| 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 |
| 2968d15 | Avinash Ramu | 28 May 2014, 20:27:37 UTC | update converge stats | 28 May 2014, 21:56:43 UTC |
| a46a39d | Avinash Ramu | 28 May 2014, 20:27:04 UTC | update clin-seq file accessors | 28 May 2014, 21:56:42 UTC |
| ed5ba2f | Avinash Ramu | 28 May 2014, 02:13:42 UTC | whitespace | 28 May 2014, 21:56:42 UTC |
| 0edb47b | Avinash Ramu | 27 May 2014, 23:18:54 UTC | update test data | 28 May 2014, 21:56:42 UTC |
| de71acc | Avinash Ramu | 27 May 2014, 22:44:03 UTC | update wgs summary dir | 28 May 2014, 21:56:41 UTC |
| 7808a8b | Avinash Ramu | 27 May 2014, 22:37:53 UTC | update doc | 28 May 2014, 21:56:41 UTC |
| a05cc14 | Avinash Ramu | 26 May 2014, 04:50:09 UTC | add converge stats | 28 May 2014, 21:56:40 UTC |
| b200161 | Avinash Ramu | 26 May 2014, 04:49:18 UTC | skip header better | 28 May 2014, 21:56:40 UTC |
| 7d5489a | Avinash Ramu | 26 May 2014, 04:48:08 UTC | use builds to get bam-qc results See RT 99337 | 28 May 2014, 21:56:40 UTC |
| 5ef307f | Avinash Ramu | 26 May 2014, 04:47:08 UTC | fix data-type | 28 May 2014, 21:56:39 UTC |
| e0e4726 | Avinash Ramu | 26 May 2014, 04:46:10 UTC | handle copycat | 28 May 2014, 21:56:39 UTC |
| 618a75a | Avinash Ramu | 26 May 2014, 04:45:14 UTC | use rsync to skip bam copies | 28 May 2014, 21:56:38 UTC |
| 4a073fd | Avinash Ramu | 26 May 2014, 04:44:19 UTC | make runcnview handle copycat | 28 May 2014, 21:56:38 UTC |
| d682333 | Avinash Ramu | 26 May 2014, 04:43:43 UTC | add self | 28 May 2014, 21:56:38 UTC |
| 0410fff | Avinash Ramu | 26 May 2014, 04:43:11 UTC | whitespace | 28 May 2014, 21:56:37 UTC |
| 03bcc70 | Avinash Ramu | 26 May 2014, 04:42:08 UTC | make clonality handle copycat results | 28 May 2014, 21:56:37 UTC |
| 6160e31 | Avinash Ramu | 26 May 2014, 04:40:41 UTC | reorganize cnv summary | 28 May 2014, 21:56:36 UTC |
| 7552745 | Avinash Ramu | 23 May 2014, 18:11:34 UTC | add file accessors | 28 May 2014, 21:56:36 UTC |
| 133fabb | Avinash Ramu | 23 May 2014, 13:36:18 UTC | ignore header | 28 May 2014, 21:56:35 UTC |
| d7b85b0 | Avinash Ramu | 23 May 2014, 13:35:51 UTC | handle copycat | 28 May 2014, 21:56:35 UTC |
| 777f546 | Avinash Ramu | 23 May 2014, 13:35:29 UTC | whitespace | 28 May 2014, 21:56:35 UTC |
| d12499c | Avinash Ramu | 23 May 2014, 13:34:38 UTC | whitespace | 28 May 2014, 21:56:34 UTC |
| a2eede6 | Thomas Mooney | 28 May 2014, 21:25:10 UTC | Change test to test the new, not-so-different ordering. | 28 May 2014, 21:25:10 UTC |
| 0c0c62b | Thomas Mooney | 28 May 2014, 21:22:14 UTC | More reliable ordering of builds: use created_at (This goes with commit 105e45dfc433911cff8bac4bcbee1e8baa5b776e.) | 28 May 2014, 21:22:14 UTC |
| 105e45d | Thomas Mooney | 28 May 2014, 20:58:12 UTC | More reliable ordering of builds: use created_at | 28 May 2014, 20:58:12 UTC |
| fad638c | Thomas Mooney | 28 May 2014, 15:46:18 UTC | Add Analysis Projects to search. | 28 May 2014, 15:46:18 UTC |
| a268869 | Avinash Ramu | 28 May 2014, 15:19:13 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 May 2014, 15:19:13 UTC |
| bac3e00 | Avinash Ramu | 28 May 2014, 15:18:22 UTC | Merge branch 'master' of github.com:genome/gms-core | 28 May 2014, 15:18:22 UTC |
| 775dc65 | APipe Tester | 28 May 2014, 15:11:52 UTC | updated ur submodule to 8d96d64 | 28 May 2014, 15:11:52 UTC |
| 4367582 | Anthony Brummett | 23 May 2014, 16:20:07 UTC | rename function to better reflect what it does | 28 May 2014, 13:55:26 UTC |
| 4b5c52a | Anthony Brummett | 22 May 2014, 19:57:11 UTC | extract method to return a build's metrics as a hashref of metric_name => value | 28 May 2014, 13:55:26 UTC |
| dbf7bae | Anthony Brummett | 22 May 2014, 19:51:07 UTC | _diff_metrics_hashrefs() now deals with metric names and values, instead of names and metric objects | 28 May 2014, 13:55:25 UTC |
| 4a82587 | Anthony Brummett | 22 May 2014, 19:00:01 UTC | extract function to diff metrics hashrefs directly | 28 May 2014, 13:55:24 UTC |
| 121840e | Anthony Brummett | 22 May 2014, 18:49:46 UTC | extract method to remove ignored metrics | 28 May 2014, 13:55:24 UTC |
| 71a2552 | Anthony Brummett | 22 May 2014, 16:26:16 UTC | use map in the more standard way | 28 May 2014, 13:55:23 UTC |
| 69e15c6 | Avinash Ramu | 28 May 2014, 02:01:29 UTC | update clin-seq blessed | 28 May 2014, 02:01:29 UTC |
| ca6f547 | Nathaniel Nutter | 27 May 2014, 21:45:26 UTC | fix issue that broke piping to xargs -0 | 27 May 2014, 22:09:04 UTC |
| d16f673 | Nathaniel Nutter | 27 May 2014, 21:41:11 UTC | even a single ID needs to be null terminated | 27 May 2014, 22:09:02 UTC |
| 84d6268 | Nathaniel Nutter | 27 May 2014, 21:37:44 UTC | add failing test for bug when piped to xargs -0 It looks like `xargs -0` expects single arguments to also be null terminated. | 27 May 2014, 22:09:01 UTC |
| 99e2127 | Nathaniel Nutter | 27 May 2014, 21:37:09 UTC | refactor print_model_ids for easier testing | 27 May 2014, 22:08:58 UTC |
| e8b86ef | Eddie Belter | 27 May 2014, 21:56:49 UTC | Model: copy inputs filter desc | 27 May 2014, 21:57:17 UTC |
| a787abf | Eddie Belter | 23 May 2014, 20:45:58 UTC | Model Input: add copy method | 27 May 2014, 21:57:16 UTC |
| 31fa4b9 | Brian White | 27 May 2014, 16:24:15 UTC | Removed a whitespace from a file path | 27 May 2014, 16:24:15 UTC |
| 838bfb2 | Nathaniel Nutter | 27 May 2014, 15:22:22 UTC | fix crashing bug in should_run_as | 27 May 2014, 15:22:22 UTC |
| cb5092c | Nathaniel Nutter | 27 May 2014, 15:22:12 UTC | fix bug introduced when pulling method up from Build | 27 May 2014, 15:22:12 UTC |
| 1c7cc5e | Nathaniel Nutter | 27 May 2014, 15:21:28 UTC | add failing test case for an uncaught bug | 27 May 2014, 15:21:28 UTC |
| a857101 | Nathaniel Nutter | 27 May 2014, 14:48:28 UTC | remove comment | 27 May 2014, 14:49:15 UTC |
| df9ae88 | Nathaniel Nutter | 27 May 2014, 14:24:21 UTC | approved new test output with an updated last_succeeded_build Avi built a new build of H_KA-763312-1224733.somatic_variation-2 on 2014-05-24 so its last_succeeded_build updated. | 27 May 2014, 14:26:16 UTC |
| dc1b71d | Eddie Belter | 23 May 2014, 20:05:46 UTC | Annotation: genotype vaf filter | 23 May 2014, 20:25:28 UTC |
