| 5d79a67 | Callie Federer | 14 August 2014, 15:47:19 UTC | updating | 14 August 2014, 15:47:19 UTC |
| 18c2749 | Thomas Mooney | 14 August 2014, 14:19:56 UTC | Don't keep detailed files when use_short_roi_names in effect. (AUE-319) | 14 August 2014, 14:19:56 UTC |
| b91adae | APipe Tester | 14 August 2014, 12:17:27 UTC | Updated `gmt` tab completion. | 14 August 2014, 12:17:27 UTC |
| a2bd29a | APipe Tester | 14 August 2014, 12:16:45 UTC | Updated `genome` tab completion. | 14 August 2014, 12:16:45 UTC |
| 99fd77a | APipe Tester | 14 August 2014, 12:15:07 UTC | Updated class browser cache. | 14 August 2014, 12:15:07 UTC |
| 530ca9d | Jason Walker | 13 August 2014, 17:07:15 UTC | Add AML_RMG to full cle report. | 13 August 2014, 17:07:15 UTC |
| c2f7411 | Jason Walker | 13 August 2014, 17:05:42 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 August 2014, 17:05:42 UTC |
| eea9994 | Miranda Fulton | 13 August 2014, 16:42:53 UTC | changed the paths so that it will run on any machine | 13 August 2014, 16:44:22 UTC |
| 02eba26 | Miranda Fulton | 13 August 2014, 16:41:49 UTC | adds extra output for when the test fails | 13 August 2014, 16:44:22 UTC |
| f8705fb | Miranda Fulton | 12 August 2014, 20:57:22 UTC | Removed the params hash and renamed variables | 13 August 2014, 16:44:21 UTC |
| 472716e | Miranda Fulton | 12 August 2014, 19:34:34 UTC | removed temporary variables | 13 August 2014, 16:44:21 UTC |
| 7122c39 | Miranda Fulton | 12 August 2014, 19:23:08 UTC | more changes ugh! | 13 August 2014, 16:44:20 UTC |
| ab5cdc1 | Miranda Fulton | 12 August 2014, 19:11:06 UTC | Rempved a bit of excess code | 13 August 2014, 16:44:20 UTC |
| 09b8926 | Miranda Fulton | 12 August 2014, 18:44:37 UTC | Removed the extra debug and print statments | 13 August 2014, 16:44:19 UTC |
| cdc666c | Miranda Fulton | 12 August 2014, 18:43:47 UTC | removed the extra print statments | 13 August 2014, 16:44:19 UTC |
| 6bc9262 | Miranda Fulton | 11 August 2014, 18:37:57 UTC | Fixed the version test error | 13 August 2014, 16:44:18 UTC |
| 8cf7eb5 | Miranda Fulton | 11 August 2014, 18:22:49 UTC | Added a test to make sure the version exists | 13 August 2014, 16:44:18 UTC |
| 8f28018 | Miranda Fulton | 11 August 2014, 18:21:43 UTC | added a test to make sure the version exists | 13 August 2014, 16:44:17 UTC |
| f495327 | Miranda Fulton | 11 August 2014, 16:16:23 UTC | Incororated versioning into the program | 13 August 2014, 16:44:17 UTC |
| f8dd786 | Miranda Fulton | 11 August 2014, 16:15:09 UTC | incorporated versioning into the program | 13 August 2014, 16:44:16 UTC |
| e79cfc7 | Miranda Fulton | 06 August 2014, 21:53:09 UTC | DB2 lumpy wrote tests to check lumpy script methods | 13 August 2014, 16:44:16 UTC |
| 21df0bd | Miranda Fulton | 06 August 2014, 21:51:59 UTC | DB2 lumpy made methods to find lumpy scripts | 13 August 2014, 16:44:15 UTC |
| d1861ab | Miranda Fulton | 06 August 2014, 20:29:19 UTC | DV2 lumpy: mean and stdev temp file storage | 13 August 2014, 16:44:14 UTC |
| f9d163b | Miranda Fulton | 04 August 2014, 16:52:09 UTC | Changed some of the print statements to debug | 13 August 2014, 16:44:14 UTC |
| af53ea4 | Miranda Fulton | 04 August 2014, 16:47:21 UTC | added a Matched samples test | 13 August 2014, 16:44:13 UTC |
| 959f5d1 | Miranda Fulton | 28 July 2014, 15:28:49 UTC | Parameters and the histo files were put in a hash | 13 August 2014, 16:44:13 UTC |
| 32a7df2 | Miranda Fulton | 25 July 2014, 17:09:56 UTC | rearranged the sr parameters to see if they would work | 13 August 2014, 16:44:12 UTC |
| cc03d83 | Miranda Fulton | 25 July 2014, 17:07:03 UTC | updated and improved pe_cmd_arrangement & its test | 13 August 2014, 16:44:12 UTC |
| c25caa3 | Miranda Fulton | 25 July 2014, 15:51:16 UTC | changed mean and stdv to a hash | 13 August 2014, 16:44:11 UTC |
| f110094 | Miranda Fulton | 25 July 2014, 14:46:27 UTC | added a subtest to test the absence of split reads in the bam_file | 13 August 2014, 16:44:10 UTC |
| acec6fd | Miranda Fulton | 25 July 2014, 14:12:08 UTC | Lumpy fixed mean and stdev subroutine | 13 August 2014, 16:44:10 UTC |
| 9afe92a | Miranda Fulton | 24 July 2014, 15:38:14 UTC | Changed the sam-bam converter to picard tools | 13 August 2014, 16:44:09 UTC |
| 8430473 | Miranda Fulton | 23 July 2014, 18:43:32 UTC | PE & SR command subroutines and tests added | 13 August 2014, 16:44:09 UTC |
| 6ec2145 | Miranda Fulton | 23 July 2014, 17:06:57 UTC | Lumpy wrapper - removed read_params command | 13 August 2014, 16:44:08 UTC |
| b8b7574 | Miranda Fulton | 22 July 2014, 20:45:37 UTC | lumpy stage2 - runs with multiple libraries | 13 August 2014, 16:44:08 UTC |
| f7d6eb2 | Miranda Fulton | 17 July 2014, 18:21:22 UTC | Lumpy test1 | 13 August 2014, 16:44:07 UTC |
| 889b061 | Miranda Fulton | 17 July 2014, 15:48:27 UTC | initial commit | 13 August 2014, 16:44:06 UTC |
| 7739781 | Callie Federer | 13 August 2014, 15:15:24 UTC | adding .. | 13 August 2014, 15:15:24 UTC |
| aaa6c02 | Jason Walker | 13 August 2014, 15:14:07 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 August 2014, 15:14:07 UTC |
| 9709ef2 | Thomas Mooney | 13 August 2014, 14:49:51 UTC | New FeatureList importer designed for LIMS capture set use. Provides additional validation and sanitization around creation so that the FL is suitable for use as an ROI in pipelines. | 13 August 2014, 14:49:51 UTC |
| 070480c | Thomas Mooney | 13 August 2014, 14:41:47 UTC | Extract track parsing and format calculation up into FeatureList itself Use the former for our other track parsing. | 13 August 2014, 14:41:47 UTC |
| c8f61f1 | Thomas Mooney | 12 August 2014, 21:46:46 UTC | Clear out the temp dir to avoid double-counting in reallocate. | 12 August 2014, 21:46:46 UTC |
| 0234e62 | Dave Larson | 12 August 2014, 20:37:23 UTC | update readcount version to 0.6 | 12 August 2014, 20:37:23 UTC |
| ba79fc7 | Callie Federer | 12 August 2014, 20:33:06 UTC | adding | 12 August 2014, 20:33:06 UTC |
| f2677b0 | Jason Walker | 12 August 2014, 20:25:31 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 August 2014, 20:25:31 UTC |
| 54ee538 | apregier | 12 August 2014, 20:15:47 UTC | Merge branch 'copy' into gb_master | 12 August 2014, 20:15:47 UTC |
| 7bd9fc4 | apregier | 12 August 2014, 20:12:09 UTC | Header not required for this subroutine | 12 August 2014, 20:12:41 UTC |
| f87d06a | apregier | 12 August 2014, 20:11:10 UTC | Don't insert bamreadcount info for positions where there is both an insertion and deletion, but also don't get hung up on these positions. | 12 August 2014, 20:12:39 UTC |
| 2a64b2b | Jason Walker | 12 August 2014, 19:45:54 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 August 2014, 19:45:54 UTC |
| 9b40be1 | Jason Walker | 12 August 2014, 19:44:56 UTC | Add additional status message and capture dirmove errors on purge. | 12 August 2014, 19:44:56 UTC |
| fe67e35 | Callie Federer | 12 August 2014, 19:25:41 UTC | adding | 12 August 2014, 19:25:41 UTC |
| b1b2a50 | apregier | 12 August 2014, 17:47:35 UTC | Merge branch 'copy' into gb_master | 12 August 2014, 17:47:35 UTC |
| 74d8914 | apregier | 12 August 2014, 17:46:04 UTC | Update blessed builds | 12 August 2014, 17:46:35 UTC |
| 9b43dd9 | Michael J. Kiwala | 12 August 2014, 17:40:22 UTC | Add explicit 'use Bio::SeqIO' | 12 August 2014, 17:45:58 UTC |
| 4ef2475 | apregier | 12 August 2014, 15:54:18 UTC | Merge branch 'copy' into gb_master | 12 August 2014, 15:54:18 UTC |
| 29c30ae | apregier | 12 August 2014, 15:52:58 UTC | Use tumor bam from d30 build rather than normal bam | 12 August 2014, 15:53:18 UTC |
| 953c136 | Adam Coffman | 12 August 2014, 15:14:09 UTC | make config_item field optional in UR as well as database | 12 August 2014, 15:14:09 UTC |
| 1a5f6bc | Avinash Ramu | 12 August 2014, 14:44:30 UTC | update clinseq blessed | 12 August 2014, 14:44:49 UTC |
| 1f44741 | Thomas Mooney | 12 August 2014, 14:39:09 UTC | Adhere to standard practice of a bare return when create() fails. This will allow SR's get_or_create() to find the newly minted object when we entered create() because we had been waiting on a lock. | 12 August 2014, 14:39:09 UTC |
| c89e020 | APipe Tester | 12 August 2014, 12:16:31 UTC | Updated `genome` tab completion. | 12 August 2014, 12:16:31 UTC |
| 3b1dd65 | APipe Tester | 12 August 2014, 12:15:00 UTC | Updated class browser cache. | 12 August 2014, 12:15:00 UTC |
| d02ece9 | Avinash Ramu | 12 August 2014, 03:21:32 UTC | check for NaN | 12 August 2014, 03:29:39 UTC |
| b44b9e8 | Avinash Ramu | 12 August 2014, 03:20:30 UTC | annotate filtered file | 12 August 2014, 03:29:38 UTC |
| 9832d12 | Avinash Ramu | 11 August 2014, 04:38:18 UTC | update Cnmops test | 12 August 2014, 03:29:37 UTC |
| 7a5c99a | Avinash Ramu | 10 August 2014, 02:31:41 UTC | get posterior probs from Cnmops | 12 August 2014, 03:29:37 UTC |
| 71bd926 | Avinash Ramu | 10 August 2014, 02:31:03 UTC | update test | 12 August 2014, 03:29:37 UTC |
| 0a72a5e | Avinash Ramu | 21 July 2014, 18:45:56 UTC | add type of change | 12 August 2014, 03:29:36 UTC |
| 2669a6b | Avinash Ramu | 21 July 2014, 18:31:11 UTC | add clinseq file accessors | 12 August 2014, 03:29:36 UTC |
| 028f0f1 | Avinash Ramu | 21 July 2014, 18:29:48 UTC | add cancerrelevancescore converge tool | 12 August 2014, 03:29:35 UTC |
| 34ae163 | Avinash Ramu | 18 July 2014, 15:40:20 UTC | update exome_cnv cnvhmm file | 12 August 2014, 03:29:34 UTC |
| b9791dc | Avinash Ramu | 15 July 2014, 19:56:50 UTC | Add mutspec clinseq file access | 12 August 2014, 03:29:34 UTC |
| 58e080e | Avinash Ramu | 14 July 2014, 16:35:38 UTC | add mutation-spectrum converge | 12 August 2014, 03:29:34 UTC |
| 0612607 | Avinash Ramu | 09 July 2014, 15:37:28 UTC | change column header | 12 August 2014, 03:29:33 UTC |
| 4b86ded | Avinash Ramu | 09 July 2014, 15:26:05 UTC | add header line | 12 August 2014, 03:29:33 UTC |
| c396866 | Avinash Ramu | 07 July 2014, 20:30:37 UTC | get data-source from path | 12 August 2014, 03:29:32 UTC |
| 1e4907f | Avinash Ramu | 07 July 2014, 20:29:56 UTC | use different temp-sorted file | 12 August 2014, 03:29:32 UTC |
| dacacc7 | Avinash Ramu | 07 July 2014, 17:42:10 UTC | add stats files | 12 August 2014, 03:29:31 UTC |
| 7d1ccf8 | Avinash Ramu | 07 July 2014, 17:08:31 UTC | add file accessors | 12 August 2014, 03:29:31 UTC |
| de0db0d | Thomas Mooney | 11 August 2014, 17:41:32 UTC | Initial version of a FeatureList merge tool. BED-merging code taken from GSCApp::BEDFile. | 11 August 2014, 22:54:41 UTC |
| a148dbf | apregier | 11 August 2014, 22:34:31 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 22:34:31 UTC |
| 25c11cb | apregier | 11 August 2014, 22:33:49 UTC | If there is no information about the af for an allele, always pass the filter | 11 August 2014, 22:33:49 UTC |
| 3bca94b | apregier | 11 August 2014, 22:27:11 UTC | When no CAF is available, it should pass | 11 August 2014, 22:27:11 UTC |
| ae980b3 | apregier | 11 August 2014, 22:16:57 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 22:16:57 UTC |
| fb3b1fe | apregier | 11 August 2014, 22:14:15 UTC | Revert "Revert "Bump vcf_version due to a bump in the default joinx version"" This reverts commit 578c984a0092b71b2bf8c143897cdcdcedc14421. No takesies backsies!!! | 11 August 2014, 22:14:15 UTC |
| c77d7a0 | Thomas Mooney | 11 August 2014, 22:11:49 UTC | Make generic SR expunge process for when deleting an object. Use it for InstrumentData and Sample deletion. | 11 August 2014, 22:11:49 UTC |
| 9675e04 | apregier | 11 August 2014, 21:54:43 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 21:54:43 UTC |
| 99f6fc4 | apregier | 11 August 2014, 21:50:46 UTC | Make verify bam id code respect test name and add user relationship | 11 August 2014, 21:51:38 UTC |
| 62394d6 | Eddie Belter | 11 August 2014, 19:48:48 UTC | File VCF: rm dumper statement | 11 August 2014, 19:49:09 UTC |
| 9f0c7d3 | apregier | 11 August 2014, 19:35:53 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 19:35:53 UTC |
| 7447f1d | apregier | 11 August 2014, 19:31:06 UTC | snv detection strategy is optional | 11 August 2014, 19:33:25 UTC |
| 578c984 | dmorton | 11 August 2014, 19:20:48 UTC | Revert "Bump vcf_version due to a bump in the default joinx version" This reverts commit 5993ebd598c94bba2847bcd8cdcc17a049ca7311. | 11 August 2014, 19:20:48 UTC |
| 5993ebd | dmorton | 11 August 2014, 19:06:22 UTC | Bump vcf_version due to a bump in the default joinx version | 11 August 2014, 19:06:22 UTC |
| 6ac75e1 | Thomas Mooney | 11 August 2014, 15:22:34 UTC | Use build factory for benefit of setup_reference_sequence_build. | 11 August 2014, 15:22:34 UTC |
| 247869f | APipe Tester | 09 August 2014, 12:17:13 UTC | Updated `gmt` tab completion. | 09 August 2014, 12:17:13 UTC |
| 0ef1383 | APipe Tester | 09 August 2014, 12:16:31 UTC | Updated `genome` tab completion. | 09 August 2014, 12:16:31 UTC |
| 8a00921 | Charles Lu | 08 August 2014, 21:33:26 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 08 August 2014, 21:33:26 UTC |
| 9b12b69 | Charles Lu | 08 August 2014, 21:33:18 UTC | fixed few bugs with the plot coverage tool. Added --highlight option to the tool | 08 August 2014, 21:33:18 UTC |
| 6227599 | Adam Coffman | 08 August 2014, 20:26:11 UTC | return empty string on method mismatch instead of shift // empty | 08 August 2014, 20:26:11 UTC |
| 55e4f0d | Adam Coffman | 08 August 2014, 20:24:12 UTC | check if a method exists before calling it: AUE-291 | 08 August 2014, 20:24:12 UTC |
| 139fe24 | Gabriel Sanderson | 25 July 2014, 19:58:39 UTC | No longer die when we find no gene. Instead we print a summary of transcript types that contained no gene at the end. | 08 August 2014, 19:54:10 UTC |
