| cefae91 | Thomas B. Mooney | 12 January 2015, 15:03:28 UTC | Merge pull request #396 from tmooney/speedup_copycat_annotation_lister Speedup CopyCat Annotation Lister | 12 January 2015, 15:03:28 UTC |
| 16d01a4 | Susanna Siebert | 09 January 2015, 15:37:15 UTC | Merge pull request #394 from susannasiebert/igv Handle bam path urls in igv sessions correctly | 09 January 2015, 15:37:15 UTC |
| 55df8a1 | APipe Tester | 09 January 2015, 13:16:14 UTC | Updated `genome` tab completion. | 09 January 2015, 13:16:14 UTC |
| 5e7841f | Feiyu Du | 08 January 2015, 22:50:04 UTC | Merge pull request #393 from dufeiyu/fix Add bam_header and comparison_flagstat as required parameters | 08 January 2015, 22:50:04 UTC |
| c11f272 | David Morton | 08 January 2015, 21:34:24 UTC | Merge pull request #382 from davidlmorton/bam_readcount_version Use BamReadcount version 0.7 in VariantReporting | 08 January 2015, 21:34:24 UTC |
| 4574a45 | Feiyu Du | 08 January 2015, 20:46:15 UTC | make bam_header and comparison_flagstat not optional | 08 January 2015, 20:46:15 UTC |
| 391fee9 | Susanna Siebert | 08 January 2015, 20:25:06 UTC | code simplifications | 08 January 2015, 20:25:06 UTC |
| fc030ea | Thomas B. Mooney | 08 January 2015, 19:40:35 UTC | Merge pull request #392 from tmooney/process_test_factory Test Factory for Genome::Process | 08 January 2015, 19:40:35 UTC |
| 8c6de4d | Susanna Siebert | 08 January 2015, 17:39:04 UTC | improve the way bam paths get resolved | 08 January 2015, 17:39:20 UTC |
| 3e22c6b | Susanna Siebert | 08 January 2015, 17:37:13 UTC | use URI instead of File::Spec to create bam path URI | 08 January 2015, 17:37:13 UTC |
| edb3836 | Susanna Siebert | 08 January 2015, 17:36:33 UTC | use URI instead of URI::URL | 08 January 2015, 17:36:33 UTC |
| 6c7091c | Malachi Griffith | 08 January 2015, 16:07:15 UTC | Merge pull request #395 from nnutter/RT/103295 Proposed Fixes for RT#103295 | 08 January 2015, 16:07:15 UTC |
| 299dfa9 | Thomas Mooney | 08 January 2015, 14:47:54 UTC | Add a default "show" that includes only the essential columns. | 08 January 2015, 14:47:54 UTC |
| f35f5fa | Thomas Mooney | 08 January 2015, 14:46:28 UTC | Don't hint at properties which lead to excessive joins. | 08 January 2015, 14:46:28 UTC |
| 907464d | Jim Weible | 08 January 2015, 14:23:02 UTC | Merge pull request #388 from jweible/AUE-383 Add tag parameter to AddConfigFile for AUE-383 | 08 January 2015, 14:23:02 UTC |
| d8ada26 | APipe Tester | 08 January 2015, 13:16:38 UTC | Updated `gmt` tab completion. | 08 January 2015, 13:16:38 UTC |
| d6aac14 | APipe Tester | 08 January 2015, 13:15:55 UTC | Updated `genome` tab completion. | 08 January 2015, 13:15:55 UTC |
| 9146e17 | APipe Tester | 08 January 2015, 13:14:25 UTC | Updated class browser cache. | 08 January 2015, 13:14:25 UTC |
| fd27b3c | David Morton | 08 January 2015, 03:17:49 UTC | Merge pull request #378 from davidlmorton/manditory_names Make library_names and sample_names manditory inputs | 08 January 2015, 03:17:49 UTC |
| 296c978 | dmorton | 08 January 2015, 03:11:36 UTC | Fix grammar and missing punctuation | 08 January 2015, 03:11:36 UTC |
| a596d34 | Thomas B. Mooney | 07 January 2015, 23:52:23 UTC | Merge pull request #341 from tmooney/refseq_conversion Reference-Sequence Conversion Improvements for Merging | 07 January 2015, 23:52:23 UTC |
| b73dd72 | Eddie Belter | 07 January 2015, 22:25:16 UTC | Merge pull request #390 from ebelter/instdata-import-use-names InstData Import: use names instead of library object for steps interacting | 07 January 2015, 22:25:16 UTC |
| a9e5795 | Nathaniel Nutter | 07 January 2015, 21:43:11 UTC | should not call region_of_interest_set_bed_file multiple times This should not call region_of_interest_set_bed_file multiple times with different arguments because that would produce multiple files due to (intentional) side effects. | 07 January 2015, 21:43:11 UTC |
| 0353d41 | Ian Ferguson | 07 January 2015, 20:41:32 UTC | Merge pull request #350 from iferguson90/methratio-fix Update GMT::Bsmap::MethRatio | 07 January 2015, 20:41:32 UTC |
| 3f6ce05 | Nathaniel Nutter | 07 January 2015, 20:03:08 UTC | explicitly unlink file if copy fails | 07 January 2015, 20:34:44 UTC |
| d255e48 | Nathaniel Nutter | 07 January 2015, 19:53:27 UTC | check file size not just existence We had a problem where this failed in a prior process due to the volume being full in which case it left behind a zero size file. This then caused a late error in future processes. | 07 January 2015, 20:34:43 UTC |
| 04a5b11 | Nathaniel Nutter | 07 January 2015, 19:51:17 UTC | store region_of_interest_set_bed_file in a temp file Since this only uses the region_of_interest_set_bed_file in order to intersect them they can probably just be stored in temp. This is trying to avoid the problem of the build's data directory no longer being writable. | 07 January 2015, 20:34:42 UTC |
| 4d34b29 | Nathaniel Nutter | 07 January 2015, 19:50:07 UTC | allow an output path to be specified for region_of_interest_set_bed_file Instead of always writing to the default location in the build directory allow the path to be specified by the caller. | 07 January 2015, 20:34:41 UTC |
| 14563a2 | Ian Ferguson | 07 January 2015, 20:32:03 UTC | Use subtest | 07 January 2015, 20:32:03 UTC |
| 43455ef | Thomas B. Mooney | 07 January 2015, 20:13:56 UTC | Merge pull request #384 from tmooney/determine_error_tweaks Tweaks to DetermineError | 07 January 2015, 20:13:56 UTC |
| e150df8 | Susanna Siebert | 07 January 2015, 18:53:53 UTC | make bam paths into urls | 07 January 2015, 18:53:53 UTC |
| 2ed6e1b | Feiyu Du | 07 January 2015, 18:28:55 UTC | Add bam_header as optional parameter | 07 January 2015, 18:28:55 UTC |
| cfe08d9 | Thomas Mooney | 07 January 2015, 17:54:23 UTC | A test factory for Processes. | 07 January 2015, 17:54:23 UTC |
| 1e9ccda | Thomas Mooney | 07 January 2015, 17:53:34 UTC | Must re-call with concrete class to avoid running create() twice. | 07 January 2015, 17:53:34 UTC |
| b2dda48 | Susanna Siebert | 07 January 2015, 14:06:12 UTC | if bam path is a URI, don't call abs_path on it | 07 January 2015, 14:06:12 UTC |
| 105151e | APipe Tester | 07 January 2015, 13:16:47 UTC | Updated `gmt` tab completion. | 07 January 2015, 13:16:47 UTC |
| 00b453e | APipe Tester | 07 January 2015, 13:16:06 UTC | Updated `genome` tab completion. | 07 January 2015, 13:16:06 UTC |
| 5a22ce1 | APipe Tester | 07 January 2015, 13:14:36 UTC | Updated class browser cache. | 07 January 2015, 13:14:36 UTC |
| 9548f4a | Eddie Belter | 07 January 2015, 00:15:48 UTC | InstData Import: use names instead of library object for steps interacting with gmt picard fastq to sam | 07 January 2015, 00:15:48 UTC |
| 5b0038e | Ian Ferguson | 06 January 2015, 21:18:57 UTC | Remove unused $DEFAULT_VERSION | 06 January 2015, 21:18:57 UTC |
| a961e98 | Ian Ferguson | 06 January 2015, 21:12:48 UTC | Test execution in MethRatio tests | 06 January 2015, 21:12:48 UTC |
| 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 |
| 43f7904 | Jim Weible | 06 January 2015, 16:58:12 UTC | test with multiple tags | 06 January 2015, 17:00:30 UTC |
| 3a7042b | Jim Weible | 06 January 2015, 16:27:36 UTC | Add tag parameter to AddConfigFile for AUE-383 | 06 January 2015, 17:00:29 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 |
| 07f20e2 | Thomas Mooney | 06 January 2015, 00:01:48 UTC | Test the code in the current directory. | 06 January 2015, 00:05:06 UTC |
| e87fb53 | Thomas Mooney | 06 January 2015, 00:01:04 UTC | We really want the last error in the log. | 06 January 2015, 00:04:17 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 |
| 92791e1 | dmorton | 05 January 2015, 18:39:54 UTC | Make tests a little more verbose | 05 January 2015, 18:39:54 UTC |
| 836c68b | dmorton | 05 January 2015, 18:39:12 UTC | Ensure we are using at least BamReadcount 0.7 | 05 January 2015, 18:39:12 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 |
| df839da | dmorton | 04 January 2015, 00:37:21 UTC | Make library_names and sample_names manditory inputs Some care has to be taken for the SoftwareResult subclasses (reports) since they have to be listed as 'input' or 'param' or the SoftwareResult infrastructure will yell about ambiguous properties. | 04 January 2015, 04:33:50 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 |
