| b1bf4bc | dmorton | 21 March 2013, 19:34:52 UTC | Add *.swp to .gitignore | 22 March 2013, 19:46:55 UTC |
| b1db994 | Chris Miller | 22 March 2013, 19:06:12 UTC | added error logs so that we can go back and see if these bsubbed jobs failed during troubleshooting | 22 March 2013, 19:07:42 UTC |
| bb3229e | Malachi Griffith | 22 March 2013, 18:57:23 UTC | Minor update to cn-view to improve visibilty of copy gains/losses | 22 March 2013, 18:57:23 UTC |
| 33f3fb0 | Dan Koboldt | 22 March 2013, 16:59:43 UTC | Addressing some updates in analysis tools Merge branch 'master' of git+ssh://git/srv/git/genome | 22 March 2013, 16:59:43 UTC |
| c11c83d | Dan Koboldt | 22 March 2013, 16:54:00 UTC | A tool to compute FET p-value expectations based on cases/controls | 22 March 2013, 16:54:00 UTC |
| a187d13 | Dan Koboldt | 22 March 2013, 16:52:59 UTC | New tool for identifying RHRO regions in a VCF | 22 March 2013, 16:52:59 UTC |
| fa3a175 | Dan Koboldt | 22 March 2013, 16:52:33 UTC | Updates to analysis tools | 22 March 2013, 16:52:33 UTC |
| 698dd89 | Dan Koboldt | 22 March 2013, 16:52:20 UTC | Fixed something in refcov reporting | 22 March 2013, 16:52:20 UTC |
| 4593c10 | Dan Koboldt | 22 March 2013, 16:52:02 UTC | Update to Scoring methods | 22 March 2013, 16:52:02 UTC |
| 267f2c5 | Dan Koboldt | 22 March 2013, 16:25:51 UTC | Update to encourage compatibility | 22 March 2013, 16:25:51 UTC |
| c07eade | Malachi Griffith | 22 March 2013, 15:51:30 UTC | Fixed a bug in the display scale for Both_AllChrs.jpeg in cn-view output | 22 March 2013, 15:51:30 UTC |
| dd81eb4 | Jason Walker | 22 March 2013, 14:58:48 UTC | Add the primary_alignment_strategy option to select primary alignment when mutliple alignments are reported per read | 22 March 2013, 14:58:48 UTC |
| 9632873 | Jason Walker | 22 March 2013, 14:57:37 UTC | The param for read_list_file was corrected. | 22 March 2013, 14:57:37 UTC |
| 9c214ce | Jason Walker | 22 March 2013, 14:56:36 UTC | Up the BWASW memory requirement to 16G | 22 March 2013, 14:56:36 UTC |
| 9c7bc7f | nnutter | 22 March 2013, 02:46:10 UTC | add tests for split_dbSNPBuildID | 22 March 2013, 02:53:17 UTC |
| b4382e1 | nnutter | 22 March 2013, 02:45:53 UTC | switch to eval/abort | 22 March 2013, 02:53:16 UTC |
| a4b75e8 | nnutter | 22 March 2013, 02:44:23 UTC | fix uninitialized warning | 22 March 2013, 02:53:16 UTC |
| 3d2140f | nnutter | 22 March 2013, 02:43:52 UTC | add abort | 22 March 2013, 02:53:15 UTC |
| 93e4919 | Gabriel Sanderson | 21 March 2013, 23:18:33 UTC | Merge branch 'master' into gb_master | 21 March 2013, 23:18:33 UTC |
| 1a600f4 | Gabriel Sanderson | 21 March 2013, 23:18:00 UTC | Fixed test data for somatic and somatic-capture models coming back into existence | 21 March 2013, 23:18:28 UTC |
| 5e4b028 | Chris Miller | 21 March 2013, 22:00:41 UTC | bugfix | 21 March 2013, 22:00:48 UTC |
| 087e81f | Gabriel Sanderson | 21 March 2013, 21:36:35 UTC | Merge branch 'varscan' into gb_master | 21 March 2013, 21:36:35 UTC |
| 3be2be0 | Gabriel Sanderson | 21 March 2013, 21:28:29 UTC | Make varscan_validation_version a parameter to PullOneTwoBpIndels. Gather this param from the processing profile of the build | 21 March 2013, 21:36:12 UTC |
| 1bcb1aa | Malachi Griffith | 21 March 2013, 21:29:24 UTC | ClinSeq - update display output in update-analysis and improve figures generated by converge all-events | 21 March 2013, 21:29:24 UTC |
| 291c76a | Eddie Belter | 21 March 2013, 20:03:59 UTC | InstData Solexa: add support for sx trimmer params to have no in the front | 21 March 2013, 20:04:05 UTC |
| fb975bb | Gabriel Sanderson | 21 March 2013, 19:33:30 UTC | Merge branch 'varscan' into gb_master | 21 March 2013, 19:33:30 UTC |
| d38aa27 | Gabriel Sanderson | 21 March 2013, 19:33:20 UTC | Added varscan_validation_version to control varscan version in the validation steps | 21 March 2013, 19:33:20 UTC |
| 2530c3a | Chris Miller | 21 March 2013, 19:16:54 UTC | bsub resource req fix | 21 March 2013, 19:17:06 UTC |
| 59f7ebd | APipe Tester | 21 March 2013, 18:47:50 UTC | updated workflow submodule to 7d78744 | 21 March 2013, 18:47:50 UTC |
| de049aa | nnutter | 21 March 2013, 18:15:35 UTC | Merge branch 'somatic-restore' | 21 March 2013, 18:15:35 UTC |
| cb11c45 | nnutter | 21 March 2013, 18:09:10 UTC | strip down Somatic and SomaticCapture Both have been deprecated and mostly removed. These exist so old models and builds can still be viewed on web and in listers. | 21 March 2013, 18:15:14 UTC |
| 23b5beb | nnutter | 21 March 2013, 17:49:37 UTC | partially restore Somatic and SomaticCapture deletions | 21 March 2013, 18:15:14 UTC |
| 5e874df | Adam Coffman | 21 March 2013, 17:50:48 UTC | increase size of initial allocation request | 21 March 2013, 17:50:48 UTC |
| 56f857d | Eddie Belter | 21 March 2013, 17:31:07 UTC | InstData Import bam: sort before importing; verify paired | 21 March 2013, 17:31:07 UTC |
| 457afc8 | APipe Tester | 21 March 2013, 15:32:55 UTC | updated jenkins submodule to 0d45367 | 21 March 2013, 15:32:55 UTC |
| 9817512 | Kyung Kim | 21 March 2013, 15:23:30 UTC | Added additional functionality params and new versions | 21 March 2013, 15:23:30 UTC |
| 8ee4475 | nnutter | 21 March 2013, 01:43:12 UTC | make test more resilient to GENOME_TEST_INPUTS move After moving GENOME_TEST_INPUTS this test started failing because permissions were not preserved. I made the test actually create the expected filesystem state instead of relying on it from GENOME_TEST_INPUTS. I also corrected an ambiguous test so that there are no two tests; one for each interpretation of the ambiguity. | 21 March 2013, 01:43:12 UTC |
| 422f8d2 | nnutter | 21 March 2013, 00:58:44 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 21 March 2013, 00:58:44 UTC |
| b705b9b | nnutter | 21 March 2013, 00:40:41 UTC | replace test_suite_data path for comparison | 21 March 2013, 00:40:41 UTC |
| dbf2c9a | dmorton | 20 March 2013, 23:17:18 UTC | Fix missing quotes | 20 March 2013, 23:17:18 UTC |
| d3267a9 | dmorton | 20 March 2013, 22:55:45 UTC | Merge branch 'ViewPreview' Adds preview of log files | 20 March 2013, 22:55:45 UTC |
| 936414d | dmorton | 20 March 2013, 22:44:41 UTC | gmb view shows preview of errors or it shows the last line in the error file | 20 March 2013, 22:53:27 UTC |
| 849b052 | dmorton | 20 March 2013, 22:48:17 UTC | Merge branch 'ChimerascanTesting' Fixes tests | 20 March 2013, 22:48:17 UTC |
| e32834c | dmorton | 20 March 2013, 22:40:26 UTC | Add quotes around cmd line args | 20 March 2013, 22:46:40 UTC |
| 07c2840 | dmorton | 20 March 2013, 22:37:25 UTC | Fix test inadvertently testing wrong class | 20 March 2013, 22:46:40 UTC |
| 7423202 | apregier | 20 March 2013, 19:25:56 UTC | Allow dbsnp imports where vcf is split by chromosome | 20 March 2013, 19:26:12 UTC |
| fead616 | Thomas Mooney | 20 March 2013, 14:44:32 UTC | Add picard-tools submodule. | 20 March 2013, 14:44:32 UTC |
| 4f8baa8 | Thomas Mooney | 20 March 2013, 14:37:19 UTC | Add support for packaged picard-tools versions under /usr/share/java/. | 20 March 2013, 14:37:19 UTC |
| 239dfb7 | nnutter | 20 March 2013, 03:58:14 UTC | additional cleanup | 20 March 2013, 04:13:08 UTC |
| fcd13f1 | nnutter | 20 March 2013, 03:47:16 UTC | data_dir changes - split into separate data_dir - support optional test version - validate package | 20 March 2013, 04:13:07 UTC |
| fb6213c | Scott Smith | 20 March 2013, 04:07:05 UTC | updated docs on htseq | 20 March 2013, 04:07:05 UTC |
| 21f0d31 | Scott Smith | 20 March 2013, 03:22:44 UTC | ensure the display of alignment results includes the test name | 20 March 2013, 03:22:44 UTC |
| 580af2a | nnutter | 20 March 2013, 00:13:32 UTC | refactor, no feature changes | 20 March 2013, 00:34:16 UTC |
| 8bd58ca | nnutter | 20 March 2013, 00:12:44 UTC | formalize file order: got, expected - invert diff so it's relative to second/expected file - rename vars to indicate expected - place expected in correct position | 20 March 2013, 00:33:35 UTC |
| 28b8a1e | nnutter | 19 March 2013, 23:24:05 UTC | cleanup test | 20 March 2013, 00:16:58 UTC |
| 83f6207 | nnutter | 19 March 2013, 23:23:26 UTC | add data_dir_ok | 20 March 2013, 00:16:57 UTC |
| 3465523 | nnutter | 19 March 2013, 23:02:35 UTC | builder is supposed to be called in functions not just once | 20 March 2013, 00:16:57 UTC |
| 7da90b3 | nnutter | 19 March 2013, 23:01:25 UTC | cleanup | 20 March 2013, 00:16:56 UTC |
| 0d98d46 | nnutter | 19 March 2013, 23:01:08 UTC | add replace option for compare_ok | 20 March 2013, 00:16:56 UTC |
| 09f2780 | APipe Tester | 19 March 2013, 21:35:49 UTC | updated ur submodule to 22f91bc | 19 March 2013, 21:35:49 UTC |
| cfa2ab1 | Adam Coffman | 19 March 2013, 19:57:35 UTC | add get_all_allocations_for_path method | 19 March 2013, 19:57:35 UTC |
| 36ac5c7 | Scott Smith | 19 March 2013, 19:01:20 UTC | updated merge logic for Genome::Command::WithSavedResults, and updated the HTSeq implementation | 19 March 2013, 19:01:20 UTC |
| 59e4b96 | Thomas Mooney | 19 March 2013, 18:42:53 UTC | Remove color codes from EOLs of expected output. | 19 March 2013, 18:42:53 UTC |
| a4130b2 | Kyung Kim | 19 March 2013, 17:07:45 UTC | update to create cleaned scaffolds.fasta that matches metrics | 19 March 2013, 17:07:45 UTC |
| ddfda17 | APipe Tester | 19 March 2013, 16:21:07 UTC | Updated `genome` tab completion. | 19 March 2013, 16:21:07 UTC |
| 8736045 | APipe Tester | 19 March 2013, 16:14:18 UTC | Updated `genome` tab completion. | 19 March 2013, 16:15:24 UTC |
| ea1c282 | APipe Tester | 19 March 2013, 16:07:32 UTC | updated ur submodule to 491b87b | 19 March 2013, 16:07:32 UTC |
| 5a0edb6 | Thomas Mooney | 19 March 2013, 13:53:14 UTC | Automatically decide the number of threads to use for PerLaneTophat. | 19 March 2013, 13:53:14 UTC |
| f511fc7 | Adam Coffman | 18 March 2013, 23:11:29 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 March 2013, 23:11:29 UTC |
| f9d70b7 | Adam Coffman | 18 March 2013, 23:11:21 UTC | add get_active_volume method to volume | 18 March 2013, 23:11:21 UTC |
| b76f661 | dmorton | 18 March 2013, 22:50:55 UTC | use arrow instead of . (PERL is not Python) | 18 March 2013, 22:50:55 UTC |
| 21c1796 | dmorton | 18 March 2013, 22:09:50 UTC | Merge branch 'ChimerascanBase' | 18 March 2013, 22:09:50 UTC |
| d33163f | dmorton | 15 March 2013, 15:39:04 UTC | Fix instrument_data->bam_file to be bam_path | 18 March 2013, 21:44:13 UTC |
| 43b9764 | dmorton | 08 March 2013, 18:18:33 UTC | Make ChimerascanResult use ChimerascanBase | 18 March 2013, 21:44:13 UTC |
| 843bc99 | dmorton | 08 March 2013, 18:17:20 UTC | Stop using build->model->x in Chimerascan command | 18 March 2013, 21:44:12 UTC |
| d67929e | dmorton | 08 March 2013, 18:16:18 UTC | Made ChimerascanBase Class | 18 March 2013, 21:44:12 UTC |
| 762dc8b | dmorton | 07 March 2013, 16:50:37 UTC | Added back in the old Chimerascan (not vrl) | 18 March 2013, 21:44:12 UTC |
| 2482a18 | Brian Derickson | 18 March 2013, 21:01:42 UTC | use rmdir instead of Genome::Sys->remove_directory_tree | 18 March 2013, 21:03:44 UTC |
| fb2a015 | Brian Derickson | 18 March 2013, 20:44:56 UTC | Changes to CreateForExisting allocation command Renamed to import. Primitivized method arguments for easier testing. | 18 March 2013, 21:03:44 UTC |
| 41501aa | Eddie Belter | 18 March 2013, 18:25:21 UTC | MetaShot: extract unaligned from meta nr | 18 March 2013, 20:14:32 UTC |
| 31b927b | Eddie Belter | 18 March 2013, 18:19:22 UTC | MetaShot: align to - consolidate some methods, rm dies | 18 March 2013, 20:14:32 UTC |
| b928764 | Eddie Belter | 15 March 2013, 15:16:40 UTC | MetaShot: build if necessary takes only one model; rm commit | 18 March 2013, 20:14:32 UTC |
| 9f5b327 | Eddie Belter | 15 March 2013, 15:10:41 UTC | MetaShot: separate assign inst data and build in align to | 18 March 2013, 20:14:31 UTC |
| d5fcde4 | Eddie Belter | 15 March 2013, 14:40:44 UTC | MetaShot: update align to to use inst data assign/unassign command to add/rm inst data | 18 March 2013, 20:14:31 UTC |
| 801efae | dmorton | 18 March 2013, 19:23:04 UTC | Fix gmb view for builds with no results. | 18 March 2013, 19:26:28 UTC |
| 8056b86 | apregier | 18 March 2013, 18:25:57 UTC | Sleep before retry | 18 March 2013, 18:25:57 UTC |
| f9d09b3 | apregier | 18 March 2013, 17:02:37 UTC | Report/Email.pm | 18 March 2013, 18:12:28 UTC |
| 7f07900 | apregier | 18 March 2013, 16:15:00 UTC | Build with no results can still be viewed | 18 March 2013, 16:15:33 UTC |
| 55d0b63 | APipe Tester | 18 March 2013, 16:13:11 UTC | Updated `gmt` tab completion. | 18 March 2013, 16:13:11 UTC |
| 4eb7c45 | APipe Tester | 18 March 2013, 16:12:08 UTC | Updated `genome` tab completion. | 18 March 2013, 16:12:08 UTC |
| afbd9eb | APipe Tester | 18 March 2013, 16:05:08 UTC | Updated `gmt` tab completion. | 18 March 2013, 16:05:10 UTC |
| 78b7fb5 | APipe Tester | 18 March 2013, 16:04:06 UTC | Updated `genome` tab completion. | 18 March 2013, 16:05:10 UTC |
| 51a074c | apregier | 18 March 2013, 15:53:33 UTC | Merge branch 'fireteam2' into gb_master | 18 March 2013, 15:53:33 UTC |
| 06126ae | apregier | 18 March 2013, 15:48:40 UTC | Fix table names for ucsc gap-list | 18 March 2013, 15:48:40 UTC |
| f18e957 | nnutter | 16 March 2013, 05:31:18 UTC | fix for when there are no changed perl files | 16 March 2013, 05:31:18 UTC |
| 072877e | APipe Tester | 16 March 2013, 04:08:13 UTC | updated workflow submodule to a730105 | 16 March 2013, 04:08:13 UTC |
| 88c984a | apregier | 15 March 2013, 23:17:18 UTC | Merge branch 'updated2' into gb_master | 15 March 2013, 23:17:18 UTC |
| 5d504e7 | apregier | 15 March 2013, 23:16:55 UTC | Remove amplicon assembly from summary of builds test | 15 March 2013, 23:17:04 UTC |
| 332c02e | nnutter | 15 March 2013, 23:07:46 UTC | Merge branch 'perl-tests' | 15 March 2013, 23:07:46 UTC |
| 95a6f69 | nnutter | 15 March 2013, 23:06:56 UTC | 135722070 was approved by Malachi Griffith | 15 March 2013, 23:06:56 UTC |
