| 77520cd | Susanna Siebert | 13 January 2015, 17:01:45 UTC | Merge pull request #380 from susannasiebert/variant_reporting_masterplan Add test for missing parameter in plan file | 13 January 2015, 17:01:45 UTC |
| 9d087f5 | APipe Tester | 13 January 2015, 13:17:04 UTC | Updated `gmt` tab completion. | 13 January 2015, 13:17:04 UTC |
| 51d2ce8 | APipe Tester | 13 January 2015, 13:16:20 UTC | Updated `genome` tab completion. | 13 January 2015, 13:16:20 UTC |
| 4413cb7 | APipe Tester | 13 January 2015, 13:14:42 UTC | Updated class browser cache. | 13 January 2015, 13:14:42 UTC |
| dafe6bf | Feiyu Du | 12 January 2015, 21:13:13 UTC | Merge pull request #398 from dufeiyu/fix Fix a bug on comparing flagstat | 12 January 2015, 21:13:13 UTC |
| facf81f | Feiyu Du | 12 January 2015, 19:51:56 UTC | rework compare_flagstat with one line diff expected based on code review | 12 January 2015, 19:51:56 UTC |
| 341aada | Susanna Siebert | 12 January 2015, 15:23:34 UTC | Merge pull request #391 from susannasiebert/process Add functionality to compare Genome::Process output files | 12 January 2015, 15:23:34 UTC |
| 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 |
| fb85a7b | Feiyu Du | 09 January 2015, 20:17:08 UTC | fix a bug on comparing flagstat | 09 January 2015, 20:17:08 UTC |
| 07823e8 | Susanna Siebert | 09 January 2015, 19:46:57 UTC | use original file paths for diff message | 09 January 2015, 19:46:57 UTC |
| 775353d | Susanna Siebert | 09 January 2015, 19:35:38 UTC | always use relative paths for diff hash keys | 09 January 2015, 19:35:38 UTC |
| 79f06fb | Susanna Siebert | 09 January 2015, 19:34:42 UTC | remove unneeded subroutine | 09 January 2015, 19:34:42 UTC |
| 0b0043a | Susanna Siebert | 09 January 2015, 17:29:54 UTC | Resolve symlinks at beginning of callback This ensures that we're also handling cases where symlinks point to files/directories where one of the targets exists but not the other | 09 January 2015, 17:33:12 UTC |
| f65be90 | Susanna Siebert | 09 January 2015, 17:27:31 UTC | Use a template string for sprintf | 09 January 2015, 17:27:31 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 |
| 5dda01e | Susanna Siebert | 06 January 2015, 16:11:17 UTC | Implement comparison subroutine _compare_output_files specific to processes The behavior is intended to mirror that of Genome::Model::Build::_compare_output_files and _compare_output_directories | 07 January 2015, 15:52:54 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 |
| d8bee5d | Susanna Siebert | 05 January 2015, 21:06:21 UTC | Allow test interpreter to specify which info field to use | 06 January 2015, 16:16:47 UTC |
| 3e28071 | Susanna Siebert | 02 January 2015, 20:07:46 UTC | Change test expert and test expert with translations to use set_info_field - Otherwise they will stomp on each other when used together | 06 January 2015, 16:16:47 UTC |
| e9c0a4c | Susanna Siebert | 31 December 2014, 18:14:16 UTC | Implement compare_output subroutine similar to G::M::B::compare_output | 06 January 2015, 16:16:47 UTC |
| c7fdcab | Susanna Siebert | 31 December 2014, 18:13:05 UTC | Bugfix: this would fail if the call to users returns more than one | 06 January 2015, 16:16:47 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 |
| d97e753 | Susanna Siebert | 05 January 2015, 15:32:38 UTC | add test for missing parameter in plan file | 05 January 2015, 15:32:38 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 |
