| 76e92c9 | Thomas B. Mooney | 10 December 2014, 23:11:40 UTC | Merge pull request #302 from tmooney/update_mg_copy_for_ur_update Use regex directly in Genome::ModelGroup::Command::Copy. | 10 December 2014, 23:11:40 UTC |
| bd94a0c | apregier | 10 December 2014, 22:13:03 UTC | Merge pull request #303 from davidlmorton/avoid-sr-get Avoid using SR->get with args other than ID | 10 December 2014, 22:13:03 UTC |
| b3b296b | apregier | 10 December 2014, 22:08:36 UTC | Merge pull request #305 from apregier/fix_coverage_summary_for_cle Fix coverage summary for cle | 10 December 2014, 22:08:36 UTC |
| ca03b7e | apregier | 10 December 2014, 22:08:14 UTC | Merge pull request #307 from apregier/fix_library_names_for_cle_full_report Fix library names for cle full report | 10 December 2014, 22:08:14 UTC |
| 1253f2c | apregier | 10 December 2014, 21:28:38 UTC | Somatic validation builds need to get the region_of_interest_set_name indirectly | 10 December 2014, 21:34:17 UTC |
| 7bfcc50 | apregier | 10 December 2014, 21:30:02 UTC | Library names need to be unique | 10 December 2014, 21:30:02 UTC |
| b026ca0 | apregier | 10 December 2014, 21:26:44 UTC | Add test name to software result query | 10 December 2014, 21:26:44 UTC |
| 68675e1 | apregier | 10 December 2014, 19:36:12 UTC | SeparatedValueWriter dies instead of returning undef Otherwise if you are writing, you would have to check the error messages to know whether you were successful or not | 10 December 2014, 19:36:12 UTC |
| 01258c6 | dmorton | 10 December 2014, 19:00:17 UTC | Avoid using SR->get with args other than ID This will eliminate a non-fatal but noisy error message that has been bothering users. | 10 December 2014, 19:00:17 UTC |
| dd44e07 | Nathaniel Nutter | 10 December 2014, 16:26:39 UTC | Merge pull request #289 from nnutter/RT/102784 if either allele is 'N' then 'N' seems like the most correct IUB | 10 December 2014, 16:26:39 UTC |
| 1140b26 | Anthony Brummett | 10 December 2014, 15:41:57 UTC | Merge pull request #277 from brummett/logging_db Die with a useful error if we can't connect to the logging DB | 10 December 2014, 15:41:57 UTC |
| de7c98d | APipe Tester | 10 December 2014, 13:16:47 UTC | Updated `gmt` tab completion. | 10 December 2014, 13:16:47 UTC |
| dc8a11f | APipe Tester | 10 December 2014, 13:16:06 UTC | Updated `genome` tab completion. | 10 December 2014, 13:16:06 UTC |
| c0bd474 | Thomas B. Mooney | 09 December 2014, 23:46:38 UTC | Merge pull request #288 from tmooney/add_sample_accessors Add our standard "experimental" and "control" accessors. | 09 December 2014, 23:46:38 UTC |
| 3dbca00 | Thomas B. Mooney | 09 December 2014, 23:46:20 UTC | Merge pull request #290 from tmooney/qc_segmented_results Find the result specific to our event. | 09 December 2014, 23:46:20 UTC |
| 9d5e7f4 | Thomas Mooney | 09 December 2014, 22:24:52 UTC | Replace call to removed UR internal subroutine with its constant value. | 09 December 2014, 22:24:52 UTC |
| 43e9827 | apregier | 09 December 2014, 22:09:14 UTC | Merge pull request #299 from apregier/fix_caf_doc Fix documentation string for caf | 09 December 2014, 22:09:14 UTC |
| 6a2748b | apregier | 09 December 2014, 22:06:55 UTC | Merge pull request #300 from apregier/change_cle_plans acmg report only needed by germline plans, not somatic plans | 09 December 2014, 22:06:55 UTC |
| 60fabe1 | David Morton | 09 December 2014, 21:55:26 UTC | Merge pull request #297 from davidlmorton/joinx-version Make sure we specify joinx version for merge | 09 December 2014, 21:55:26 UTC |
| 41c36df | Chris Miller | 09 December 2014, 21:23:17 UTC | Merge pull request #298 from chrisamiller/master adding additional documentation | 09 December 2014, 21:23:17 UTC |
| d780407 | Chris Miller | 09 December 2014, 21:22:00 UTC | whitespace for readability | 09 December 2014, 21:22:00 UTC |
| 4ce8e4c | apregier | 09 December 2014, 20:49:45 UTC | merged reports don't have plan or legend files | 09 December 2014, 20:49:45 UTC |
| a2db004 | apregier | 09 December 2014, 20:18:05 UTC | dbsnp af is reported as ratio, not percent | 09 December 2014, 20:18:05 UTC |
| eb50ebc | apregier | 09 December 2014, 19:43:59 UTC | acmg report only needed by germline plans, not somatic plans | 09 December 2014, 20:14:23 UTC |
| 87655ae | Chris Miller | 09 December 2014, 19:31:14 UTC | adding additional documentation | 09 December 2014, 19:31:14 UTC |
| ebff702 | apregier | 09 December 2014, 19:16:24 UTC | Fix documentation string for caf | 09 December 2014, 19:16:43 UTC |
| 8edbc42 | apregier | 09 December 2014, 18:54:42 UTC | Merge pull request #279 from apregier/make_svr_die SeparatedValueReader dies when columns don't match | 09 December 2014, 18:54:42 UTC |
| 4691b93 | dmorton | 09 December 2014, 17:52:06 UTC | Make sure we specify joinx version for merge | 09 December 2014, 17:52:06 UTC |
| 8a51b42 | Nathaniel Nutter | 09 December 2014, 17:22:27 UTC | update test to current belief of having an 'N' in alleles | 09 December 2014, 17:22:27 UTC |
| 7d1e728 | Thomas Mooney | 09 December 2014, 17:06:02 UTC | Try calling the new accessors. | 09 December 2014, 17:06:02 UTC |
| 2e160fa | Gabriel Sanderson | 09 December 2014, 16:47:13 UTC | Merge pull request #270 from gsanders/tcga Tcga metadata update | 09 December 2014, 16:47:13 UTC |
| 958e822 | APipe Tester | 09 December 2014, 13:16:40 UTC | Updated `genome` tab completion. | 09 December 2014, 13:16:40 UTC |
| 97a691b | APipe Tester | 09 December 2014, 13:14:58 UTC | Updated class browser cache. | 09 December 2014, 13:14:58 UTC |
| 1078980 | David Morton | 08 December 2014, 23:09:15 UTC | Merge pull request #293 from davidlmorton/validate-cle-disk Add command to verify a process for CLE | 08 December 2014, 23:09:15 UTC |
| 5857a11 | dmorton | 08 December 2014, 23:07:50 UTC | Don't include cle_solexa_sequence in cle_disk_group_names | 08 December 2014, 23:07:50 UTC |
| 955f7ea | dmorton | 08 December 2014, 22:57:11 UTC | Add command to verify a process for CLE | 08 December 2014, 22:57:11 UTC |
| 850cb8a | Thomas Mooney | 08 December 2014, 21:45:49 UTC | Find the result specific to our event. | 08 December 2014, 21:45:49 UTC |
| 1556312 | apregier | 08 December 2014, 21:42:09 UTC | Merge pull request #284 from apregier/update_somatic_reports Update somatic reports to match cle trio reports | 08 December 2014, 21:42:09 UTC |
| 789329a | Nathaniel Nutter | 08 December 2014, 20:30:00 UTC | if either allele is 'N' then 'N' seems like the most correct IUB | 08 December 2014, 21:23:46 UTC |
| f85e006 | apregier | 08 December 2014, 21:13:02 UTC | Merge pull request #283 from apregier/fix_per_library_merge_problem Tell the full report what libraries to get vaf info for | 08 December 2014, 21:13:02 UTC |
| 7c84669 | apregier | 08 December 2014, 20:48:13 UTC | Pass label into ModelPair | 08 December 2014, 20:48:25 UTC |
| dad3ee3 | apregier | 08 December 2014, 20:15:51 UTC | Undo overzealous search and replace | 08 December 2014, 20:15:51 UTC |
| ce6e11c | apregier | 08 December 2014, 20:13:22 UTC | Need to return an array ref | 08 December 2014, 20:13:22 UTC |
| 1ac851e | David Morton | 08 December 2014, 20:06:12 UTC | Merge pull request #287 from davidlmorton/listers Listers | 08 December 2014, 20:06:12 UTC |
| fd2d6b2 | Thomas Mooney | 08 December 2014, 19:46:05 UTC | Add our standard "experimental" and "control" accessors. (This way refaligns can also be used as the source builds in `genome model somatic-validation manual-result`.) | 08 December 2014, 19:46:05 UTC |
| 491f173 | dmorton | 08 December 2014, 19:37:15 UTC | Add order_by for list-recent | 08 December 2014, 19:37:15 UTC |
| bb2c80c | dmorton | 08 December 2014, 18:58:11 UTC | Add listers for VariantReporting processes | 08 December 2014, 18:58:11 UTC |
| bcadce5 | dmorton | 08 December 2014, 18:44:20 UTC | Add command to list recently run processes | 08 December 2014, 18:48:47 UTC |
| 1653304 | apregier | 08 December 2014, 18:43:33 UTC | Update expected test data that was missed before | 08 December 2014, 18:43:33 UTC |
| d2c2aa1 | apregier | 08 December 2014, 18:02:25 UTC | Merge pull request #281 from davidlmorton/sr-simple Remove extra / from begining of allocation_path | 08 December 2014, 18:02:25 UTC |
| 8d07692 | apregier | 08 December 2014, 17:54:08 UTC | More efficient library lookup | 08 December 2014, 17:54:08 UTC |
| 92ec53a | apregier | 08 December 2014, 17:43:02 UTC | Plan updates for gold evaluation reports | 08 December 2014, 17:43:02 UTC |
| f5105b0 | Anthony Brummett | 08 December 2014, 17:39:58 UTC | Print a warning when terminating instead of dying immediately This way, the warning message is more likely to be seen than it it were mixed in with the program's output at the beginning. | 08 December 2014, 17:39:58 UTC |
| 282adcc | Dave Larson | 08 December 2014, 17:01:29 UTC | Merge pull request #285 from ernfrid/joinx_version_check Refactor version checking in Joinx. This fixes VcfAnnotate for | 08 December 2014, 17:01:29 UTC |
| 4f0558f | Dave Larson | 08 December 2014, 15:33:35 UTC | use version module in Joinx.pm | 08 December 2014, 15:33:35 UTC |
| 95b76bc | apregier | 08 December 2014, 14:44:08 UTC | Remove separate germline reports | 08 December 2014, 14:44:08 UTC |
| 7be75eb | apregier | 08 December 2014, 14:42:47 UTC | Use the same plan file for single model germline report as cle | 08 December 2014, 14:42:47 UTC |
| 66a17a0 | Dave Larson | 08 December 2014, 05:27:54 UTC | accept minimum version as argument and drop version module from VcfAnnotate | 08 December 2014, 05:27:54 UTC |
| 671e2c0 | Dave Larson | 08 December 2014, 03:35:16 UTC | Refactor version checking in Joinx. This fixes VcfAnnotate for v1.10 and provides a basis for centralizing Joinx version checking as there are other modules that will fail with v1.10 as well. | 08 December 2014, 03:35:16 UTC |
| 875918d | apregier | 08 December 2014, 01:56:26 UTC | Update somatic reports to match cle trio reports | 08 December 2014, 01:57:03 UTC |
| e12b17e | APipe Tester | 08 December 2014, 01:47:50 UTC | Merge pull request #282 from apregier/update_joinx_version | 08 December 2014, 01:47:50 UTC |
| 7148517 | apregier | 08 December 2014, 00:05:31 UTC | Tell the full report what libraries to get vaf info for This way they will all have the same columns even if some have no variants with coverage for a particular library. This makes the hacky "split columns" step during the merge unnecessary | 08 December 2014, 00:07:51 UTC |
| e900908 | apregier | 07 December 2014, 03:30:33 UTC | Use joinx1.10 for vcf-annotate This will give a very large performance improvement | 07 December 2014, 03:46:04 UTC |
| af5d265 | APipe Tester | 06 December 2014, 20:12:00 UTC | updated ur submodule to 6324bbd | 06 December 2014, 20:12:00 UTC |
| 7b28f87 | dmorton | 06 December 2014, 19:52:23 UTC | Remove extra / from begining of allocation_path | 06 December 2014, 19:52:23 UTC |
| 32f71e6 | Nathaniel Nutter | 06 December 2014, 17:37:59 UTC | Merge pull request #273 from nnutter/RT/102920 update tests to not write to GENOME_TEST_INPUTS | 06 December 2014, 17:37:59 UTC |
| 851082e | Nathaniel Nutter | 06 December 2014, 17:10:56 UTC | Merge pull request #269 from iferguson90/mode-fix Fix bitwise bug in G::Utility::File::Mode | 06 December 2014, 17:10:56 UTC |
| c280f69 | APipe Tester | 06 December 2014, 13:16:53 UTC | Updated `genome` tab completion. | 06 December 2014, 13:16:53 UTC |
| fe6e515 | APipe Tester | 06 December 2014, 13:15:06 UTC | Updated class browser cache. | 06 December 2014, 13:15:06 UTC |
| 43a50ee | Nathaniel Nutter | 06 December 2014, 11:01:26 UTC | Merge pull request #280 from nnutter/genome_test_inputs make tests more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 11:01:26 UTC |
| a24f44a | Nathaniel Nutter | 06 December 2014, 09:59:32 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:04:07 UTC |
| da7fcb2 | Nathaniel Nutter | 06 December 2014, 09:57:27 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:04:05 UTC |
| a900853 | Nathaniel Nutter | 06 December 2014, 09:55:03 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:04:02 UTC |
| 728e3a8 | Nathaniel Nutter | 06 December 2014, 09:55:19 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:03:56 UTC |
| f26902f | Nathaniel Nutter | 06 December 2014, 09:45:31 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:02:10 UTC |
| 3c1b1b9 | Nathaniel Nutter | 06 December 2014, 09:38:16 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:02:08 UTC |
| 2ffa3e3 | Nathaniel Nutter | 06 December 2014, 09:29:45 UTC | make test more resilient to GENOME_TEST_INPUTS changes This makes use of the new `compare_dirs` test function and updated test inputs to make this test more resilient to GENOME_TEST_INPUTS changes. | 06 December 2014, 10:02:06 UTC |
| 18646f2 | Nathaniel Nutter | 06 December 2014, 09:28:40 UTC | add compare_dirs Adds a compare_dirs test function for comparing the files in two directories. | 06 December 2014, 10:02:04 UTC |
| a3faf3b | Nathaniel Nutter | 06 December 2014, 02:40:18 UTC | remove commented out debug code | 06 December 2014, 10:02:02 UTC |
| a149b94 | Nathaniel Nutter | 06 December 2014, 02:39:48 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:02:00 UTC |
| 2157afe | David Morton | 06 December 2014, 04:45:50 UTC | Merge pull request #276 from davidlmorton/trio Trio | 06 December 2014, 04:45:50 UTC |
| ed62145 | dmorton | 06 December 2014, 03:41:57 UTC | Merge branch 'master' of github.com:genome/genome into trio Conflicts: lib/perl/Genome/Model/SomaticValidation/Command/CoverageStatsSummary.pm | 06 December 2014, 03:41:57 UTC |
| dac6531 | dmorton | 06 December 2014, 03:34:14 UTC | Add plan_yaml to expected directories | 06 December 2014, 03:39:09 UTC |
| 6f01097 | dmorton | 06 December 2014, 03:32:57 UTC | Allow transient properties in show-docs | 06 December 2014, 03:39:09 UTC |
| c7d7ef8 | dmorton | 06 December 2014, 03:31:37 UTC | Make compare_directories work more intuitivly is and is_deeply use (got, expected) so we changed the order. | 06 December 2014, 03:39:09 UTC |
| 0f67826 | dmorton | 06 December 2014, 03:30:36 UTC | Remove overly sensitive test | 06 December 2014, 03:39:08 UTC |
| cbc72d7 | dmorton | 06 December 2014, 01:54:59 UTC | Allowing withManySampleNames to live on DB backed objects. | 06 December 2014, 03:39:08 UTC |
| 10eee49 | dmorton | 06 December 2014, 01:54:34 UTC | Fix extra \t in full-reporter | 06 December 2014, 03:39:08 UTC |
| 9ecd767 | dmorton | 06 December 2014, 01:53:44 UTC | Fixed compare_directories in TestHelper | 06 December 2014, 03:39:07 UTC |
| e57c7d2 | dmorton | 06 December 2014, 00:39:52 UTC | Eliminate redundant definition | 06 December 2014, 03:39:07 UTC |
| 72224b9 | dmorton | 06 December 2014, 00:38:46 UTC | Disable Report Object validation during Plan validation | 06 December 2014, 03:39:07 UTC |
| 6f14d1c | dmorton | 06 December 2014, 00:35:38 UTC | Report::WithHeader validates during initialize It was being validated when the Report Plan was validated, but now that it isn't we validate at runtime. At least this way we still see the nice error messages, albiet later than we used to. | 06 December 2014, 02:08:34 UTC |
| e506d33 | dmorton | 05 December 2014, 23:56:27 UTC | Remove combination_label from test data | 06 December 2014, 02:08:34 UTC |
| 527719c | dmorton | 05 December 2014, 23:55:40 UTC | Make CreateMergedReports dag name generic | 06 December 2014, 02:08:33 UTC |
| d93177e | dmorton | 05 December 2014, 23:19:26 UTC | Delete transient after Results are got/created The transients sometimes contain values that Flow cannot serialize/deserialize. It shouldn't affect anything since they were transient (i.e. not persisted to the db). | 06 December 2014, 02:08:33 UTC |
| 19b52f4 | dmorton | 05 December 2014, 22:42:00 UTC | Fix required/requires oversight | 06 December 2014, 02:08:33 UTC |
| df97b17 | apregier | 06 December 2014, 02:01:24 UTC | SeparatedValueReader dies when columns don't match otherwise when you are looping through a file using next, it will just truncate the file and print an error message, without any other clue that something is wrong. | 06 December 2014, 02:06:23 UTC |
| 1bb098c | dmorton | 05 December 2014, 21:08:42 UTC | Add resassuring message | 06 December 2014, 02:02:14 UTC |
| 794fa45 | Nathaniel Nutter | 06 December 2014, 01:43:30 UTC | Merge pull request #267 from nnutter/apipe_ci add apipe_ci as valid disk group | 06 December 2014, 01:43:30 UTC |
| 1ddeaac | Nathaniel Nutter | 06 December 2014, 01:25:44 UTC | Merge pull request #278 from nnutter/cross_sample_test replace test_dir with TEST_INPUTS_DIR | 06 December 2014, 01:25:44 UTC |
