| 56940f7 | Thomas B. Mooney | 06 January 2015, 19:46:03 UTC | Merge pull request #381 from tmooney/delegatestoresult_default_input_hash_implementation A default implementation of G:C:DelegatesToResult->input_hash() | 06 January 2015, 19:46:03 UTC |
| 8700bfb | Avinash Ramu | 06 January 2015, 17:32:34 UTC | Merge pull request #385 from gatoravi/clinseq-docm-update add baseq, mapq parameters for docm bamrc. | 06 January 2015, 17:32:34 UTC |
| d7e97b4 | Avinash Ramu | 06 January 2015, 14:55:33 UTC | add baseq, mapq parameters for docm bamrc. control the mapping quality and base quality parameters for bam-readcounting for DOCM sites. We need to be as sensitive as possible so set these to the absolute minimum. | 06 January 2015, 14:55:33 UTC |
| 15231af | Thomas B. Mooney | 06 January 2015, 14:45:46 UTC | Merge pull request #383 from tmooney/remove_withsavedresults_and_buildstepwrapper Fixes for HtseqCount in RnaSeq; Final Removal of WithSavedResults and BuildStepWrapper. | 06 January 2015, 14:45:46 UTC |
| fcc13d1 | APipe Tester | 06 January 2015, 13:17:40 UTC | Updated `gmt` tab completion. | 06 January 2015, 13:17:40 UTC |
| ec8a590 | APipe Tester | 06 January 2015, 13:16:56 UTC | Updated `genome` tab completion. | 06 January 2015, 13:16:56 UTC |
| 3aa21a0 | APipe Tester | 06 January 2015, 13:15:12 UTC | Updated class browser cache. | 06 January 2015, 13:15:12 UTC |
| 3756b93 | David Morton | 06 January 2015, 02:18:12 UTC | Merge pull request #379 from davidlmorton/optional_plan_inputs Optional plan inputs | 06 January 2015, 02:18:12 UTC |
| ee44751 | Thomas Mooney | 05 January 2015, 20:38:45 UTC | Link the result of HtseqCount into the RnaSeq build directory. | 05 January 2015, 22:26:16 UTC |
| dc50be0 | Thomas Mooney | 05 January 2015, 20:04:19 UTC | Remove "BuildStepWrapper". | 05 January 2015, 22:26:15 UTC |
| f7fc4b9 | Thomas Mooney | 05 January 2015, 20:00:41 UTC | Stop using BuildStepWrapper in RnaSeq. This fixes the inconsistency introduced in #375 wherein the wrapper was still called even though the underlying command no longer is a WithSavedResults. | 05 January 2015, 22:26:15 UTC |
| 7552dad | Thomas Mooney | 05 January 2015, 19:05:48 UTC | Remove G:C:WithSavedResults and SR::Default. | 05 January 2015, 22:26:14 UTC |
| fa8953e | Travis Abbott | 02 January 2015, 20:46:55 UTC | add bedtools_version to params params_for_merged_alignment the merged alignment result needs it so it can find the alignment results to merge. | 05 January 2015, 21:17:33 UTC |
| 7e5e8d4 | Travis Abbott | 31 December 2014, 20:48:45 UTC | add bedtools version to params_for_alignment | 05 January 2015, 21:17:32 UTC |
| 92e8d9a | Travis Abbott | 31 December 2014, 20:48:26 UTC | remove unused processing_profile_params_for_alignment from refalign | 05 January 2015, 21:17:32 UTC |
| ab4980e | Travis Abbott | 31 December 2014, 20:44:55 UTC | add debug messages about program versions | 05 January 2015, 21:17:32 UTC |
| 42c16be | Travis Abbott | 31 December 2014, 18:40:57 UTC | wire up bedtools_version in composite alignment workflows | 05 January 2015, 21:17:31 UTC |
| 28be8b1 | Travis Abbott | 31 December 2014, 18:36:30 UTC | add bedtools version to AlignReads command this optional param will now be passed in when running an InstrumentData::Composite::Workflow | 05 January 2015, 21:17:31 UTC |
| 32f5eb3 | Travis Abbott | 31 December 2014, 18:37:44 UTC | fix samtools version in aligner api v6 it was supposed to be 0.1.19 | 05 January 2015, 21:17:30 UTC |
| 99c6502 | Travis Abbott | 24 December 2014, 09:51:40 UTC | fix outdated comments about file descriptor juggling | 05 January 2015, 21:17:30 UTC |
| 78b9788 | Travis Abbott | 22 December 2014, 23:20:54 UTC | add bedtools_version param to alignment result this can also go in reference alignment processing profiles and exists as part of the aligner api starting with v6 | 05 January 2015, 21:17:29 UTC |
| 5b45717 | Travis Abbott | 22 December 2014, 22:51:03 UTC | simplify file descriptor juggling now, we swap stdin/stderr and use tee to a) keep the original stderr b) have another copy to mess with for warning checking of course we swap them back later on :) | 05 January 2015, 21:17:29 UTC |
| 64b73fe | Travis Abbott | 22 December 2014, 18:26:37 UTC | add bam input to gmt bwa run-mem this lets us stream from bam -> fastq rather than dumping fastqs to /tmp | 05 January 2015, 21:17:28 UTC |
| 2b8a624 | Travis Abbott | 20 December 2014, 02:00:18 UTC | add bedtools 2.17.0 to valid versions This is already installed, we just didn't have it in the version hash. Some other minor module cleanup (whitespace/errmsgs) too. | 05 January 2015, 21:17:27 UTC |
| 6d639bb | Travis Abbott | 20 December 2014, 01:50:18 UTC | import fixups removing some unused imports. | 05 January 2015, 21:17:27 UTC |
| 5adb8a3 | Travis Abbott | 19 December 2014, 20:38:01 UTC | update bamqc error-rate version selection test for bwa mem: $name eq 'bwamem' # do not want $name =~ /^bwamem/ # much better (matches bwamem-stream) | 05 January 2015, 21:17:26 UTC |
| cd64e00 | Travis Abbott | 18 December 2014, 20:30:00 UTC | add bwamem-stream aligner module runs bwa mem | sort | calmd to avoid touching /tmp so much | 05 January 2015, 21:17:26 UTC |
| cc9d5d8 | Travis Abbott | 18 December 2014, 17:17:11 UTC | remove -f param from samtools sort (v0.1.19) there's a samtools bug that will cause a crash if the bam is large enough to cause temp files to be written. | 05 January 2015, 21:17:25 UTC |
| 2725bae | Thomas B. Mooney | 05 January 2015, 20:42:40 UTC | Merge pull request #366 from tmooney/polymutt_denovo_print Minor PolymuttDenovo Filter Improvements | 05 January 2015, 20:42:40 UTC |
| d4552cf | Thomas B. Mooney | 05 January 2015, 18:47:52 UTC | Merge pull request #373 from tmooney/remove_nonfunctional_cosmic_importer Remove WithSavedResults from Genome::Db::Cosmic::Command::Import | 05 January 2015, 18:47:52 UTC |
| bdbde82 | Ian Ferguson | 05 January 2015, 18:15:37 UTC | Merge pull request #348 from iferguson90/bsmap-fix Disable fillmd/BamQc for bsmap | 05 January 2015, 18:15:37 UTC |
| 65f0356 | Anthony Brummett | 05 January 2015, 17:39:58 UTC | Merge pull request #357 from brummett/iterate iterate_file_lines() | 05 January 2015, 17:39:58 UTC |
| 5ccff61 | Thomas Mooney | 05 January 2015, 16:14:23 UTC | Remove subclass implementations of input_hash() that can use default. | 05 January 2015, 16:14:23 UTC |
| d562ce6 | Thomas Mooney | 05 January 2015, 15:03:32 UTC | Add a default implementation of input_hash() in G:C:DelegatesToResult (Pulled up from GMT:Htseq::Count.) | 05 January 2015, 15:03:32 UTC |
| dc5f8ca | Thomas B. Mooney | 05 January 2015, 14:34:28 UTC | Merge pull request #375 from tmooney/htseq_count_delegates_to_result Convert GMT::Htseq::Count to a G:C::DelegatesToResult | 05 January 2015, 14:34:28 UTC |
| aa8c819 | Thomas B. Mooney | 05 January 2015, 14:27:47 UTC | Merge pull request #376 from tmooney/dont_use_models_inputs Query reference alignment build directly for inputs. | 05 January 2015, 14:27:47 UTC |
| fc35e14 | Thomas B. Mooney | 05 January 2015, 14:27:29 UTC | Merge pull request #372 from tmooney/correct_refalign_get_alignments get_alignments() defers to existing method to get each alignment. | 05 January 2015, 14:27:29 UTC |
| e3fd955 | Thomas B. Mooney | 05 January 2015, 14:24:46 UTC | Merge pull request #371 from tmooney/remove_old_subclassification_methods Remove old subclassification methods from ReferenceAlignment. | 05 January 2015, 14:24:46 UTC |
| a81d05b | Thomas B. Mooney | 05 January 2015, 14:24:23 UTC | Merge pull request #369 from tmooney/file_summaries_only_of_allocations Don't generate file summaries if we can't reach the target directory. | 05 January 2015, 14:24:23 UTC |
| b816121 | APipe Tester | 05 January 2015, 13:15:59 UTC | Updated `genome` tab completion. | 05 January 2015, 13:15:59 UTC |
| 96d4e1f | Avinash Ramu | 04 January 2015, 19:13:47 UTC | Merge pull request #355 from gatoravi/clinseq_converge_stats_update clinseq-converge-stats update | 04 January 2015, 19:13:47 UTC |
| 607d340 | dmorton | 04 January 2015, 01:48:38 UTC | Die if no translations given for is_many translated input We were previously only checking that an entry exists in the translations file, now it will die if there is an entry that is an empty array-ref as well. | 04 January 2015, 04:34:36 UTC |
| ac84fa8 | dmorton | 04 January 2015, 00:39:16 UTC | Allow optional is_many translated plan inputs This was not working as intended, because if the plan didn't specify the optional input then it would be undef, which cannot be dereferenced as an array. | 04 January 2015, 04:34:36 UTC |
| 627bfb3 | Thomas Mooney | 31 December 2014, 21:42:54 UTC | Query build directly for inputs. The model inputs might have changed from what's recorded on the build as we progress. The builds then cannot be trusted. | 31 December 2014, 21:42:54 UTC |
| 5a1fa3a | Thomas B. Mooney | 31 December 2014, 20:47:07 UTC | Merge pull request #370 from tmooney/respect_active_flag_in_ar Respect the active flag when deciding if it's safe to delete children. | 31 December 2014, 20:47:07 UTC |
| 8deb956 | David Morton | 31 December 2014, 20:22:30 UTC | Merge pull request #347 from davidlmorton/header_labels Header labels | 31 December 2014, 20:22:30 UTC |
| 59c1336 | dmorton | 31 December 2014, 20:20:42 UTC | Fix show-docs expected output This changed when we started use 'pp' to format default values. | 31 December 2014, 20:20:42 UTC |
| 7b948ca | Thomas Mooney | 31 December 2014, 20:00:43 UTC | Convert GMT::Htseq::Count to a G:C::DelegatesToResult | 31 December 2014, 20:00:43 UTC |
| 84d6cde | dmorton | 31 December 2014, 19:35:56 UTC | Merge remote-tracking branch 'origin/master' into header_labels Conflicts: lib/perl/Genome/VariantReporting/Command/ShowDocs.t.expected-output/interpreters/variant-callers | 31 December 2014, 19:35:56 UTC |
| 001e804 | dmorton | 31 December 2014, 18:36:58 UTC | bugfix (grep properties not property names) | 31 December 2014, 19:03:41 UTC |
| 65a175d | David Morton | 31 December 2014, 18:39:30 UTC | Merge pull request #349 from apregier/fix_bam_readcount Fix bam readcount | 31 December 2014, 18:39:30 UTC |
| 6dfa223 | David Morton | 31 December 2014, 17:28:12 UTC | Merge pull request #351 from apregier/add_valid_variant_callers Variant callers interpreter takes a list of valid callers | 31 December 2014, 17:28:12 UTC |
| ff9c01c | dmorton | 31 December 2014, 17:25:14 UTC | Combine two lines into one line (readability) | 31 December 2014, 17:25:14 UTC |
| da2cbad | dmorton | 31 December 2014, 17:00:04 UTC | Grep results of all_* instead of duplicating logic | 31 December 2014, 17:00:04 UTC |
| dcdbe66 | Thomas Mooney | 31 December 2014, 16:46:18 UTC | Remove WithSavedResults from outline of cosmic importer. | 31 December 2014, 16:56:33 UTC |
| 68796e6 | dmorton | 31 December 2014, 16:53:18 UTC | Suppress warning when no error occurs | 31 December 2014, 16:53:18 UTC |
| e477cf1 | Thomas Mooney | 31 December 2014, 15:26:16 UTC | get_alignments() defers to existing method to get each alignment. The other method correctly handles segment data. | 31 December 2014, 15:26:16 UTC |
| 82434c6 | Thomas Mooney | 31 December 2014, 14:54:13 UTC | Remove old subclassification methods from ReferenceAlignment. These were replaced by the calculated+immutable version in 2010 (in 35a703b98545aca94785442a997a95fc2b9178ae before the redaction). | 31 December 2014, 14:54:13 UTC |
| 0b6bda9 | Ian Ferguson | 30 December 2014, 22:31:05 UTC | Disable alignment summary for Bsmap | 30 December 2014, 22:31:05 UTC |
| 7184935 | APipe Tester | 30 December 2014, 20:33:45 UTC | updated ur submodule to ef244bd | 30 December 2014, 20:33:45 UTC |
| 67686c7 | Thomas Mooney | 30 December 2014, 18:17:29 UTC | Respect the active flag when deciding if it's safe to delete children. | 30 December 2014, 18:17:29 UTC |
| d4257bc | Mark Burnett | 30 December 2014, 17:54:01 UTC | Merge pull request #345 from mark-burnett/purge-orphaned-allocations Purge orphaned allocations | 30 December 2014, 17:54:01 UTC |
| dfa34da | Anthony Brummett | 29 December 2014, 22:44:15 UTC | Fix regex for the exception-finding case The reverse search looks for a die or warn, not preceded by "ERROR:" | 29 December 2014, 22:44:15 UTC |
| 5e4da5e | Anthony Brummett | 29 December 2014, 21:53:16 UTC | Extract important parts from the giant regex We'll be reusing the parts for another regex | 29 December 2014, 21:53:16 UTC |
| bce2c33 | Thomas Mooney | 29 December 2014, 20:35:17 UTC | Don't generate file summaries if we can't reach the target directory. Otherwise we end up with summaries for whatever arbitrary directory we happened to be in. | 29 December 2014, 20:44:14 UTC |
| 1ed72f4 | Feiyu Du | 29 December 2014, 18:33:31 UTC | Merge pull request #368 from dufeiyu/bug_fix Resolve the warnings for G::M::T::Dbsnp::Import and G::M::C::Define::ImportedVariationList | 29 December 2014, 18:33:31 UTC |
| 1febffe | Thomas B. Mooney | 29 December 2014, 14:18:18 UTC | Merge pull request #365 from tmooney/replace_dv2_result_detector_pm_comments Replace confusing comments in DV2 result modules. | 29 December 2014, 14:18:18 UTC |
| 3cbd9ab | Avinash Ramu | 28 December 2014, 03:12:33 UTC | remove manual directory concatenation. | 28 December 2014, 03:12:33 UTC |
| 81ad3f2 | Feiyu Du | 24 December 2014, 19:33:24 UTC | changed to defined | 24 December 2014, 19:33:24 UTC |
| 7e4ab98 | Feiyu Du | 24 December 2014, 19:17:57 UTC | bug fix | 24 December 2014, 19:17:57 UTC |
| f2f1db9 | Thomas Mooney | 24 December 2014, 18:48:57 UTC | Use Genome::Sys->copy_file instead of `cp`. | 24 December 2014, 18:48:57 UTC |
| a503c1b | Thomas Mooney | 24 December 2014, 18:48:16 UTC | Replace STDERR->print with status_message. | 24 December 2014, 18:48:16 UTC |
| 4b3ed2a | Thomas B. Mooney | 24 December 2014, 16:13:07 UTC | Merge pull request #361 from tmooney/quiet_composite_test_warnings Quiet G:ID:Composite Warnings | 24 December 2014, 16:13:07 UTC |
| 02d0cf9 | Thomas Mooney | 24 December 2014, 15:02:00 UTC | Replace confusing comments in result modules. | 24 December 2014, 15:02:00 UTC |
| 7fbdd81 | Susanna Siebert | 24 December 2014, 14:50:30 UTC | Merge pull request #362 from susannasiebert/joinx_version use version package so that version comparison works for 1.10 and up | 24 December 2014, 14:50:30 UTC |
| c901f1b | Eddie Belter | 23 December 2014, 23:47:42 UTC | Merge pull request #364 from ebelter/rm-gsc-perl-from-tests Use /usr/bin/env genome-perl in tests instead of /gsc/bin/perl | 23 December 2014, 23:47:42 UTC |
| 6d11d16 | Eddie Belter | 23 December 2014, 23:31:26 UTC | Merge pull request #363 from ebelter/anp-cli-doc AnP CLI help and tests update. | 23 December 2014, 23:31:26 UTC |
| 07082ed | Eddie Belter | 23 December 2014, 23:13:14 UTC | AnP CLI: use env gneome-perl in test | 23 December 2014, 23:13:14 UTC |
| 1ecc9c2 | Eddie Belter | 23 December 2014, 23:09:18 UTC | Use /usr/bin/env genome-perl in tests instead of /gsc/bin/perl | 23 December 2014, 23:09:18 UTC |
| 23748f8 | Eddie Belter | 23 December 2014, 22:49:24 UTC | AnP CLI: add tests for disable config file | 23 December 2014, 22:49:24 UTC |
| 73c8aa4 | Eddie Belter | 23 December 2014, 22:48:54 UTC | AnP CLI: add test to config for instdata | 23 December 2014, 22:48:54 UTC |
| 2b45aed | Eddie Belter | 23 December 2014, 22:47:16 UTC | AnP CLI: add help brief to disable config file and config for instdata | 23 December 2014, 22:48:12 UTC |
| b3e1b00 | Susanna Siebert | 23 December 2014, 18:29:18 UTC | need to prepend 'v' to the version number so it gets parsed correctly | 23 December 2014, 18:29:18 UTC |
| de17f51 | Susanna Siebert | 23 December 2014, 16:39:50 UTC | use version package so that version comparison works for 1.10 and up | 23 December 2014, 17:00:32 UTC |
| df7f808 | Thomas Mooney | 23 December 2014, 16:02:59 UTC | Avoid null in-clause warning when we know we have no IDs. | 23 December 2014, 16:02:59 UTC |
| a7c3143 | Thomas Mooney | 23 December 2014, 16:02:16 UTC | Fill in output_dir in mocked SRs to quiet warnings. | 23 December 2014, 16:02:16 UTC |
| 8595d1b | Susanna Siebert | 23 December 2014, 15:59:44 UTC | Merge pull request #359 from susannasiebert/epitope_prediction Use wildtype sequence length if it is shorter than desired peptide sequence length | 23 December 2014, 15:59:44 UTC |
| ace556a | APipe Tester | 23 December 2014, 13:16:57 UTC | Updated `gmt` tab completion. | 23 December 2014, 13:16:57 UTC |
| 917a2e4 | APipe Tester | 23 December 2014, 13:16:15 UTC | Updated `genome` tab completion. | 23 December 2014, 13:16:15 UTC |
| 9eae308 | APipe Tester | 23 December 2014, 13:14:38 UTC | Updated class browser cache. | 23 December 2014, 13:14:38 UTC |
| 95b8dc7 | Avinash Ramu | 22 December 2014, 23:25:28 UTC | use File::Spec methods | 22 December 2014, 23:25:28 UTC |
| ca0bc2e | Avinash Ramu | 22 December 2014, 21:59:25 UTC | use valid_values attribute | 22 December 2014, 21:59:25 UTC |
| 43f79bd | Eddie Belter | 22 December 2014, 21:09:30 UTC | Merge pull request #334 from ebelter/cghub-import-instdata InstData Import: pull out retrieve file methods into separate modules | 22 December 2014, 21:09:30 UTC |
| 7a96079 | Mark Burnett | 22 December 2014, 21:07:31 UTC | Merge pull request #354 from mark-burnett/dv2-purged-allocations DV2 DetectionBase knows more about allocation statuses | 22 December 2014, 21:07:31 UTC |
| 8a3add5 | Thomas B. Mooney | 22 December 2014, 19:45:05 UTC | Merge pull request #344 from tmooney/import_instrument_data_sort_order_in_test Stop depending on being able to determine the order in which the two results were created. | 22 December 2014, 19:45:05 UTC |
| 7d3b7c5 | Eddie Belter | 22 December 2014, 19:42:55 UTC | InstData Import: spell/grammar check | 22 December 2014, 19:42:55 UTC |
| 75da1c4 | Mark Burnett | 22 December 2014, 19:23:52 UTC | fix missing `$_ eq` in grep | 22 December 2014, 19:23:52 UTC |
| d6e54b3 | Thomas Mooney | 22 December 2014, 18:48:47 UTC | Don't sort--grab the correct instrument data directly. | 22 December 2014, 18:48:47 UTC |
| fd9f651 | Thomas B. Mooney | 22 December 2014, 18:31:19 UTC | Merge pull request #340 from tmooney/remove_commented_code Clean Up Old Comments and Commented-Out Code | 22 December 2014, 18:31:19 UTC |
| 4c64a38 | Thomas B. Mooney | 22 December 2014, 18:28:55 UTC | Merge pull request #342 from tmooney/drop_featurelist_file_id Drop model.feature_list.file_id | 22 December 2014, 18:28:55 UTC |
