| d8981b5 | Thomas Mooney | 09 December 2013, 20:20:29 UTC | Fallback on any available GTF file for the annotation build. | 09 December 2013, 21:05:06 UTC |
| a1da992 | Feiyu Du | 09 December 2013, 20:59:34 UTC | add solution for another case of indelfilter normal genotype | 09 December 2013, 20:59:34 UTC |
| bfa13b1 | Adam Coffman | 09 December 2013, 18:41:40 UTC | update analysis project lister | 09 December 2013, 18:41:40 UTC |
| cf12f8b | Adam Coffman | 09 December 2013, 17:00:01 UTC | small CQID fixes | 09 December 2013, 17:00:01 UTC |
| 83ef80b | Susanna Siebert | 09 December 2013, 16:29:25 UTC | sort instrument data by read group instead of date | 09 December 2013, 16:29:25 UTC |
| e587bed | Jim Weible | 09 December 2013, 15:07:45 UTC | update apipe-test-rnaseq to have new processing profile param | 09 December 2013, 15:08:14 UTC |
| 8b10e7b | Jim Weible | 06 December 2013, 19:49:53 UTC | add Annotation to RnaSeq fusion detection | 09 December 2013, 15:08:13 UTC |
| 64117b2 | APipe Tester | 07 December 2013, 13:17:07 UTC | Updated `genome` tab completion. | 07 December 2013, 13:17:07 UTC |
| c331c02 | APipe Tester | 07 December 2013, 13:15:30 UTC | Updated class browser cache. | 07 December 2013, 13:15:30 UTC |
| d18093b | apregier | 06 December 2013, 22:31:12 UTC | Merge branch 'copy' into gb_master | 06 December 2013, 22:31:12 UTC |
| 7c7abe8 | apregier | 06 December 2013, 22:29:51 UTC | Use topTags to get adjusted p-value | 06 December 2013, 22:30:56 UTC |
| 995c846 | apregier | 06 December 2013, 22:11:16 UTC | Use topTags to get adjusted p-value | 06 December 2013, 22:30:55 UTC |
| 60b967f | Anthony Brummett | 06 December 2013, 21:20:55 UTC | tag the sqitch schema as synced with production | 06 December 2013, 21:36:13 UTC |
| 6e7f5ae | Anthony Brummett | 04 December 2013, 22:18:39 UTC | rename indexes to match the production database | 06 December 2013, 21:36:12 UTC |
| 0a331d7 | Anthony Brummett | 04 December 2013, 21:33:24 UTC | rename index to match what is in production DB | 06 December 2013, 21:36:12 UTC |
| 29ee6be | Anthony Brummett | 04 December 2013, 21:12:33 UTC | set permissions on config.instrument_data_analysis_project_bridge | 06 December 2013, 21:36:11 UTC |
| c472f04 | Anthony Brummett | 04 December 2013, 21:01:48 UTC | change the name of the index to match what is in the production DB | 06 December 2013, 21:36:10 UTC |
| 7625257 | Anthony Brummett | 04 December 2013, 20:53:49 UTC | drop column disk.preserved and add NOT NULL to archive_after_time and status | 06 December 2013, 21:36:09 UTC |
| 24bcedc | apregier | 06 December 2013, 21:14:39 UTC | Merge branch 'copy' into gb_master | 06 December 2013, 21:14:39 UTC |
| 02157e4 | apregier | 06 December 2013, 21:12:48 UTC | Add header to counts_file | 06 December 2013, 21:12:48 UTC |
| e88cb6d | apregier | 06 December 2013, 20:34:33 UTC | Don't explicitly set groups in DGEList object | 06 December 2013, 20:34:33 UTC |
| 90031cc | Susanna Siebert | 06 December 2013, 17:14:01 UTC | Replaced the rnaseq tumor and normal parameters with clinseq parameter | 06 December 2013, 20:16:23 UTC |
| 73f5ee2 | Susanna Siebert | 06 December 2013, 15:27:41 UTC | subjects_list and groups_list are optional parameters | 06 December 2013, 20:16:23 UTC |
| 4a506fa | Susanna Siebert | 05 December 2013, 22:36:28 UTC | Added test to ensure that the gene columns of the input files are identical | 06 December 2013, 20:16:22 UTC |
| d421890 | Susanna Siebert | 05 December 2013, 22:30:33 UTC | Added test to ensure that the joined output file is as expected | 06 December 2013, 20:16:21 UTC |
| c2b7cd1 | Susanna Siebert | 05 December 2013, 21:50:51 UTC | added new module to make a joined gene counts file for multiple RnaSeq builds | 06 December 2013, 20:16:21 UTC |
| b405955 | Susanna Siebert | 04 December 2013, 17:57:02 UTC | Added validation and test to ensure that each subject is in each group at least once | 06 December 2013, 20:16:20 UTC |
| 3a1abe0 | Susanna Siebert | 04 December 2013, 17:36:47 UTC | Added validation and test to ensure that number of groups and subjects are the same | 06 December 2013, 20:16:20 UTC |
| c7c7266 | Susanna Siebert | 04 December 2013, 17:28:18 UTC | Added validation and test to ensure that more than one subject is being used | 06 December 2013, 20:16:19 UTC |
| 783d23e | Susanna Siebert | 04 December 2013, 17:25:50 UTC | Added validation and test to ensure that each subject is being used more than once | 06 December 2013, 20:16:19 UTC |
| e506ee9 | Susanna Siebert | 04 December 2013, 17:12:53 UTC | Added validation and test for having more than one group | 06 December 2013, 20:16:18 UTC |
| e39bc2f | Susanna Siebert | 04 December 2013, 17:00:30 UTC | Factored out the validate params tests into Base.t | 06 December 2013, 20:16:17 UTC |
| 31fc275 | Susanna Siebert | 04 December 2013, 16:49:57 UTC | updated the documentation for the GLM module | 06 December 2013, 20:16:17 UTC |
| 6056ea0 | Susanna Siebert | 04 December 2013, 16:48:23 UTC | refactored the parameter validation | 06 December 2013, 20:16:16 UTC |
| d8d8140 | Susanna Siebert | 03 December 2013, 22:41:27 UTC | added edgeR GLM functionality and tests | 06 December 2013, 20:16:16 UTC |
| e08309c | Susanna Siebert | 03 December 2013, 22:40:33 UTC | factored out the generate_counts_file subroutine into the base class so it can be used by both tests for classic and glm | 06 December 2013, 20:16:15 UTC |
| b6f9ab4 | Susanna Siebert | 03 December 2013, 21:30:28 UTC | updated documentation to correspond to edgeR's updated output file header names | 06 December 2013, 20:16:15 UTC |
| 57ff7aa | Susanna Siebert | 03 December 2013, 21:23:46 UTC | factored out common functionality into EdgeR::Base and made EdgeR::Classic a child class | 06 December 2013, 20:16:14 UTC |
| c4cd085 | Gabriel Sanderson | 06 December 2013, 16:32:34 UTC | Merge branch 'master' into gb_master | 06 December 2013, 16:32:34 UTC |
| 0c260eb | Gabriel Sanderson | 06 December 2013, 16:31:24 UTC | Make sure we do not have double slashes causing an invalid URL | 06 December 2013, 16:31:24 UTC |
| a907880 | Gabriel Sanderson | 06 December 2013, 16:16:29 UTC | Expanded Copy.t beyond just a use_ok | 06 December 2013, 16:24:11 UTC |
| f06b9a3 | APipe Tester | 06 December 2013, 13:17:17 UTC | Updated `genome` tab completion. | 06 December 2013, 13:17:17 UTC |
| e69195f | Chris Miller | 05 December 2013, 22:21:51 UTC | fixing bug with var allele matching | 05 December 2013, 22:23:50 UTC |
| df8f213 | Chris Miller | 05 December 2013, 21:56:25 UTC | update AddRsid to handle the case where there are multiple variants at the same position. Also has the nice side effect of preserving the order of the input list | 05 December 2013, 22:23:50 UTC |
| 7729044 | Travis Abbott | 05 December 2013, 19:36:59 UTC | add max_output_files to split variant mtx to avoid running out of fds | 05 December 2013, 19:36:59 UTC |
| e979a4f | Charles Lu | 05 December 2013, 17:52:22 UTC | Add a feature where if user specifies somatic_variation_id, readcounts will be done from the normal and tumor BAMs associated with the som_var_model | 05 December 2013, 17:52:22 UTC |
| e260269 | Thomas Mooney | 05 December 2013, 14:44:57 UTC | Add "is_capture" for benefit of AP Config rule specification. | 05 December 2013, 14:44:57 UTC |
| 7996fcb | APipe Tester | 05 December 2013, 13:54:03 UTC | updated workflow submodule to 214c3f7 | 05 December 2013, 13:54:03 UTC |
| 7db41fa | APipe Tester | 05 December 2013, 13:17:03 UTC | Updated `genome` tab completion. | 05 December 2013, 13:17:03 UTC |
| b6285eb | APipe Tester | 05 December 2013, 13:15:25 UTC | Updated class browser cache. | 05 December 2013, 13:15:25 UTC |
| 8ab2989 | APipe Tester | 05 December 2013, 05:00:02 UTC | updated workflow submodule to 6e78a48 | 05 December 2013, 05:00:02 UTC |
| 5c68ec0 | Thomas Mooney | 05 December 2013, 00:03:00 UTC | Test the module that is the namesake of our test! | 05 December 2013, 00:03:00 UTC |
| 72c4606 | Gabriel Sanderson | 04 December 2013, 23:55:33 UTC | Merge branch 'master' into gb_master | 04 December 2013, 23:55:33 UTC |
| 720f0d6 | Gabriel Sanderson | 04 December 2013, 23:54:57 UTC | Remove the hardcoded -m param. Allow default memory usage. RT95163 | 04 December 2013, 23:54:57 UTC |
| 3b284c6 | Thomas Mooney | 04 December 2013, 22:30:00 UTC | Skip user confirmation in the test. | 04 December 2013, 22:30:00 UTC |
| 87ff465 | Thomas Mooney | 04 December 2013, 22:27:05 UTC | Prompt for what kinds of analysis to run. | 04 December 2013, 22:27:05 UTC |
| c1d9c56 | Adam Coffman | 04 December 2013, 22:19:19 UTC | add factory method for creating profiles from an already existing config file | 04 December 2013, 22:19:19 UTC |
| 8650ada | Adam Coffman | 04 December 2013, 21:42:12 UTC | make analysis menu items optional for config profile items | 04 December 2013, 21:42:12 UTC |
| 7090b25 | Adam Coffman | 04 December 2013, 21:39:31 UTC | change column to be nullable | 04 December 2013, 21:39:31 UTC |
| 3b3e5aa | Adam Coffman | 04 December 2013, 21:10:14 UTC | get test factory test for analysis projects working | 04 December 2013, 21:10:14 UTC |
| 996fed8 | Mark Burnett | 04 December 2013, 20:40:36 UTC | fix parallel by bug in WorkflowBuilder | 04 December 2013, 20:41:02 UTC |
| 1894923 | Mark Burnett | 04 December 2013, 15:58:12 UTC | improve error message of mandatory inputs | 04 December 2013, 20:41:02 UTC |
| 3e44c9c | Adam Coffman | 04 December 2013, 20:00:42 UTC | get analysis project test passing again | 04 December 2013, 20:00:42 UTC |
| ff58c9b | Adam Coffman | 04 December 2013, 19:54:32 UTC | get CQID test passing again | 04 December 2013, 19:54:32 UTC |
| 92bda68 | Thomas Mooney | 04 December 2013, 19:50:47 UTC | If the aligner doesn't support multiple references only make one index. The specified annotation build will need to have the entirety of the desired annotation for this to work properly. | 04 December 2013, 19:50:47 UTC |
| a231b9a | Adam Coffman | 04 December 2013, 19:44:12 UTC | fix class definitions so they are valid | 04 December 2013, 19:44:12 UTC |
| 345e9fd | Feiyu Du | 04 December 2013, 18:05:32 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 December 2013, 18:05:32 UTC |
| 1e264a5 | Thomas Mooney | 04 December 2013, 17:16:07 UTC | Merge AP configuration changes into branch 'master' of ssh://git/srv/git/genome Conflicts: lib/perl/Genome/Config/Set.pm lib/perl/Genome/Config/Set.t sqitch/gms/sqitch.plan | 04 December 2013, 17:16:07 UTC |
| 8b31f87 | Adam Coffman | 04 December 2013, 17:09:40 UTC | update CQID to use new analysis project config reader | 04 December 2013, 17:09:40 UTC |
| 740d7b1 | Adam Coffman | 04 December 2013, 17:08:56 UTC | add new CQID supporting classes | 04 December 2013, 17:08:56 UTC |
| 7fdfe50 | Adam Coffman | 04 December 2013, 17:07:17 UTC | remove unused config classes and references to them | 04 December 2013, 17:07:17 UTC |
| 8e93087 | Adam Coffman | 04 December 2013, 16:57:04 UTC | Add database migrations to support CQID custom config profiles. | 04 December 2013, 16:57:04 UTC |
| a91e55b | Feiyu Du | 04 December 2013, 16:45:12 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 December 2013, 16:45:12 UTC |
| ab09272 | Feiyu Du | 04 December 2013, 16:45:04 UTC | fix unit test | 04 December 2013, 16:45:04 UTC |
| f16e8c9 | APipe Tester | 04 December 2013, 13:18:20 UTC | Updated `gmt` tab completion. | 04 December 2013, 13:18:20 UTC |
| 193d684 | APipe Tester | 04 December 2013, 13:17:38 UTC | Updated `genome` tab completion. | 04 December 2013, 13:17:38 UTC |
| 31d354d | APipe Tester | 04 December 2013, 13:16:07 UTC | Updated class browser cache. | 04 December 2013, 13:16:07 UTC |
| f4ec48c | APipe Tester | 04 December 2013, 01:39:28 UTC | updated workflow submodule to 3176de1 | 04 December 2013, 01:39:28 UTC |
| 3c6ff48 | Feiyu Du | 04 December 2013, 00:15:20 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 December 2013, 00:15:20 UTC |
| 363696e | Feiyu Du | 04 December 2013, 00:15:11 UTC | bug fix to overwrite test_name | 04 December 2013, 00:15:11 UTC |
| b304b3a | dmorton | 03 December 2013, 22:07:11 UTC | Add params to input_properties | 03 December 2013, 22:07:11 UTC |
| af93d4b | apregier | 03 December 2013, 16:33:26 UTC | Merge branch 'copy' into gb_master | 03 December 2013, 16:33:26 UTC |
| 1470d02 | apregier | 03 December 2013, 16:31:22 UTC | New version of edgeR has different column headers in DGEExact.table object | 03 December 2013, 16:31:56 UTC |
| 2f0d6ca | Jim Weible | 03 December 2013, 16:03:30 UTC | bless new apipe-test-rnaseq | 03 December 2013, 16:03:30 UTC |
| ff2c2ef | Jim Weible | 25 November 2013, 20:51:39 UTC | add filter step to chimera scan workflow | 03 December 2013, 14:11:09 UTC |
| 68c6d80 | Jim Weible | 18 November 2013, 20:27:49 UTC | move Chimerascan FilterOutput next to the other chimerascan commands | 03 December 2013, 14:11:08 UTC |
| 6aad6b1 | APipe Tester | 03 December 2013, 13:17:13 UTC | Updated `genome` tab completion. | 03 December 2013, 13:17:13 UTC |
| c3ea1ca | APipe Tester | 03 December 2013, 13:15:29 UTC | Updated class browser cache. | 03 December 2013, 13:15:29 UTC |
| 9aabaa7 | Eddie Belter | 03 December 2013, 00:28:41 UTC | InstData Import: update doc | 03 December 2013, 00:28:41 UTC |
| b4ab826 | Eddie Belter | 02 December 2013, 23:36:35 UTC | InstData Import: rm inst data output | 03 December 2013, 00:18:00 UTC |
| 4c8edcd | Eddie Belter | 02 December 2013, 23:19:47 UTC | InstData Import: print the bam paths of the created instrument data | 03 December 2013, 00:17:59 UTC |
| 4eea7e2 | Eddie Belter | 02 December 2013, 23:11:02 UTC | InstData Import: update doc | 03 December 2013, 00:17:58 UTC |
| 5683ced | Eddie Belter | 14 November 2013, 21:41:26 UTC | InstData Import: moved parsing inst data properties to helpers, retrieve error msg from there to verify correct error | 03 December 2013, 00:17:58 UTC |
| e9ee8e1 | Eddie Belter | 24 October 2013, 22:29:43 UTC | InstData Import: set subset name from inst data props or use "unknown" | 03 December 2013, 00:17:57 UTC |
| ae518cc | Eddie Belter | 24 October 2013, 22:29:14 UTC | InstData Import: do not set import format until create inst data | 03 December 2013, 00:17:57 UTC |
| 61be658 | Eddie Belter | 24 October 2013, 22:22:47 UTC | InstData Import: create inst data validates inst data props | 03 December 2013, 00:17:56 UTC |
| 9db52b0 | Eddie Belter | 24 October 2013, 22:01:55 UTC | InstData Import: create inst data uses check for previously imported inst data in helpers | 03 December 2013, 00:17:56 UTC |
| a2656c7 | Eddie Belter | 24 October 2013, 21:55:09 UTC | InstData Import: verify md5 uses check for previously imported inst data in helpers | 03 December 2013, 00:17:55 UTC |
| 98d4173 | Eddie Belter | 24 October 2013, 21:51:08 UTC | InstData Import: add check for previously imported source paths | 03 December 2013, 00:17:55 UTC |
| 7c09ff0 | Eddie Belter | 24 October 2013, 21:04:40 UTC | InstData Import: rm unused code from helpers.t | 03 December 2013, 00:17:54 UTC |
