5350a27 | Thomas Mooney | 23 September 2014, 14:02:42 UTC | Test that the correct columns are "extra". | 23 September 2014, 14:02:42 UTC |
| 0b7518e | Thomas Mooney | 23 September 2014, 13:57:51 UTC | Remove unused include. | 23 September 2014, 13:57:51 UTC |
| f6fffb7 | Mark Burnett | 23 September 2014, 13:28:09 UTC | D:D:A:Purger extract _update_allocation_status | 23 September 2014, 13:28:09 UTC |
| 91afbb6 | Mark Burnett | 23 September 2014, 13:27:11 UTC | D:D:A:Purger rename _add_timeline_event to _finalize_purge | 23 September 2014, 13:27:11 UTC |
| 20e8684 | Mark Burnett | 23 September 2014, 12:47:17 UTC | D:D:A:Purger purge archived allocations | 23 September 2014, 12:49:09 UTC |
| bed0ed1 | Mark Burnett | 23 September 2014, 12:46:27 UTC | D:D:A:Purger extract _purge_unarchived | 23 September 2014, 12:49:09 UTC |
| 95dfac4 | Mark Burnett | 23 September 2014, 12:41:27 UTC | whitespace | 23 September 2014, 12:49:09 UTC |
| b4a5c09 | Mark Burnett | 23 September 2014, 12:40:24 UTC | D:D:A:Purger extract _destination_dir method | 23 September 2014, 12:49:09 UTC |
| 7a84457 | Mark Burnett | 23 September 2014, 12:38:58 UTC | D:D:A:Purger extract _add_timeline_event | 23 September 2014, 12:49:09 UTC |
| e0120a0 | Thomas Mooney | 23 September 2014, 12:44:16 UTC | Revise file_path doc text for correctness. | 23 September 2014, 12:44:16 UTC |
| 2636e47 | APipe Tester | 23 September 2014, 12:17:08 UTC | Updated `gmt` tab completion. | 23 September 2014, 12:17:08 UTC |
| 8705cbb | APipe Tester | 23 September 2014, 12:16:23 UTC | Updated `genome` tab completion. | 23 September 2014, 12:16:23 UTC |
| 810e9a2 | APipe Tester | 23 September 2014, 12:14:44 UTC | Updated class browser cache. | 23 September 2014, 12:14:44 UTC |
| 9a7016d | Feiyu Du | 22 September 2014, 22:43:03 UTC | Change Genome/VariantReporting/Framework/Command/ to Genome/VariantReporting/Command/ | 22 September 2014, 22:43:03 UTC |
| 52fe963 | Dave Larson | 22 September 2014, 18:44:52 UTC | Merge pull request #46 from ernfrid/remove-downsample CHANGELOG: Remove genome model reference-alignment downsample command. | 22 September 2014, 18:44:52 UTC |
| 773878b | Thomas Mooney | 22 September 2014, 18:40:30 UTC | Spelling: spmething => something | 22 September 2014, 18:40:30 UTC |
| 200041b | Thomas Mooney | 22 September 2014, 17:35:29 UTC | Use List::MoreUtils::any as a shortcutting grep. | 22 September 2014, 17:35:29 UTC |
| 0dca7ee | Thomas Mooney | 22 September 2014, 17:31:39 UTC | Check that no spurious models are created when CQID fails. | 22 September 2014, 17:31:39 UTC |
| 814d905 | Mark Burnett | 22 September 2014, 15:08:50 UTC | Merge pull request #45 from nnutter/master _reload_allocation also gets called after allocations are deleted | 22 September 2014, 15:08:50 UTC |
| 590adfc | Mark Burnett | 22 September 2014, 15:04:29 UTC | Merge pull request #48 from mark-burnett/remove-bio-db-fasta Delete G:M:T:BioDbFasta* | 22 September 2014, 15:04:29 UTC |
| d1e3159 | Mark Burnett | 22 September 2014, 14:56:59 UTC | Merge pull request #42 from mark-burnett/fix-bam-readcount-header-skipping Skip possible header lines less aggressively in G:M:T:A:Coverage:BamReadcount | 22 September 2014, 14:56:59 UTC |
| 7922dfc | Mark Burnett | 22 September 2014, 14:49:29 UTC | delete G:M:T:BioDbFasta* | 22 September 2014, 14:49:29 UTC |
| 3c75f8b | Mark Burnett | 22 September 2014, 14:46:01 UTC | gmt a cov add- & bam-readcount: fix header regexes | 22 September 2014, 14:46:01 UTC |
| e7e2ae8 | Susanna Siebert | 22 September 2014, 14:22:53 UTC | Merge pull request #37 from susannasiebert/cle_legend_file Create a legend file for CLE reports | 22 September 2014, 14:22:53 UTC |
| ccb366f | Mark Burnett | 22 September 2014, 13:15:55 UTC | Merge pull request #44 from mark-burnett/fix-cleanup-archive-directory Fix G:D:A _cleanup_archive_directory | 22 September 2014, 13:15:55 UTC |
| 136be01 | Mark Burnett | 22 September 2014, 13:15:18 UTC | Merge pull request #39 from mark-burnett/delete-archived-allocation Allow archived disk allocations to be deleted directly from tape | 22 September 2014, 13:15:18 UTC |
| 1a5449c | Dave Larson | 21 September 2014, 03:25:18 UTC | CHANGELOG: Remove genome model reference-alignment downsample command. Downsampling is now best done via genome instrument-data import basic. | 21 September 2014, 03:25:18 UTC |
| 906ad1b | APipe Tester | 20 September 2014, 12:15:20 UTC | Updated `genome` tab completion. | 20 September 2014, 12:15:20 UTC |
| c6db398 | APipe Tester | 20 September 2014, 12:13:49 UTC | Updated class browser cache. | 20 September 2014, 12:13:49 UTC |
| 4d92317 | Nathaniel Nutter | 20 September 2014, 04:34:23 UTC | _reload_allocation also gets called after allocations are deleted | 20 September 2014, 04:34:23 UTC |
| 3ce2000 | Mark Burnett | 19 September 2014, 20:34:47 UTC | D:A notify of failure when `rm` from tape fails | 19 September 2014, 20:34:47 UTC |
| 469335e | Mark Burnett | 19 September 2014, 20:33:11 UTC | D:A bugfix - test whether $directory is a dir `-a` seems to test whether it's a file or directory, which does not seem to be the intent. | 19 September 2014, 20:33:11 UTC |
| 85f1899 | Mark Burnett | 19 September 2014, 20:32:57 UTC | D:A bugfix - invalid test syntax | 19 September 2014, 20:32:57 UTC |
| cd4cc9b | Susanna Siebert | 19 September 2014, 14:56:53 UTC | Write a sample legend alongside the resource.yaml file | 19 September 2014, 19:06:46 UTC |
| 90cbb92 | Susanna Siebert | 19 September 2014, 18:50:58 UTC | Encode the list of filters to be excluded from the legend file in a more generic way | 19 September 2014, 18:50:58 UTC |
| ae449bb | Susanna Siebert | 19 September 2014, 18:37:42 UTC | Bugfix: Legend file name needs to be unique When there are multiple reports in a plan file they will be written to the same directory. The legend files are unique to a report. With the old naming scheme the legend file names would clash if there were more than one. Now they're being created uniquely by using each report's name. | 19 September 2014, 18:37:42 UTC |
| 07fbad7 | Jason Walker | 19 September 2014, 17:48:03 UTC | Add the homopolymer filter/expert to the somatic indel report. | 19 September 2014, 17:48:03 UTC |
| 3f494de | Jason Walker | 19 September 2014, 17:31:05 UTC | Separate commands for gold evaluations. Also consolidate the germline/somatic wrappers into a ModelReport command. This time with the new wrappers added. | 19 September 2014, 17:31:05 UTC |
| a55054c | Jason Walker | 19 September 2014, 16:40:52 UTC | Separate commands for gold evaluations. Also consolidate the germline/somatic wrappers into a ModelReport command. | 19 September 2014, 16:40:52 UTC |
| a02ed2b | Mark Burnett | 19 September 2014, 15:28:55 UTC | gmt a cov bam-readcount - only check for header on first line | 19 September 2014, 15:28:55 UTC |
| dc5a0a3 | Mark Burnett | 19 September 2014, 15:26:57 UTC | gmt a cov bam-readcount - use same header regex as AddReadcounts | 19 September 2014, 15:26:57 UTC |
| 92348ac | Mark Burnett | 19 September 2014, 15:24:55 UTC | gmt a cov add-readcounts - simplify header regex | 19 September 2014, 15:24:55 UTC |
| 1ce2c94 | Jim Weible | 19 September 2014, 14:56:33 UTC | Merge pull request #41 from jweible/master Remove check for useless, deleted default database | 19 September 2014, 14:56:33 UTC |
| 1cd240b | Jim Weible | 19 September 2014, 13:04:23 UTC | Remove check for useless, deleted default database Despite evidence to the contrary, the user claims this is still in use. Remove the offending line in the test that references data she claims is not in use so that tests pass. | 19 September 2014, 13:04:23 UTC |
| 0c59396 | apregier | 18 September 2014, 22:10:40 UTC | Merge pull request #35 from apregier/indel_position Correctly report coordinates and alleles for indels | 18 September 2014, 22:10:40 UTC |
| 832c3b4 | apregier | 18 September 2014, 22:02:14 UTC | Move utility methods to G::Utility::Vcf | 18 September 2014, 22:02:14 UTC |
| 3ede914 | Thomas Mooney | 18 September 2014, 21:46:05 UTC | CQID respects tags set on mappings when deciding what models to create. | 18 September 2014, 21:46:05 UTC |
| 51a0fa6 | Thomas Mooney | 18 September 2014, 21:45:18 UTC | Set is_mutable so can add_tag() to these. | 18 September 2014, 21:45:18 UTC |
| f493588 | Mark Burnett | 18 September 2014, 21:33:18 UTC | D:A extract get_deletion_observers | 18 September 2014, 21:35:11 UTC |
| 0055b1b | Mark Burnett | 18 September 2014, 21:28:52 UTC | D:A move duplicate lines out of if/else | 18 September 2014, 21:28:52 UTC |
| e0e2a37 | Mark Burnett | 18 September 2014, 21:28:05 UTC | D:A delete archive inside commit observer | 18 September 2014, 21:28:05 UTC |
| a23ca5f | Mark Burnett | 18 September 2014, 21:18:00 UTC | whitespace | 18 September 2014, 21:18:00 UTC |
| 3bac170 | Mark Burnett | 18 September 2014, 21:17:21 UTC | D:A delete timeline events when deleting archived allocation | 18 September 2014, 21:17:21 UTC |
| 36c71d6 | Mark Burnett | 18 September 2014, 21:16:54 UTC | D:A extract _delete_timeline_events | 18 September 2014, 21:16:54 UTC |
| 1bb552a | Mark Burnett | 18 September 2014, 21:05:27 UTC | D:Allocation directly delete archived allocations | 18 September 2014, 21:05:27 UTC |
| 787a0e4 | apregier | 18 September 2014, 20:34:03 UTC | Make condition clearer | 18 September 2014, 20:34:03 UTC |
| a039f0d | apregier | 18 September 2014, 19:33:43 UTC | Use coordinate converter to get correct indel positions | 18 September 2014, 19:33:43 UTC |
| b892188 | apregier | 18 September 2014, 19:33:20 UTC | Update test so offset insertion is unambiguous | 18 September 2014, 19:33:20 UTC |
| 4d8fbc3 | Susanna Siebert | 18 September 2014, 19:16:19 UTC | make tests pass | 18 September 2014, 19:21:43 UTC |
| 17df87e | Susanna Siebert | 18 September 2014, 15:53:27 UTC | Field descriptions for interpreters | 18 September 2014, 19:21:42 UTC |
| 1b8b6fb | Susanna Siebert | 18 September 2014, 14:27:05 UTC | Framework for writing a legend file | 18 September 2014, 19:21:42 UTC |
| 68c2701 | Thomas B. Mooney | 18 September 2014, 19:15:38 UTC | Merge pull request #33 from tmooney/software_result_test_name_collision Reload the owner after taking action on a disk allocation. | 18 September 2014, 19:15:38 UTC |
| 13b432a | apregier | 18 September 2014, 18:45:15 UTC | Refactor - move coordinate converting code to a utility class | 18 September 2014, 18:45:54 UTC |
| b4d49f4 | Michael J. Kiwala | 18 September 2014, 17:23:45 UTC | update blessed gene-prediction-bacterial build | 18 September 2014, 17:24:48 UTC |
| a5e71fe | Thomas Mooney | 18 September 2014, 15:04:28 UTC | Consolidate get() attempts to single statement. | 18 September 2014, 15:08:17 UTC |
| a7aeee9 | Thomas Mooney | 18 September 2014, 14:55:54 UTC | Add support for setting tags when creating subject mappings. | 18 September 2014, 15:08:17 UTC |
| dfbc49e | Thomas Mooney | 18 September 2014, 14:53:47 UTC | Create add_ methods for links to profile items and subject mappings. | 18 September 2014, 14:53:47 UTC |
| b24fe8a | Thomas Mooney | 18 September 2014, 14:50:16 UTC | spelling: preceed* => preced* | 18 September 2014, 14:51:48 UTC |
| 5bded51 | Thomas Mooney | 18 September 2014, 14:34:32 UTC | Rename "ignore_extra_columns" to "allow_extra_columns". We're not just ignoring them any more! | 18 September 2014, 14:34:32 UTC |
| 8762c15 | Thomas Mooney | 18 September 2014, 14:28:46 UTC | Whitespace. | 18 September 2014, 14:28:46 UTC |
| d2ba0e1 | Thomas Mooney | 18 September 2014, 14:16:47 UTC | Allow access to the additional columns that were found. | 18 September 2014, 14:28:18 UTC |
| 914f36a | Thomas Mooney | 18 September 2014, 14:08:57 UTC | Whitespace. | 18 September 2014, 14:08:57 UTC |
