| 3a82e98 | Avinash Ramu | 03 June 2014, 22:19:32 UTC | don't diff jpegs | 03 June 2014, 22:19:53 UTC |
| 6db380e | ygindin | 03 June 2014, 22:15:47 UTC | Add OncoPrint | 03 June 2014, 22:15:47 UTC |
| fe901d0 | Avinash Ramu | 03 June 2014, 21:54:01 UTC | update clin-seq blessed | 03 June 2014, 21:56:46 UTC |
| ee90fb6 | Avinash Ramu | 03 June 2014, 21:53:14 UTC | update test data | 03 June 2014, 21:56:45 UTC |
| 9645148 | Avinash Ramu | 03 June 2014, 19:43:38 UTC | undo test change | 03 June 2014, 21:56:45 UTC |
| 139e4e6 | Avinash Ramu | 03 June 2014, 19:41:47 UTC | get lrr from function | 03 June 2014, 21:56:44 UTC |
| 5364671 | Avinash Ramu | 03 June 2014, 16:29:43 UTC | add checks to bam-qc tools | 03 June 2014, 21:56:44 UTC |
| 83ccc9f | Avinash Ramu | 03 June 2014, 16:28:32 UTC | add cnview to exome-cnv | 03 June 2014, 21:56:43 UTC |
| 9693d2d | Nathaniel Nutter | 03 June 2014, 20:19:42 UTC | remove write instead of setting absolute permissions | 03 June 2014, 21:03:15 UTC |
| 7321a94 | Nathaniel Nutter | 03 June 2014, 20:30:41 UTC | remove write instead of setting absolute permissions | 03 June 2014, 21:02:26 UTC |
| 8f21491 | Nathaniel Nutter | 03 June 2014, 20:03:36 UTC | remove write instead of setting absolute permissions | 03 June 2014, 21:01:44 UTC |
| 35429fd | Nathaniel Nutter | 02 June 2014, 19:59:31 UTC | don't need to check regex first | 03 June 2014, 21:00:58 UTC |
| 7ab1e28 | Nathaniel Nutter | 03 June 2014, 21:00:16 UTC | remove write instead of setting absolute permissions | 03 June 2014, 21:00:16 UTC |
| 1cb4d2c | Nathaniel Nutter | 03 June 2014, 20:59:26 UTC | make setgid optional, transient was still preventing commit | 03 June 2014, 20:59:26 UTC |
| b74b244 | Thomas Mooney | 03 June 2014, 20:27:43 UTC | Add api v5 with Picard 1.113 | 03 June 2014, 20:27:43 UTC |
| 4291332 | Feiyu Du | 03 June 2014, 19:28:04 UTC | add ref_seq_build check | 03 June 2014, 19:28:04 UTC |
| 3d203f4 | APipe Tester | 03 June 2014, 17:19:22 UTC | updated jenkins submodule to 7d04db6 | 03 June 2014, 17:19:22 UTC |
| 2a0f3f4 | APipe Tester | 03 June 2014, 12:17:31 UTC | Updated `genome` tab completion. | 03 June 2014, 12:17:31 UTC |
| 9fa4454 | APipe Tester | 03 June 2014, 12:15:53 UTC | Updated class browser cache. | 03 June 2014, 12:15:53 UTC |
| b437395 | Nathaniel Nutter | 02 June 2014, 21:32:36 UTC | sort use statements | 03 June 2014, 02:14:35 UTC |
| 1606150 | Nathaniel Nutter | 02 June 2014, 21:30:11 UTC | preserve setgid bit when chowning Due, I think, to root_squash on NFS the setgid bit is not preserved when chowning even though it would be on a local filesystem. Therefore, this should more correctly model Linux's default behavior. | 03 June 2014, 02:14:34 UTC |
| f036861 | Nathaniel Nutter | 02 June 2014, 21:11:29 UTC | switch to 'mode' | 03 June 2014, 02:14:32 UTC |
| 4a88bd0 | Nathaniel Nutter | 02 June 2014, 21:04:00 UTC | switch to File::stat | 03 June 2014, 02:14:31 UTC |
| 481ff93 | Nathaniel Nutter | 02 June 2014, 21:01:36 UTC | sort use statements | 03 June 2014, 02:14:29 UTC |
| cd33249 | APipe Tester | 02 June 2014, 21:04:39 UTC | updated ur submodule to f9a7c8d | 02 June 2014, 21:04:39 UTC |
| 2c28fbc | APipe Tester | 02 June 2014, 20:12:22 UTC | updated ur submodule to 0b8c6be | 02 June 2014, 20:12:22 UTC |
| 0ddc7b2 | Nathaniel Nutter | 02 June 2014, 20:00:14 UTC | add add/rm method and additional accessors to 'mode' objects | 02 June 2014, 20:01:32 UTC |
| 6cd3cce | Nathaniel Nutter | 02 June 2014, 19:49:21 UTC | check initial and final permissions in case of side effects | 02 June 2014, 20:01:30 UTC |
| 551c0bf | Nathaniel Nutter | 02 June 2014, 19:52:21 UTC | add all_* methods | 02 June 2014, 20:01:28 UTC |
| 1d45175 | Nathaniel Nutter | 02 June 2014, 19:48:55 UTC | add mode, path, and perm instance methods | 02 June 2014, 20:01:26 UTC |
| 23632ac | Nathaniel Nutter | 02 June 2014, 19:28:45 UTC | flip bit/name hash I'm going to add some compound bits so I want to move the bit to the RHS. | 02 June 2014, 20:01:24 UTC |
| 3c7c2db | Nathaniel Nutter | 02 June 2014, 19:21:06 UTC | extract method: set_mode | 02 June 2014, 20:01:22 UTC |
| 0bed757 | Nathaniel Nutter | 02 June 2014, 18:59:10 UTC | add the add/rm methods | 02 June 2014, 20:01:21 UTC |
| 52d6291 | Nathaniel Nutter | 02 June 2014, 18:24:52 UTC | refactor to allow additional methods to be added | 02 June 2014, 20:01:18 UTC |
| d949340 | dmorton | 02 June 2014, 19:14:55 UTC | Use Memoize instead of caching by hand | 02 June 2014, 19:15:14 UTC |
| 91f09eb | Nathaniel Nutter | 30 May 2014, 23:00:20 UTC | add --queue option to unarchive command | 02 June 2014, 19:05:18 UTC |
| 2d5bce6 | Nathaniel Nutter | 02 June 2014, 16:29:12 UTC | refactor file mode tests into new module Refactor Genome::Utility::Test::Stat into Genome::Utility::File::Mode. Implementing as a Test::Builder module limited reuse and defined unnecessary test methods. | 02 June 2014, 16:31:26 UTC |
| 2dc6418 | Nathaniel Nutter | 02 June 2014, 16:26:59 UTC | remove deprecated module | 02 June 2014, 16:31:25 UTC |
| 4147a53 | Nathaniel Nutter | 02 June 2014, 16:26:36 UTC | rename test | 02 June 2014, 16:31:24 UTC |
| 08a21fc | Nathaniel Nutter | 02 June 2014, 16:25:53 UTC | convert test to use 'mode' instead of 'has_bit' | 02 June 2014, 16:31:22 UTC |
| 44299d1 | Nathaniel Nutter | 02 June 2014, 16:11:48 UTC | convert test to use 'mode' instead of 'has_bit' | 02 June 2014, 16:31:21 UTC |
| bed83fb | Nathaniel Nutter | 02 June 2014, 15:59:55 UTC | remove duplicated functionality | 02 June 2014, 16:31:19 UTC |
| 12d5d8c | Nathaniel Nutter | 02 June 2014, 15:59:34 UTC | add Genome::Utility::File::Mode | 02 June 2014, 16:31:18 UTC |
| a5337d1 | Nathaniel Nutter | 02 June 2014, 15:50:37 UTC | fix typo | 02 June 2014, 16:31:16 UTC |
| 5fbda39 | Eddie Belter | 02 June 2014, 16:00:33 UTC | InstData: update lister doc | 02 June 2014, 16:00:33 UTC |
| 2edce28 | Mark Burnett | 02 June 2014, 12:35:27 UTC | G:S:Lock: use 2 hour TTL with Nessy | 02 June 2014, 12:35:27 UTC |
| dc20022 | dmorton | 01 June 2014, 21:21:19 UTC | Fix some missed renames | 01 June 2014, 21:21:19 UTC |
| 135c348 | dmorton | 01 June 2014, 20:32:14 UTC | Fix test and print message about errors. | 01 June 2014, 20:32:14 UTC |
| 3ece69b | dmorton | 01 June 2014, 20:23:26 UTC | Bugfix: Generate more correct header when splitting vep entries | 01 June 2014, 20:24:13 UTC |
| 42b91ed | APipe Tester | 31 May 2014, 12:18:18 UTC | Updated `genome` tab completion. | 31 May 2014, 12:18:18 UTC |
| d276195 | APipe Tester | 31 May 2014, 12:16:40 UTC | Updated class browser cache. | 31 May 2014, 12:16:40 UTC |
| 930559e | Dave Larson | 31 May 2014, 03:31:42 UTC | draft of tool for exome qc metrics for ADSP | 31 May 2014, 03:31:50 UTC |
| c7fcc81 | APipe Tester | 30 May 2014, 23:24:36 UTC | updated ur submodule to 658e160 | 30 May 2014, 23:24:36 UTC |
| 8f500e3 | dmorton | 30 May 2014, 18:16:34 UTC | Bugfix: Vep plugin runtime configuration points to proper locations | 30 May 2014, 20:54:12 UTC |
| 84bfdca | dmorton | 30 May 2014, 16:59:38 UTC | Renamed Genome::Annotation to Genome::VariantReporting | 30 May 2014, 20:54:12 UTC |
| 01d53b2 | APipe Tester | 30 May 2014, 20:52:47 UTC | updated ur submodule to 95b19dc | 30 May 2014, 20:52:47 UTC |
| d7ba99b | APipe Tester | 30 May 2014, 18:53:12 UTC | updated ur submodule to 9211480 | 30 May 2014, 18:53:12 UTC |
| 04ff67e | apregier | 30 May 2014, 18:31:31 UTC | Merge branch 'updated' into gb_master | 30 May 2014, 18:31:31 UTC |
| 9c1a1fe | apregier | 30 May 2014, 18:26:18 UTC | Use default empty hash so we can always set new entries | 30 May 2014, 18:29:44 UTC |
| e083d98 | apregier | 27 May 2014, 20:44:40 UTC | Tumor-only report | 30 May 2014, 18:29:43 UTC |
| d245946 | apregier | 27 May 2014, 19:56:43 UTC | Gmaf interpreter | 30 May 2014, 18:29:43 UTC |
| 6c48f63 | apregier | 27 May 2014, 19:48:45 UTC | Add gmaf filter | 30 May 2014, 18:29:42 UTC |
| 73632c7 | apregier | 27 May 2014, 19:42:57 UTC | strand and transcript_status not available from vep | 30 May 2014, 18:29:42 UTC |
| d614f3f | apregier | 27 May 2014, 19:41:32 UTC | bed file for vep needs to be processed and sorted Since FeatureList.t now calls processed_bed_file with two different sets of parameters, we need to make sure that the processed bed file gets recalculated if the parameters are different. To do this, we calculate a processed_bed_file_name based on the parameters and cache each processed_bed_file in a hash with the name as a key | 30 May 2014, 18:29:41 UTC |
| 5ac6990 | apregier | 27 May 2014, 19:40:20 UTC | Needs to implement requires_experts | 30 May 2014, 18:29:41 UTC |
| d050cee | apregier | 27 May 2014, 19:38:30 UTC | Dbsnp needs result_class defined | 30 May 2014, 18:29:40 UTC |
| 0b939af | apregier | 27 May 2014, 19:36:57 UTC | Interpreters also need their params translated | 30 May 2014, 18:29:40 UTC |
| 93cd6cc | apregier | 23 May 2014, 15:13:53 UTC | Add ref_count and var_count to vaf interpreter | 30 May 2014, 18:29:39 UTC |
| a42b09b | APipe Tester | 30 May 2014, 12:17:37 UTC | Updated `genome` tab completion. | 30 May 2014, 12:17:37 UTC |
| 16ada9e | APipe Tester | 30 May 2014, 12:16:01 UTC | Updated class browser cache. | 30 May 2014, 12:16:01 UTC |
| 0d0b2c8 | Gabriel Sanderson | 29 May 2014, 21:12:48 UTC | Avoid crashing when info is undefined. | 29 May 2014, 21:21:22 UTC |
| ef6ad1d | Gabriel Sanderson | 29 May 2014, 21:05:36 UTC | Avoid crashing when transcripts comes back undefined. | 29 May 2014, 21:21:21 UTC |
| cb5e182 | Nathaniel Nutter | 29 May 2014, 18:10:07 UTC | add ability to assign new model to model-group | 29 May 2014, 20:29:50 UTC |
| ab3fd27 | Nathaniel Nutter | 29 May 2014, 18:08:40 UTC | truncate log messages that are longer than MAX_SYSLOG_MSG_LEN | 29 May 2014, 20:29:48 UTC |
| 8039355 | Nathaniel Nutter | 27 May 2014, 14:21:48 UTC | get supported archive types from the archive operation | 29 May 2014, 20:29:47 UTC |
| c1eeb5a | Nathaniel Nutter | 27 May 2014, 14:21:08 UTC | extract method: _operation_class_from_name | 29 May 2014, 20:29:45 UTC |
| 4fd78fa | Eddie Belter | 29 May 2014, 20:04:17 UTC | VarReport: changed coverage/vaf mapping handling in filter | 29 May 2014, 20:05:11 UTC |
| 45ad246 | Eddie Belter | 29 May 2014, 17:53:53 UTC | Variant Report: add coverage vaf filter | 29 May 2014, 20:05:09 UTC |
| 2208c3d | apregier | 28 May 2014, 18:52:29 UTC | Switch return values to reflect max | 29 May 2014, 20:05:08 UTC |
| feb1845 | apregier | 28 May 2014, 18:51:13 UTC | Rename to max | 29 May 2014, 20:05:08 UTC |
| c55240e | Eddie Belter | 27 May 2014, 22:19:26 UTC | Annotation: filter for indel size | 29 May 2014, 20:05:06 UTC |
| ea13b99 | Nathaniel Nutter | 29 May 2014, 19:03:12 UTC | missing newline in logger output (breaks TAP also) | 29 May 2014, 19:03:12 UTC |
| 4c7639f | Nathaniel Nutter | 29 May 2014, 15:34:31 UTC | remove 'run_as' customizations to _launch 'run_as' is now handled outside the code so these customizations are no longer needed | 29 May 2014, 18:18:31 UTC |
| 058095b | Nathaniel Nutter | 29 May 2014, 15:29:20 UTC | remove BuildQueuedModels This was "simplified" into "two" pieces. The first just lists model IDs to build, i.e. ListBuildQueue, taking into account customizations we made in BuildQueuedModels, e.g. genotype first. The second could just be the standard start command however since we also are supporting the 'run_as' behaviour in practice it would be an alternate tool that handles 'run_as'. | 29 May 2014, 18:18:29 UTC |
| 0f66e82 | Nathaniel Nutter | 29 May 2014, 15:26:27 UTC | multiple changes to ListBuildQueue - Add type_name != 'genotype microarray' to the second iterator. - Loop over each run_as value so that we don't have to iterate through the whole list of queued models. | 29 May 2014, 18:18:28 UTC |
| 1186ba9 | Gabriel Sanderson | 29 May 2014, 17:47:20 UTC | Fix crash bug when we have no params | 29 May 2014, 17:47:35 UTC |
| 154f699 | Gabriel Sanderson | 27 May 2014, 20:06:07 UTC | Raise priority of VEP so it runs before FPKM. | 29 May 2014, 17:47:35 UTC |
| d77c788 | Thomas Mooney | 29 May 2014, 15:33:23 UTC | Remove duplicate variable declaration. | 29 May 2014, 15:33:23 UTC |
| a6c0fd2 | Thomas Mooney | 29 May 2014, 15:32:21 UTC | whitespace | 29 May 2014, 15:33:03 UTC |
| f12fc52 | Thomas Mooney | 29 May 2014, 15:02:37 UTC | Add a test for the downsample command. | 29 May 2014, 15:02:37 UTC |
| 54dcb8d | Thomas Mooney | 29 May 2014, 15:02:04 UTC | Simplify library creation now that is has locked construction. | 29 May 2014, 15:02:04 UTC |
| c63eb0e | Thomas Mooney | 29 May 2014, 14:50:22 UTC | Reconnect downsample command to imported instrument data. | 29 May 2014, 14:59:28 UTC |
| df986ea | Dave Larson | 29 May 2014, 13:40:42 UTC | Remove any trace of the lolli stick if suppressing the labels | 29 May 2014, 13:40:42 UTC |
| f9478f2 | APipe Tester | 29 May 2014, 12:17:22 UTC | Updated `genome` tab completion. | 29 May 2014, 12:17:22 UTC |
| 8638387 | APipe Tester | 29 May 2014, 12:15:49 UTC | Updated class browser cache. | 29 May 2014, 12:15:49 UTC |
| 95d9913 | Dave Larson | 29 May 2014, 02:42:07 UTC | * Add option to suppress labels below max frequency * Change default length of lolli sticks | 29 May 2014, 02:42:07 UTC |
| 19c47d8 | Nathaniel Nutter | 28 May 2014, 20:33:25 UTC | simplify ListBuildQueue | 28 May 2014, 22:10:27 UTC |
| 6505eba | Avinash Ramu | 28 May 2014, 21:55:53 UTC | update clinseq blessed | 28 May 2014, 21:56:44 UTC |
| 3e62737 | Avinash Ramu | 28 May 2014, 20:34:24 UTC | do not regenerate single bam cnvs | 28 May 2014, 21:56:44 UTC |
| b3a04be | Avinash Ramu | 28 May 2014, 20:28:04 UTC | update test data | 28 May 2014, 21:56:43 UTC |
