| ff32652 | APipe Tester | 29 October 2013, 12:18:37 UTC | Updated `gmt` tab completion. | 29 October 2013, 12:18:37 UTC |
| 7c60a01 | APipe Tester | 29 October 2013, 12:17:48 UTC | Updated `genome` tab completion. | 29 October 2013, 12:17:48 UTC |
| 3ad8e3c | APipe Tester | 29 October 2013, 12:16:01 UTC | Updated class browser cache. | 29 October 2013, 12:16:01 UTC |
| adaa33c | Thomas Mooney | 28 October 2013, 22:32:56 UTC | Changes to more efficiently grab the models for the entities. Call a different optimized path based on the class of entity we're looking up. | 28 October 2013, 22:32:56 UTC |
| dd1f48f | dmorton | 28 October 2013, 20:24:32 UTC | Move tmp directory creation back into loop The temp directory/directories need to be made in the loop or the files will not be uniquely named. | 28 October 2013, 20:35:14 UTC |
| 44b2a91 | Jim Weible | 28 October 2013, 20:22:35 UTC | add a test | 28 October 2013, 20:22:46 UTC |
| d7bba5b | Jim Weible | 28 October 2013, 20:22:19 UTC | fix bugs | 28 October 2013, 20:22:46 UTC |
| 66bd550 | Jim Weible | 28 October 2013, 20:19:59 UTC | grab allocations correctly | 28 October 2013, 20:22:45 UTC |
| 43af83c | Mark Burnett | 28 October 2013, 18:56:05 UTC | add tests for allocation file permission setting | 28 October 2013, 18:57:05 UTC |
| e23636c | Jim Weible | 28 October 2013, 18:14:32 UTC | lister for copycat annotation data | 28 October 2013, 18:14:32 UTC |
| 78cee39 | Mark Burnett | 28 October 2013, 15:41:32 UTC | add AddAnnotationData command for CopyCat | 28 October 2013, 15:41:32 UTC |
| 87e0134 | Mark Burnett | 28 October 2013, 15:41:09 UTC | add AnnotationData software result for CopyCat | 28 October 2013, 15:41:09 UTC |
| b68b4d1 | Mark Burnett | 28 October 2013, 15:38:09 UTC | add set_permissions_read_only This method depends on File::Find::Rule, which needs to be included in genome-snapshot-deps still. | 28 October 2013, 15:38:09 UTC |
| 96dd7e3 | Thomas Mooney | 28 October 2013, 14:20:49 UTC | Don't count LqUnion results as candidates for the final result. | 28 October 2013, 14:20:49 UTC |
| 1845d28 | APipe Tester | 28 October 2013, 12:16:10 UTC | Updated `genome` tab completion. | 28 October 2013, 12:16:10 UTC |
| ab924d8 | APipe Tester | 27 October 2013, 12:17:12 UTC | Updated `genome` tab completion. | 27 October 2013, 12:17:12 UTC |
| 7d428ea | APipe Tester | 26 October 2013, 12:17:23 UTC | Updated `genome` tab completion. | 26 October 2013, 12:17:23 UTC |
| 23c5a83 | Ian Ferguson | 25 October 2013, 22:49:10 UTC | Use debug_message in AlignmentResult/Bwasw | 25 October 2013, 22:51:42 UTC |
| 1a6d979 | Ian Ferguson | 25 October 2013, 22:47:33 UTC | Disconnect dbhandle in AlignmentResult/Bwasw | 25 October 2013, 22:51:42 UTC |
| ce5159c | Ian Ferguson | 25 October 2013, 22:04:55 UTC | Add comments to AlignmentResult/Bwasw | 25 October 2013, 22:51:41 UTC |
| 61a2be8 | APipe Tester | 25 October 2013, 22:30:57 UTC | Updated `genome` tab completion. | 25 October 2013, 22:30:57 UTC |
| 24c3345 | APipe Tester | 25 October 2013, 22:26:07 UTC | Updated `genome` tab completion. | 25 October 2013, 22:26:07 UTC |
| b1d9192 | APipe Tester | 25 October 2013, 22:20:43 UTC | Updated `genome` tab completion. | 25 October 2013, 22:20:43 UTC |
| 0331c8c | APipe Tester | 25 October 2013, 22:15:59 UTC | Updated `genome` tab completion. | 25 October 2013, 22:15:59 UTC |
| b479c07 | APipe Tester | 25 October 2013, 22:11:24 UTC | Updated `genome` tab completion. | 25 October 2013, 22:11:24 UTC |
| 103c1a7 | APipe Tester | 25 October 2013, 22:06:57 UTC | Updated `gmt` tab completion. | 25 October 2013, 22:06:57 UTC |
| 73565bb | APipe Tester | 25 October 2013, 22:06:01 UTC | Updated `genome` tab completion. | 25 October 2013, 22:06:01 UTC |
| 2d4cd88 | APipe Tester | 25 October 2013, 22:04:20 UTC | Updated class browser cache. | 25 October 2013, 22:04:20 UTC |
| a896c24 | APipe Tester | 25 October 2013, 22:00:44 UTC | Updated `genome` tab completion. | 25 October 2013, 22:01:41 UTC |
| fe8acea | Feiyu Du | 25 October 2013, 21:59:55 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 October 2013, 21:59:55 UTC |
| 887da4b | Feiyu Du | 25 October 2013, 21:56:31 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 October 2013, 21:56:31 UTC |
| 2b3b212 | Feiyu Du | 25 October 2013, 21:56:21 UTC | change to Command::V2 | 25 October 2013, 21:56:21 UTC |
| 95bbdcb | APipe Tester | 25 October 2013, 21:55:52 UTC | Updated `genome` tab completion. | 25 October 2013, 21:55:52 UTC |
| 0cf4952 | APipe Tester | 25 October 2013, 21:50:16 UTC | Updated `genome` tab completion. | 25 October 2013, 21:50:16 UTC |
| 25c5ebc | APipe Tester | 25 October 2013, 21:44:53 UTC | Updated `genome` tab completion. | 25 October 2013, 21:44:53 UTC |
| 1301823 | APipe Tester | 25 October 2013, 21:39:19 UTC | Updated `genome` tab completion. | 25 October 2013, 21:39:19 UTC |
| 33f2903 | APipe Tester | 25 October 2013, 21:34:09 UTC | Updated `genome` tab completion. | 25 October 2013, 21:34:09 UTC |
| 33f833e | APipe Tester | 25 October 2013, 21:28:30 UTC | Updated `genome` tab completion. | 25 October 2013, 21:28:30 UTC |
| 0797b4a | APipe Tester | 25 October 2013, 21:23:46 UTC | Updated `genome` tab completion. | 25 October 2013, 21:23:46 UTC |
| 226e9b9 | APipe Tester | 25 October 2013, 19:19:59 UTC | Updated `genome` tab completion. | 25 October 2013, 19:19:59 UTC |
| fcd1839 | APipe Tester | 25 October 2013, 19:15:06 UTC | Updated `genome` tab completion. | 25 October 2013, 19:15:06 UTC |
| 69bcd15 | APipe Tester | 25 October 2013, 19:09:59 UTC | Updated `genome` tab completion. | 25 October 2013, 19:09:59 UTC |
| cf4c7b0 | APipe Tester | 25 October 2013, 19:05:08 UTC | Updated `genome` tab completion. | 25 October 2013, 19:05:08 UTC |
| 03dd413 | APipe Tester | 25 October 2013, 19:00:06 UTC | Updated `genome` tab completion. | 25 October 2013, 19:00:06 UTC |
| 18fc2f5 | APipe Tester | 25 October 2013, 18:55:16 UTC | Updated `genome` tab completion. | 25 October 2013, 18:55:16 UTC |
| 39a7d8c | APipe Tester | 25 October 2013, 18:50:27 UTC | Updated `genome` tab completion. | 25 October 2013, 18:50:27 UTC |
| 1ac06ef | Ben Ainscough | 25 October 2013, 18:29:08 UTC | updated version of circos | 25 October 2013, 18:29:08 UTC |
| bcabbc1 | Jasreet Hundal | 25 October 2013, 17:00:37 UTC | Updated help | 25 October 2013, 17:00:37 UTC |
| d921f2e | APipe Tester | 25 October 2013, 11:19:10 UTC | Updated `genome` tab completion. | 25 October 2013, 11:19:10 UTC |
| 766d01b | APipe Tester | 25 October 2013, 06:05:47 UTC | Updated `genome` tab completion. | 25 October 2013, 06:05:47 UTC |
| 55132dc | Nathan Nutter | 25 October 2013, 01:51:02 UTC | looks like a bunch of things got renamed to tst1 | 25 October 2013, 01:52:20 UTC |
| 0efc99d | Adam Coffman | 24 October 2013, 23:43:19 UTC | purging should set kb_{used,requested} to 0 | 24 October 2013, 23:43:19 UTC |
| f89a011 | Thomas Mooney | 24 October 2013, 22:23:25 UTC | Skip any parts that don't point to valid entities. | 24 October 2013, 22:23:25 UTC |
| 949d7a4 | Ben Ainscough | 24 October 2013, 22:12:27 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 24 October 2013, 22:12:27 UTC |
| 914bf35 | Ben Ainscough | 24 October 2013, 22:11:01 UTC | updated regex for snvs and indels to be more robust | 24 October 2013, 22:11:01 UTC |
| acf5f5e | APipe Tester | 24 October 2013, 22:10:31 UTC | Updated `gmt` tab completion. | 24 October 2013, 22:10:31 UTC |
| a075fca | APipe Tester | 24 October 2013, 22:09:43 UTC | Updated `genome` tab completion. | 24 October 2013, 22:09:43 UTC |
| a885235 | APipe Tester | 24 October 2013, 22:07:54 UTC | Updated class browser cache. | 24 October 2013, 22:07:54 UTC |
| d397a9e | Nathan Nutter | 24 October 2013, 20:32:50 UTC | remove skip over symlinks | 24 October 2013, 22:00:39 UTC |
| 7287c97 | Nathan Nutter | 24 October 2013, 21:52:53 UTC | looks like a bunch of things got renamed to tst1 | 24 October 2013, 21:52:53 UTC |
| 9ac9f8e | Adam Coffman | 24 October 2013, 21:01:55 UTC | add ability to purge allocations | 24 October 2013, 21:01:55 UTC |
| eec4e49 | Adam Coffman | 24 October 2013, 19:14:12 UTC | add create_file_summaries method to allocations | 24 October 2013, 19:14:12 UTC |
| 743d016 | Mark Burnett | 24 October 2013, 19:01:29 UTC | make `genome search` to be more like web search | 24 October 2013, 19:05:03 UTC |
| 6b98e84 | APipe Tester | 24 October 2013, 19:04:13 UTC | updated jenkins submodule to 9443f13 | 24 October 2013, 19:04:13 UTC |
| 2c219d9 | Adam Coffman | 24 October 2013, 18:52:57 UTC | add create_or_update method | 24 October 2013, 18:52:57 UTC |
| 5150d7a | Chris Miller | 24 October 2013, 18:28:23 UTC | adding somvar option | 24 October 2013, 18:28:53 UTC |
| 6fc1c0a | Adam Coffman | 24 October 2013, 18:23:40 UTC | add file summary objects to prepare for allocation purging | 24 October 2013, 18:23:40 UTC |
| 33cb819 | Nathan Nutter | 24 October 2013, 15:34:10 UTC | rm metric: disk.allocation.create.get_allocation_without_lock.selection Removed metric, disk.allocation.create.get_allocation_without_lock.selection, because it, more-or-less, completely overlapped another metric, disk.allocation.create.get_allocation_without_lock. | 24 October 2013, 15:34:10 UTC |
| c04fdc2 | Nathan Nutter | 24 October 2013, 14:30:57 UTC | add metric: disk.allocation.get_allocation_without_lock.rollback.over_used | 24 October 2013, 14:31:08 UTC |
| 3ee59e8 | Nathan Nutter | 24 October 2013, 14:30:35 UTC | add metric: disk.allocation.get_allocation_without_lock.rollback.over_allocated | 24 October 2013, 14:31:07 UTC |
| 286660a | APipe Tester | 24 October 2013, 14:25:52 UTC | Updated `genome` tab completion. | 24 October 2013, 14:25:52 UTC |
| 2fc7533 | Thomas Mooney | 24 October 2013, 13:37:38 UTC | Update the blessed build due to new fgenesh version. | 24 October 2013, 13:37:38 UTC |
| 8538776 | APipe Tester | 24 October 2013, 11:28:06 UTC | Updated `genome` tab completion. | 24 October 2013, 11:28:06 UTC |
| 3a1120f | APipe Tester | 24 October 2013, 11:26:29 UTC | Updated class browser cache. | 24 October 2013, 11:26:29 UTC |
| 3ad0fbd | Gabriel Sanderson | 23 October 2013, 23:32:16 UTC | Merge branch 'varscanparam' into gb_master | 23 October 2013, 23:32:16 UTC |
| 76a9ef9 | Gabriel Sanderson | 23 October 2013, 23:26:10 UTC | Corrected a bug that prevented baq from being turned off with --nobaq | 23 October 2013, 23:31:25 UTC |
| 684ca89 | Gabriel Sanderson | 23 October 2013, 23:06:06 UTC | Expanded VarscanBase test | 23 October 2013, 23:31:24 UTC |
| b5f8e69 | Gabriel Sanderson | 23 October 2013, 22:40:52 UTC | Move has_version into VarscanBase | 23 October 2013, 23:31:23 UTC |
| ac67136 | Gabriel Sanderson | 23 October 2013, 22:37:52 UTC | DV2 Varscan modules inherit from VarscanBase and _process_samtools_params and _split_params are moved up. | 23 October 2013, 23:31:23 UTC |
| 738bdf9 | Gabriel Sanderson | 23 October 2013, 22:33:28 UTC | Added VarscanBase | 23 October 2013, 23:31:22 UTC |
| d12468a | Gabriel Sanderson | 23 October 2013, 22:29:51 UTC | Enable samtools parameter processing in VarscanSomaticValidation (previously only worked in Varscan germline) | 23 October 2013, 23:31:21 UTC |
| f6dfd6a | Gabriel Sanderson | 23 October 2013, 22:25:58 UTC | Enable samtools parameter processing in VarscanSomatic (previously only worked in Varscan germline) | 23 October 2013, 23:31:21 UTC |
| 9d261f0 | Nathan Nutter | 23 October 2013, 22:50:10 UTC | allow expected/got count to be shown in diag | 23 October 2013, 23:12:09 UTC |
| 7fe1c6b | Nathan Nutter | 23 October 2013, 22:26:35 UTC | extract method: _existing_allocation_path_check | 23 October 2013, 23:12:08 UTC |
| 35a13e1 | Nathan Nutter | 23 October 2013, 22:14:15 UTC | add metric: disk.allocation.require | 23 October 2013, 23:12:07 UTC |
| 5ec72bf | Nathan Nutter | 23 October 2013, 21:58:39 UTC | add metric: disk.allocation.get_parent_allocation | 23 October 2013, 23:12:07 UTC |
| 59b8b0e | Nathan Nutter | 23 October 2013, 21:54:25 UTC | add metric: disk.allocation.child_allocation_query | 23 October 2013, 23:12:05 UTC |
| b163ec2 | Nathan Nutter | 23 October 2013, 21:42:21 UTC | push existing allocation_path down to _get_allocation_without_lock Checking that an allocation_path does not exist on every candidate volume is very slow due to having to mount the volume and stat a path. This pushes the check down to where each candidate volume is attempted rather than checking all candidate volumes. | 23 October 2013, 23:12:04 UTC |
| 8062269 | Nathan Nutter | 23 October 2013, 21:51:48 UTC | fix old typo | 23 October 2013, 23:12:03 UTC |
| ecc5101 | APipe Tester | 23 October 2013, 21:44:45 UTC | Updated `genome` tab completion. | 23 October 2013, 21:44:45 UTC |
| 010637b | APipe Tester | 23 October 2013, 21:43:14 UTC | Updated class browser cache. | 23 October 2013, 21:43:14 UTC |
| 37d1a20 | Mark Burnett | 23 October 2013, 18:57:01 UTC | make search work for multiple results | 23 October 2013, 21:05:23 UTC |
| 4bd0453 | Mark Burnett | 23 October 2013, 15:00:03 UTC | display single and many differently | 23 October 2013, 21:05:23 UTC |
| d91a3e2 | Mark Burnett | 23 October 2013, 14:07:30 UTC | update low score warning message | 23 October 2013, 21:05:22 UTC |
| ae63819 | Mark Burnett | 23 October 2013, 14:00:07 UTC | add basic model shower | 23 October 2013, 21:05:22 UTC |
| baed53f | Mark Burnett | 22 October 2013, 21:18:58 UTC | rename `genome show` to `genome search` | 23 October 2013, 21:05:21 UTC |
| 29ebf0b | Mark Burnett | 22 October 2013, 15:23:24 UTC | complete sketch of show command | 23 October 2013, 21:05:21 UTC |
| 175f9e6 | Mark Burnett | 22 October 2013, 14:22:35 UTC | add show to Genome::Command | 23 October 2013, 21:05:20 UTC |
| f408635 | Mark Burnett | 22 October 2013, 14:22:10 UTC | sort subcommands in Genome::Command | 23 October 2013, 21:05:20 UTC |
| 2f2fe27 | Mark Burnett | 22 October 2013, 14:21:42 UTC | whitespace | 23 October 2013, 21:05:19 UTC |
