| b5cea18 | Chris Miller | 22 February 2016, 18:11:53 UTC | Merge pull request #1267 from chrisamiller/copyconfig don't copy config if to and from projects are the same | 22 February 2016, 18:11:53 UTC |
| baf6260 | Chris Miller | 22 February 2016, 16:58:06 UTC | return instead of return 0 | 22 February 2016, 16:58:06 UTC |
| ffb4f44 | Chris Miller | 22 February 2016, 16:53:10 UTC | don't copy config if to and from projects are the same | 22 February 2016, 16:53:10 UTC |
| 33307e3 | APipe Tester | 19 February 2016, 13:17:06 UTC | Updated `genome` tab completion. | 19 February 2016, 13:17:06 UTC |
| aa096af | APipe Tester | 19 February 2016, 13:15:32 UTC | Updated class browser cache. | 19 February 2016, 13:15:32 UTC |
| fe7072e | Thomas B. Mooney | 18 February 2016, 21:56:45 UTC | Merge pull request #1263 from tmooney/remove_disused_refalign_events Remove disused ReferenceAlignment events. | 18 February 2016, 21:56:45 UTC |
| 8ee1ec4 | Thomas B. Mooney | 18 February 2016, 21:32:36 UTC | Merge pull request #1257 from tmooney/analysis_project_view_includes_environmental_configuration AnalysisProject View: Display Environment Config if One Exists. | 18 February 2016, 21:32:36 UTC |
| 1f8e53f | Thomas B. Mooney | 18 February 2016, 21:32:05 UTC | Merge pull request #1260 from tmooney/no_more_default_profile Remove Old "Default Profile"s CHANGELOG: The SomaticValidation helper commands for defining models will no longer choose a default processing-profile, so one must be explicitly specified. (This does not affect models created via Analysis Projects.) | 18 February 2016, 21:32:05 UTC |
| 9a994fc | Thomas Mooney | 18 February 2016, 21:05:00 UTC | Let read_file() decide if the file can be read. | 18 February 2016, 21:05:00 UTC |
| bc086f4 | Thomas Mooney | 11 February 2016, 22:21:19 UTC | Add a block for environment config if one exists. | 18 February 2016, 21:00:57 UTC |
| 8721a64 | Thomas Mooney | 18 February 2016, 20:57:22 UTC | Processing Profile is required, so don't need to check if it's there. | 18 February 2016, 20:57:22 UTC |
| dce87d7 | Thomas B. Mooney | 18 February 2016, 20:51:24 UTC | Merge pull request #1254 from tmooney/remove_pp_initalize_build_support Remove Delegation of `_initialize_build` to ProcessingProfiles. | 18 February 2016, 20:51:24 UTC |
| 293be2a | APipe Tester | 18 February 2016, 18:15:17 UTC | updated ur submodule to 3a5ed79 | 18 February 2016, 18:15:17 UTC |
| 053b66f | APipe Tester | 18 February 2016, 17:35:30 UTC | updated ur submodule to ec9b072 | 18 February 2016, 17:35:30 UTC |
| 6075c48 | Susanna Kiwala | 18 February 2016, 16:54:56 UTC | Merge pull request #1262 from susannasiebert/build_metrics Change G::M::B results to use result_associations instead of result_users | 18 February 2016, 16:54:56 UTC |
| 48ddecf | Eddie Belter | 17 February 2016, 23:00:21 UTC | Merge pull request #1244 from ebelter/import-fastq Import Fastq Updates | 17 February 2016, 23:00:21 UTC |
| 4e9705a | Thomas Mooney | 17 February 2016, 21:52:20 UTC | Remove disused ReferenceAlignment events. * Old builds will now see these as "Generic" events. | 17 February 2016, 21:52:20 UTC |
| 76fb75a | Thomas B. Mooney | 17 February 2016, 20:45:20 UTC | Merge pull request #1259 from tmooney/somaticvalidation_uses_workflowbuilder SomaticValidation Workflow is Instantiated with WorkflowBuilder. | 17 February 2016, 20:45:20 UTC |
| ddc7aad | Susanna Kiwala | 17 February 2016, 19:15:59 UTC | Change G::M::B results to use result_associations instead of result_users This will ensure that results returns a unique list. | 17 February 2016, 19:15:59 UTC |
| d829f6f | Thomas B. Mooney | 17 February 2016, 18:24:34 UTC | Merge pull request #1261 from tmooney/restore_known_sites_magic Restore the known_sites Magic to SomaticValidation | 17 February 2016, 18:24:34 UTC |
| a8e84ac | Thomas Mooney | 16 February 2016, 15:38:20 UTC | Remove default profile listing from SomaticValidation. Users of the "define-validation-model" command will now have to supply a processing-profile explicitly. | 16 February 2016, 22:41:59 UTC |
| 941eddd | Thomas Mooney | 16 February 2016, 20:01:39 UTC | Restore the known_sites magic removed in 2a4ac6c9d37f5ea6ae96a0886d611b26e2a9c9e7. known_sites is an is_many property, and the automatic generation of the id property is not set to happen for is_many inputs. | 16 February 2016, 20:01:39 UTC |
| 4fb7eff | Chris Miller | 16 February 2016, 15:58:50 UTC | Merge pull request #1258 from chrisamiller/conc added mm9 snps to examples | 16 February 2016, 15:58:50 UTC |
| 0c0acaa | Thomas Mooney | 16 February 2016, 15:13:53 UTC | Remove default profile listing from ReferenceAlignment. Hardcode the aligner name in the weird "default alignment" heuristic instead! | 16 February 2016, 15:13:53 UTC |
| ab22691 | Thomas Mooney | 16 February 2016, 14:40:34 UTC | SomaticValidation workflow is instantiated with WorkflowBuilder. | 16 February 2016, 14:40:34 UTC |
| 7c2230f | Eddie Belter | 15 February 2016, 23:30:40 UTC | Fastq to Bam: use sys line count | 15 February 2016, 23:30:43 UTC |
| e52b4cf | Eddie Belter | 15 February 2016, 23:29:30 UTC | Fastq to Bam: add done | 15 February 2016, 23:29:30 UTC |
| 6b8d4de | Eddie Belter | 15 February 2016, 23:29:07 UTC | Fastq to Bam: use debug messages | 15 February 2016, 23:29:07 UTC |
| 0d6802e | Chris Miller | 15 February 2016, 22:38:00 UTC | Merge remote-tracking branch 'origin/master' into conc | 15 February 2016, 22:38:00 UTC |
| f05a242 | Chris Miller | 15 February 2016, 22:37:41 UTC | added mm9 snps to examples | 15 February 2016, 22:37:41 UTC |
| 641a6c1 | Thomas B. Mooney | 15 February 2016, 19:57:44 UTC | Merge pull request #1255 from tmooney/remove_old_alignment_accessors Remove Old Alignment Accessors | 15 February 2016, 19:57:44 UTC |
| 4df8f38 | Thomas B. Mooney | 15 February 2016, 14:51:03 UTC | Merge pull request #1253 from tmooney/createreport_uses_standard_somvar_accessors SomVar CreateReport uses Build Accessors for BAMs and Reference | 15 February 2016, 14:51:03 UTC |
| 9eea86b | Chris Miller | 12 February 2016, 20:20:22 UTC | Merge pull request #1247 from chrisamiller/master typo in docs | 12 February 2016, 20:20:22 UTC |
| bf2cc96 | APipe Tester | 12 February 2016, 13:16:44 UTC | Updated `genome` tab completion. | 12 February 2016, 13:16:44 UTC |
| fe70a5d | APipe Tester | 12 February 2016, 13:15:11 UTC | Updated class browser cache. | 12 February 2016, 13:15:11 UTC |
| 9f89d66 | Thomas B. Mooney | 11 February 2016, 22:28:14 UTC | Merge pull request #1252 from tmooney/build_export_improvements Further Refinements to Build Export | 11 February 2016, 22:28:14 UTC |
| d710c88 | Thomas B. Mooney | 11 February 2016, 20:31:20 UTC | Merge pull request #1250 from tmooney/quiet_autoload_warning_in_refalign_summary_report Use GMT:Joinx::SnvConcordanceByQuality in RefAlign Summary Report. | 11 February 2016, 20:31:20 UTC |
| 6769e4d | Susanna Kiwala | 11 February 2016, 18:33:19 UTC | Merge pull request #1251 from susannasiebert/epitope_prediction_bugfix2 Add transcript id to the fasta headers to ensure uniqueness | 11 February 2016, 18:33:19 UTC |
| beeb317 | Thomas B. Mooney | 11 February 2016, 18:21:36 UTC | Merge pull request #1246 from tmooney/remove_obsolete_refalign_pp_params Remove Obsolete RefAlign ProcessingProfile Parameters | 11 February 2016, 18:21:36 UTC |
| baac23b | Eddie Belter | 11 February 2016, 17:13:02 UTC | Merge pull request #1243 from ebelter/unarchive-imported-instdata Disk Allocation Unarchive | 11 February 2016, 17:13:02 UTC |
| 176611f | Thomas Mooney | 11 February 2016, 15:11:47 UTC | Remove old instrument-data indirect accessors. The "temp hack" was added in bd502ac71a8a613e95af57f429d98b1d948abc76 on 14 July 2008 to the original Genome::Model. It was then migrated to Genome::Model::ShortRead before moving to its most recent location here in Genome::Model::ReferenceAlignment. | 11 February 2016, 15:11:47 UTC |
| f860c3e | Thomas Mooney | 11 February 2016, 15:03:44 UTC | Remove build_subclass_name from RefAlign. The TODO told me to! | 11 February 2016, 15:03:44 UTC |
| 219a27c | Thomas Mooney | 11 February 2016, 15:00:10 UTC | Remove "latest_build_bam_file". This can be listed now with latest_build.whole_rmdup_bam_file. | 11 February 2016, 15:00:10 UTC |
| d265030 | Thomas Mooney | 11 February 2016, 14:54:10 UTC | Remove accessors for .map files. Sorry, maq. | 11 February 2016, 14:54:10 UTC |
| c9640a9 | Thomas Mooney | 11 February 2016, 14:52:03 UTC | Remove old accessors for getting allocations owned by events. BAMs are "now" stored in SoftwareResults! | 11 February 2016, 14:52:03 UTC |
| 21f1ad8 | Susanna Kiwala | 11 February 2016, 14:47:15 UTC | Merge pull request #1248 from susannasiebert/epitope_prediction_bugfix Pass is_many property as an array ref | 11 February 2016, 14:47:15 UTC |
| 457b0ef | Susanna Kiwala | 11 February 2016, 14:46:49 UTC | Move iterator incrementation to a more appropriate place | 11 February 2016, 14:46:49 UTC |
| 5dc98c3 | Susanna Kiwala | 11 February 2016, 14:41:35 UTC | Simplify iterator creation | 11 February 2016, 14:41:35 UTC |
| caa6783 | Susanna Kiwala | 11 February 2016, 14:41:10 UTC | Fix test file | 11 February 2016, 14:41:10 UTC |
| 725f6d4 | Susanna Kiwala | 11 February 2016, 14:36:43 UTC | New test file for multiple transcripts | 11 February 2016, 14:36:43 UTC |
| ae9cde3 | Thomas Mooney | 11 February 2016, 14:31:29 UTC | Remove support for delegating _initialize_build to processing profiles. | 11 February 2016, 14:31:29 UTC |
| af219b7 | Thomas Mooney | 11 February 2016, 14:31:04 UTC | Move RefAlign _initialize_build to the model class. | 11 February 2016, 14:31:04 UTC |
| c58db23 | Eddie Belter | 11 February 2016, 01:02:46 UTC | Remove unused helper fastq count methods | 11 February 2016, 01:02:46 UTC |
| 10cda38 | Thomas Mooney | 10 February 2016, 23:44:04 UTC | Use standard SomVar accessors to get BAMs and references. | 10 February 2016, 23:44:04 UTC |
| a7d750b | Thomas Mooney | 10 February 2016, 23:43:33 UTC | Both input builds to SomVar should share a common reference. | 10 February 2016, 23:43:33 UTC |
| 6e49272 | Thomas Mooney | 10 February 2016, 19:34:35 UTC | Use GMT:Joinx::SnvConcordanceByQuality. This quiets the warning: Use of inherited AUTOLOAD for non-method Genome::Model::Tools::Joinx::SnvConcordanceByQuality::parse_results_file() is deprecated at .../Genome/Model/ReferenceAlignment/Report/Summary.pm line 220. | 10 February 2016, 23:15:27 UTC |
| 040c7d6 | Thomas B. Mooney | 10 February 2016, 22:11:21 UTC | Merge pull request #1242 from tmooney/resurrect_per_iteration_stat Check for directory existence each time before calling mkdir. | 10 February 2016, 22:11:21 UTC |
| 97ce67f | Eddie Belter | 10 February 2016, 22:05:34 UTC | Unarchive: check first before adding instdata to AnP | 10 February 2016, 22:05:34 UTC |
| 1c1dfc1 | Thomas Mooney | 10 February 2016, 21:43:00 UTC | Paranoidly refuse to unlink things outside our export directory. This shouldn't happen as long as our algorithm is correct, but makes modifications less scary! | 10 February 2016, 21:48:59 UTC |
| 9bf6aaa | Allison Penner Regier | 10 February 2016, 21:45:41 UTC | Merge pull request #1231 from apregier/list_hc_files Command to print out all haplotype caller output files | 10 February 2016, 21:45:41 UTC |
| 8209da2 | Thomas Mooney | 10 February 2016, 21:40:45 UTC | Handle dangling symlinks ourselves now that follow is disabled. | 10 February 2016, 21:40:45 UTC |
| 7003a5b | Susanna Kiwala | 10 February 2016, 21:40:29 UTC | Add an iterator to cover edge case where transcript id is the same | 10 February 2016, 21:40:29 UTC |
| e4ea977 | Thomas Mooney | 10 February 2016, 21:22:33 UTC | Don't follow symlinks. We're explicitly handling them in the $resolve_symlinks function. | 10 February 2016, 21:22:33 UTC |
| 0b36a87 | Thomas Mooney | 10 February 2016, 21:03:05 UTC | Only recursively find on directories. | 10 February 2016, 21:03:05 UTC |
| 69f539c | Thomas Mooney | 10 February 2016, 21:00:26 UTC | Use abs_path to get the symlink destination. $File::Find::fullname is not always defined. This brings the symlink and the dangling-symlink approach to parity. | 10 February 2016, 21:00:26 UTC |
| 3b97b8e | Thomas Mooney | 10 February 2016, 20:59:18 UTC | Friendlier error message when the target directory doesn't exist. Previously this would confusingly report the "Not enough space..." error. | 10 February 2016, 20:59:18 UTC |
| 5f960bb | Susanna Kiwala | 10 February 2016, 19:35:06 UTC | Add transcript id to the fasta headers to ensure uniqueness | 10 February 2016, 19:38:23 UTC |
| 5264956 | Susanna Kiwala | 10 February 2016, 18:47:03 UTC | Pass is_many property as an array ref | 10 February 2016, 18:47:03 UTC |
| 4a09a45 | Chris Miller | 10 February 2016, 17:45:47 UTC | typo in docs | 10 February 2016, 17:46:44 UTC |
| eb74062 | Thomas Mooney | 10 February 2016, 16:31:42 UTC | Remove "read_calibrator_name" and "read_calibrator_params". No processing profiles have these set. | 10 February 2016, 16:34:14 UTC |
| 21cff02 | Thomas Mooney | 10 February 2016, 16:27:42 UTC | Remove deprecated "capture_set_name" parameter. These have been using the "target_region_set_name" and "region_of_interest_set_name" inputs for years! | 10 February 2016, 16:34:14 UTC |
| 8be504c | Thomas Mooney | 10 February 2016, 16:26:51 UTC | Remove obsolete "prior_ref_seq" parameter. | 10 February 2016, 16:34:13 UTC |
| 2574091 | Thomas Mooney | 10 February 2016, 16:18:45 UTC | Remove things that asked to be removed. They weren't referenced anywhere, so fulfil their destiny. | 10 February 2016, 16:34:13 UTC |
| f454481 | Thomas Mooney | 10 February 2016, 16:14:34 UTC | Remove obsolete parameter "align_dist_threshold". As best I can tell this was used in "AcceptReads" in very early versions of the pipeline. | 10 February 2016, 16:34:08 UTC |
| 7bbb7d2 | Thomas Mooney | 10 February 2016, 16:02:55 UTC | Remove special-casing for "maq". This will change the returned value for some old processing profiles, but they don't work any more, anyway. | 10 February 2016, 16:02:55 UTC |
| b539f28 | Thomas Mooney | 10 February 2016, 16:00:21 UTC | Remove maq-related parameter "multi_read_fragment_strategy". | 10 February 2016, 16:00:21 UTC |
| 1b14cd3 | Thomas B. Mooney | 10 February 2016, 14:02:58 UTC | Merge pull request #1239 from tmooney/stop_subclassing_refalign_processingprofiles Stop subclassing ReferenceAlignment ProcessingProfiles on sequencing_platform. | 10 February 2016, 14:02:58 UTC |
| 84c5a63 | APipe Tester | 10 February 2016, 13:16:42 UTC | Updated `genome` tab completion. | 10 February 2016, 13:16:42 UTC |
| b02631c | APipe Tester | 10 February 2016, 13:15:11 UTC | Updated class browser cache. | 10 February 2016, 13:15:11 UTC |
| 25c2afa | Eddie Belter | 10 February 2016, 00:27:23 UTC | Make fastq to bam ahve role removes input files | 10 February 2016, 00:27:23 UTC |
| 64201d9 | Eddie Belter | 10 February 2016, 00:16:09 UTC | Import Fastqs: get and check line counts | 10 February 2016, 00:21:45 UTC |
| 0ac9199 | Eddie Belter | 09 February 2016, 23:50:37 UTC | Import Fastq: use archive extract to gunzip | 09 February 2016, 23:50:37 UTC |
| 2289a7a | Eddie Belter | 09 February 2016, 23:48:24 UTC | With Working Dir: add method to get new file name in working directory | 09 February 2016, 23:48:24 UTC |
| f2eacc5 | Eddie Belter | 09 February 2016, 21:47:57 UTC | Revert "InstData Import: do not unarchive fastqs" This reverts commit bec97f92864fcde705f5b6bb162f9502c4bf4275. Never forget - fastq to sam may or may not like your gzipped fastqs! | 09 February 2016, 22:49:44 UTC |
| 4e18ef9 | Eddie Belter | 09 February 2016, 22:47:44 UTC | Merge pull request #1234 from ebelter/import-tweaks InstData Import Fixes and Improvements | 09 February 2016, 22:47:44 UTC |
| 15fe3ae | Eddie Belter | 09 February 2016, 21:25:19 UTC | spell check | 09 February 2016, 21:25:19 UTC |
| b272c7c | Eddie Belter | 09 February 2016, 20:25:21 UTC | Spell/grammer check | 09 February 2016, 20:25:21 UTC |
| 2e609ae | Eddie Belter | 09 February 2016, 20:21:18 UTC | Merge pull request #1238 from ebelter/instdata-delete-command InstData Delete CLI | 09 February 2016, 20:21:18 UTC |
| 6cfafa4 | Eddie Belter | 09 February 2016, 19:48:35 UTC | Unarchive: convert to subtests | 09 February 2016, 19:50:19 UTC |
| 5a33a8c | Eddie Belter | 09 February 2016, 19:36:43 UTC | Unarchive: use sub install in test | 09 February 2016, 19:36:43 UTC |
| fd4ae2b | Eddie Belter | 09 February 2016, 19:36:17 UTC | Unarchive: allow imported instrument data | 09 February 2016, 19:36:17 UTC |
| 30634f3 | Thomas Mooney | 09 February 2016, 19:15:48 UTC | Check for directory existence each time before calling mkdir. This partially reverts 0a28189020054af452b08c8d496234b1734bf403 from PR #809. | 09 February 2016, 19:15:48 UTC |
| ce9b9be | Eddie Belter | 09 February 2016, 00:23:03 UTC | Unarchive: make and use create allocation function in test | 09 February 2016, 19:04:09 UTC |
| 03335f5 | Eddie Belter | 09 February 2016, 19:03:31 UTC | Set no commit in delete test | 09 February 2016, 19:03:31 UTC |
| 3cb9770 | Anthony Brummett | 09 February 2016, 14:28:08 UTC | Merge pull request #1241 from brummett/genome-test-env-alloc-cleanup Ensure allocations are cleaned up when genome-test-env exits | 09 February 2016, 14:28:08 UTC |
| 3400c40 | APipe Tester | 09 February 2016, 13:18:00 UTC | Updated `gmt` tab completion. | 09 February 2016, 13:18:00 UTC |
| 68b02d1 | APipe Tester | 09 February 2016, 13:17:18 UTC | Updated `genome` tab completion. | 09 February 2016, 13:17:18 UTC |
| c0a8cdd | APipe Tester | 09 February 2016, 13:15:46 UTC | Updated class browser cache. | 09 February 2016, 13:15:46 UTC |
| d2e80c6 | Eddie Belter | 08 February 2016, 23:46:46 UTC | InstData: delete command test ensures only imported instdata is deleted | 08 February 2016, 23:46:46 UTC |
| a8beaf0 | Eddie Belter | 08 February 2016, 21:23:11 UTC | Fix removes input files role test | 08 February 2016, 21:23:11 UTC |
