| fefc56d | Travis Abbott | 11 September 2013, 17:19:40 UTC | add BedPe reader | 11 September 2013, 17:20:07 UTC |
| 33f6839 | Mark Burnett | 11 September 2013, 15:31:15 UTC | use arrayref consistently for chromosome_list | 11 September 2013, 15:32:10 UTC |
| c0f5d06 | APipe Tester | 11 September 2013, 15:04:41 UTC | updated ur submodule to d1040b5 | 11 September 2013, 15:04:41 UTC |
| afae01c | APipe Tester | 11 September 2013, 01:24:27 UTC | Updated `gmt` tab completion. | 11 September 2013, 01:24:27 UTC |
| cdf96a4 | APipe Tester | 11 September 2013, 01:23:33 UTC | Updated `genome` tab completion. | 11 September 2013, 01:23:33 UTC |
| 415757a | APipe Tester | 11 September 2013, 01:21:50 UTC | Updated class browser cache. | 11 September 2013, 01:21:50 UTC |
| 780412d | dmorton | 11 September 2013, 00:57:26 UTC | Added gmt vcf create-cross-sample-vcf create-output-directory command | 11 September 2013, 01:06:46 UTC |
| 2d34583 | dmorton | 11 September 2013, 00:34:39 UTC | Added gmt sam get-sample-name command and tests | 11 September 2013, 01:06:46 UTC |
| e88cf03 | dmorton | 10 September 2013, 23:40:23 UTC | Made CreateCrossSampleVcf directory Moved Result into there, will end up putting indel related stuff in here too. | 11 September 2013, 01:06:45 UTC |
| 37d1bce | Travis Abbott | 10 September 2013, 23:33:19 UTC | Add test for 'peek' method in vcf reader. Sometimes, you just want to have a look at the next entry without taking it. | 10 September 2013, 23:36:02 UTC |
| 9591542 | Travis Abbott | 10 September 2013, 23:32:31 UTC | 'use base' instead of @ISA in GF:Vep:Reader | 10 September 2013, 23:36:02 UTC |
| 35036d9 | APipe Tester | 10 September 2013, 23:35:19 UTC | Updated `gmt` tab completion. | 10 September 2013, 23:35:19 UTC |
| af7b476 | APipe Tester | 10 September 2013, 23:34:11 UTC | Updated `genome` tab completion. | 10 September 2013, 23:34:11 UTC |
| bd421fe | APipe Tester | 10 September 2013, 23:32:14 UTC | Updated class browser cache. | 10 September 2013, 23:32:14 UTC |
| a36690e | dmorton | 10 September 2013, 23:04:35 UTC | Make Model/Pair.t use Model/TestHelpers instead of live database entries It is wrong to use database entries in our tests. | 10 September 2013, 23:05:46 UTC |
| e5c92f9 | dmorton | 10 September 2013, 23:04:02 UTC | Make Model-build_requested.t use Model/TestHelpers | 10 September 2013, 23:05:46 UTC |
| 4d33032 | dmorton | 10 September 2013, 23:03:10 UTC | Added Model/TestHelpers.pm to assist with testing | 10 September 2013, 23:05:46 UTC |
| 9ba43a6 | dmorton | 10 September 2013, 22:19:35 UTC | Added to gmt varscan consensus tests | 10 September 2013, 23:05:46 UTC |
| 8c9901c | dmorton | 10 September 2013, 22:02:11 UTC | Added --vcf-sample-name option to gmt varscan consensus | 10 September 2013, 23:05:46 UTC |
| 8bd22f7 | Travis Abbott | 10 September 2013, 22:13:37 UTC | refactor Genome::File::{Vcf,Vep} to share common code through a new base class Genome::File::TypedStream. future formats (e.g., BedPe) can use this as well. | 10 September 2013, 22:14:32 UTC |
| 912fec3 | Thomas Mooney | 10 September 2013, 21:48:38 UTC | Close our filehandles even when dying. | 10 September 2013, 21:48:38 UTC |
| cd3f495 | Chris Miller | 10 September 2013, 21:42:05 UTC | Allowing zero size outputs, as this is the expected behavior when there is no coverage for any site | 10 September 2013, 21:42:11 UTC |
| 2cd7fe0 | Nathan Nutter | 10 September 2013, 21:28:30 UTC | restore old default LSF queues in DV2 The argument here is that we minimize the overlap of parents and children in the same queue. workflow: Builds apipe: DV2 Child Workflow and Workers long: DV2 Dispatcher | 10 September 2013, 21:32:12 UTC |
| f0ca4bd | Chris Miller | 10 September 2013, 21:21:39 UTC | updated input options | 10 September 2013, 21:22:42 UTC |
| dbfcb7f | Nathan Nutter | 10 September 2013, 21:03:50 UTC | change the workflow queue for DV2 to long | 10 September 2013, 21:03:50 UTC |
| ae85328 | Nathan Nutter | 10 September 2013, 20:42:17 UTC | Revert "increase requested memory from LSF for the Pindel job" This reverts commit 5dd8ff26cd3bb16bfb3cdfe1d9a0ea2d987bc8b0. This is a Workflow server so cannot and should not have this much memory requested. This was discovered because it was recently changed to run in the workflow queue instead of in the long queue. Conflicts: lib/perl/Genome/Model/Tools/DetectVariants2/Pindel.pm | 10 September 2013, 20:53:32 UTC |
| fad3b4e | Anthony Brummett | 10 September 2013, 20:33:23 UTC | Enable pausing by listening for the "sequence_nextval" signal | 10 September 2013, 20:34:23 UTC |
| fe351a1 | dmorton | 10 September 2013, 20:13:29 UTC | Refactor gmt varscan consensus and add tests | 10 September 2013, 20:15:13 UTC |
| c434cc9 | dmorton | 10 September 2013, 20:12:38 UTC | Extract java_command_line method | 10 September 2013, 20:15:13 UTC |
| c7567c3 | dmorton | 10 September 2013, 18:34:07 UTC | Fix RealignWithVcf.xml links | 10 September 2013, 20:15:13 UTC |
| f377048 | dmorton | 10 September 2013, 17:42:06 UTC | Cleanup whitespace in Varscan Consensus | 10 September 2013, 20:15:13 UTC |
| eeba5ce | dmorton | 10 September 2013, 17:38:58 UTC | Update types of Varscan Consensus properties | 10 September 2013, 20:15:13 UTC |
| bad7fcd | Scott Smith | 10 September 2013, 20:14:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 September 2013, 20:14:15 UTC |
| 01de406 | Scott Smith | 10 September 2013, 20:13:31 UTC | add Genome::Model::Pair | 10 September 2013, 20:13:31 UTC |
| d21d9a8 | APipe Tester | 10 September 2013, 20:13:11 UTC | updated ur submodule to bb4c031 | 10 September 2013, 20:13:11 UTC |
| 0b020e1 | APipe Tester | 10 September 2013, 19:31:21 UTC | updated ur submodule to 9366b9e | 10 September 2013, 19:31:21 UTC |
| 60ceccb | Feiyu Du | 10 September 2013, 17:55:39 UTC | fix a version max bug | 10 September 2013, 17:55:39 UTC |
| fb6636d | Malachi Griffith | 10 September 2013, 17:17:17 UTC | clinseq - blessing new test build to accomodate expected update to illumina_info | 10 September 2013, 17:17:17 UTC |
| af4edf4 | Malachi Griffith | 10 September 2013, 17:12:49 UTC | clinseq - add option to SummarizeBuilds.t to allow full test of illumina_info as used in the clinseq pipeline | 10 September 2013, 17:12:49 UTC |
| 04a2f57 | Thomas Mooney | 10 September 2013, 15:00:27 UTC | Grab the latest build using accessor to not care about sort order. | 10 September 2013, 15:00:27 UTC |
| 684f34a | APipe Tester | 10 September 2013, 14:46:17 UTC | updated ur submodule to 6b0fbd1 | 10 September 2013, 14:46:17 UTC |
| da71dba | Dave Larson | 09 September 2013, 22:10:02 UTC | remove an unnecessary test | 09 September 2013, 22:10:02 UTC |
| 2747c0c | Dave Larson | 09 September 2013, 22:08:17 UTC | simple integration test for the Mutect tool | 09 September 2013, 22:08:17 UTC |
| eef79e2 | Cyriac Kandoth | 09 September 2013, 21:34:14 UTC | Changed the way in which temporary files are generated | 09 September 2013, 21:34:14 UTC |
| f33d305 | Scott Smith | 09 September 2013, 20:07:15 UTC | updated metadata exporter to get feature lists, associated reference sequence builds, and adaptors between refseq builds | 09 September 2013, 20:08:22 UTC |
| 00f757a | dmorton | 09 September 2013, 19:25:58 UTC | Stop using pipefail in PrepareInstrumentData Having it set causes the Flow model tests to fail, even though (oddly enough) it does not cause the Genome model tests to fail. The Flow model tests passes diff tests after running with this set, so we don't think it is a mistake to turn off pipefail here. | 09 September 2013, 19:31:20 UTC |
| 818fc57 | dmorton | 09 September 2013, 19:24:13 UTC | Add set_pipefail option to Genome::Sys->shellcmd The default is to set_pipefail for compatibility but now you can specify that you don't want pipefail set if you want to. | 09 September 2013, 19:31:19 UTC |
| 664c19c | Scott Smith | 09 September 2013, 19:05:45 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 September 2013, 19:05:45 UTC |
| 286c791 | Scott Smith | 09 September 2013, 16:32:10 UTC | blessed new clinseq build to match changes in LIMS | 09 September 2013, 16:32:59 UTC |
| 9f14446 | APipe Tester | 09 September 2013, 16:30:17 UTC | Updated `genome` tab completion. | 09 September 2013, 16:32:59 UTC |
| dcc4de0 | APipe Tester | 09 September 2013, 16:28:08 UTC | Updated class browser cache. | 09 September 2013, 16:32:58 UTC |
| 1c1d2b2 | APipe Tester | 09 September 2013, 16:30:17 UTC | Updated `genome` tab completion. | 09 September 2013, 16:30:17 UTC |
| 047216c | APipe Tester | 09 September 2013, 16:28:08 UTC | Updated class browser cache. | 09 September 2013, 16:28:08 UTC |
| 03ad763 | Scott Smith | 09 September 2013, 16:21:42 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 September 2013, 16:21:42 UTC |
| dea374b | Scott Smith | 09 September 2013, 16:21:21 UTC | add Genome::Sys::Gateway and related command tree for working with other GMSs | 09 September 2013, 16:21:21 UTC |
| 54247d2 | Jim Weible | 09 September 2013, 16:06:20 UTC | disable BQM | 09 September 2013, 16:06:20 UTC |
| 6cea71d | Jim Weible | 09 September 2013, 14:34:42 UTC | Disable BQM | 09 September 2013, 14:34:42 UTC |
| ea36bea | Dave Larson | 08 September 2013, 17:24:38 UTC | fix some pathnames and remove some cruft. | 08 September 2013, 17:24:38 UTC |
| 1e9d40c | Dave Larson | 08 September 2013, 17:17:12 UTC | simple integration test for Mutect ParallelWrapper | 08 September 2013, 17:17:12 UTC |
| 8b7ab6b | Dave Larson | 06 September 2013, 23:40:38 UTC | simple integration test for mutect merge-output-files utility | 08 September 2013, 16:47:09 UTC |
| b13ee2b | Nathan Nutter | 07 September 2013, 01:28:00 UTC | refactor Genome::Site::TGI::InstrumentData::Solexa | 07 September 2013, 01:28:00 UTC |
| 62890a0 | Nathan Nutter | 07 September 2013, 01:22:12 UTC | delegate instead of duplicate: _unprocessed_fastq_filenames code-deduplication: nnutter | 07 September 2013, 01:27:26 UTC |
| 0c01c39 | Nathan Nutter | 07 September 2013, 01:21:41 UTC | delegate instead of duplicate: run_identifier code-deduplication: nnutter | 07 September 2013, 01:27:22 UTC |
| c0014f1 | Nathan Nutter | 07 September 2013, 01:19:49 UTC | delegate instead of duplicate: total_bases_read code-deduplication: nnutter | 07 September 2013, 01:27:18 UTC |
| a4bd26f | Nathan Nutter | 07 September 2013, 01:18:40 UTC | delegate instead of duplicate: run_start_date_formatted code-deduplication: nnutter | 07 September 2013, 01:27:14 UTC |
| 567663f | Nathan Nutter | 07 September 2013, 01:16:10 UTC | delegate instead of duplicate: _calculate_total_read_count code-deduplication: nnutter | 07 September 2013, 01:27:10 UTC |
| 07d6362 | Nathan Nutter | 07 September 2013, 01:15:38 UTC | delegate instead of duplicate: resolve_external_fastq_filenames code-deduplication: nnutter | 07 September 2013, 01:27:06 UTC |
| ff94236 | Nathan Nutter | 07 September 2013, 01:15:03 UTC | delegate instead of duplicate: validate_fastq_directory code-deduplication: nnutter | 07 September 2013, 01:27:02 UTC |
| c159d39 | Nathan Nutter | 07 September 2013, 01:14:11 UTC | delegate instead of duplicate: dump_illumina_fastq_archive code-deduplication: nnutter | 07 September 2013, 01:26:57 UTC |
| f227cb3 | Nathan Nutter | 07 September 2013, 01:13:20 UTC | delegate instead of duplicate: resolve_fastq_filenames code-deduplication: nnutter | 07 September 2013, 01:26:53 UTC |
| 580d0c0 | Nathan Nutter | 07 September 2013, 01:09:07 UTC | whitespace | 07 September 2013, 01:26:46 UTC |
| 7688d5a | Nathan Nutter | 07 September 2013, 01:07:01 UTC | delegate to Genome::Sys instead of using inheritance This class strangely inherits from Genome::Sys. This changes some calls to specifically delegate to Genome::Sys. I verified that can() returned the Genome::Sys methods. code-deduplication: nnutter | 07 September 2013, 01:26:41 UTC |
| 15ec665 | Nathan Nutter | 07 September 2013, 01:02:03 UTC | delegate instead of duplicate: fragment_fastq_name code-deduplication: nnutter | 07 September 2013, 01:26:37 UTC |
| 52f4f98 | Nathan Nutter | 07 September 2013, 01:01:32 UTC | delegate instead of duplicate: read2_fastq_name code-deduplication: nnutter | 07 September 2013, 01:26:33 UTC |
| cd364d4 | Nathan Nutter | 07 September 2013, 01:00:58 UTC | delegate instead of duplicate: read1_fastq_name code-deduplication: nnutter | 07 September 2013, 01:26:28 UTC |
| 2081af9 | Nathan Nutter | 07 September 2013, 01:00:18 UTC | delegate instead of duplicate: desc code-deduplication: nnutter | 07 September 2013, 01:26:20 UTC |
| 97dfd13 | Nathan Nutter | 06 September 2013, 22:20:43 UTC | delegate instead of duplicate: dump_sanger_fastq_files (diverged code) The code appears to have diverged a bit. First, this was not passing @_ to `$self->dump_fastqs_from_bam`. Second, it was using Genome::Model::Tools::Maq::Sol2sanger instead of Genome::Model::Tools::Fastq::Sol2sanger to convert the file. However, I expect that Genome::Model::Tools::Fastq::Sol2sanger is the better choice so went ahead and delegated this method. code-deduplication: nnutter | 07 September 2013, 01:26:13 UTC |
| 60e9651 | Nathan Nutter | 06 September 2013, 22:16:13 UTC | delegate instead of duplicate: dump_solexa_fastq_files code-deduplication: nnutter | 07 September 2013, 01:26:09 UTC |
| f5ddf1f | Nathan Nutter | 06 September 2013, 22:15:33 UTC | delegate instead of duplicate: dump_illumina_fastq_files code-deduplication: nnutter | 07 September 2013, 01:26:06 UTC |
| 0cffa94 | Nathan Nutter | 06 September 2013, 22:12:18 UTC | delegate instead of duplicate: calculate_alignment_estimated_kb_usage code-deduplication: nnutter | 07 September 2013, 01:26:02 UTC |
| cf24d6e | Nathan Nutter | 06 September 2013, 22:08:14 UTC | delegate instead of duplicate: _calculate_non_paired_end_kb_usage code-deduplication: nnutter | 07 September 2013, 01:25:56 UTC |
| c2f35c8 | Nathan Nutter | 06 September 2013, 22:07:54 UTC | delegate instead of duplicate: _calculate_paired_end_kb_usage code-deduplication: nnutter | 07 September 2013, 01:25:46 UTC |
| e6acd5b | Gabriel Sanderson | 06 September 2013, 23:43:11 UTC | Merge branch 'master' into gb_master | 06 September 2013, 23:43:11 UTC |
| 4ecb2ff | Gabriel Sanderson | 06 September 2013, 23:42:47 UTC | Re-enabled test by only running on chr22 | 06 September 2013, 23:42:57 UTC |
| a54d646 | Adam Coffman | 06 September 2013, 23:34:54 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 September 2013, 23:34:54 UTC |
| 3959bf4 | Gabriel Sanderson | 06 September 2013, 23:34:28 UTC | Merge branch 'master' into gb_master | 06 September 2013, 23:34:28 UTC |
| fd6ff36 | Gabriel Sanderson | 06 September 2013, 23:33:59 UTC | Re-enable the test fully, only run on chr22. | 06 September 2013, 23:33:59 UTC |
| 254b8fb | Gabriel Sanderson | 06 September 2013, 23:19:48 UTC | Move up chromosome_list code-deduplication: gsanders | 06 September 2013, 23:21:14 UTC |
| 0aa65e4 | Gabriel Sanderson | 06 September 2013, 23:03:08 UTC | Move up _ensure_chromosome_list_set code-deduplication: gsanders | 06 September 2013, 23:21:12 UTC |
| e9e5878 | Gabriel Sanderson | 06 September 2013, 22:59:23 UTC | Move up _generate_standard_files code-deduplication: gsanders | 06 September 2013, 23:21:09 UTC |
| 88a0278 | Gabriel Sanderson | 06 September 2013, 22:58:21 UTC | Move up raw_input_for_chromosome code-deduplication: gsanders | 06 September 2013, 23:21:06 UTC |
| 8446576 | Gabriel Sanderson | 06 September 2013, 22:57:24 UTC | Move up raw_inputs code-deduplication: gsanders | 06 September 2013, 23:21:02 UTC |
| 9ec6cfe | Gabriel Sanderson | 06 September 2013, 22:56:05 UTC | Move up raw_output_file code-deduplication: gsanders | 06 September 2013, 23:20:59 UTC |
| 49bd3ca | Gabriel Sanderson | 06 September 2013, 22:54:27 UTC | Move up default_chromosomes code-deduplication: gsanders | 06 September 2013, 23:20:57 UTC |
| 4dc8ef9 | Gabriel Sanderson | 06 September 2013, 22:51:07 UTC | Copied over variant_type, raw_output_file, raw_inputs, raw_input_for_chromosome code-deduplication: gsanders | 06 September 2013, 23:20:54 UTC |
| 062bad5 | Gabriel Sanderson | 06 September 2013, 22:40:33 UTC | Copy over variant_type, raw_output_file, raw_inputs, raw_input_for_chromosome, generate_standard_files code-deduplication: gsanders | 06 September 2013, 23:20:49 UTC |
| 04bd064 | APipe Tester | 06 September 2013, 22:37:47 UTC | updated workflow submodule to f9affd1 | 06 September 2013, 22:37:47 UTC |
| e37bf22 | APipe Tester | 06 September 2013, 22:37:43 UTC | updated ur submodule to 086a619 | 06 September 2013, 22:37:43 UTC |
| 5574f32 | Mark Burnett | 06 September 2013, 16:49:36 UTC | extract variant_type code-deduplication: mburnett, gsanders | 06 September 2013, 22:26:09 UTC |
| 0704b31 | Mark Burnett | 06 September 2013, 16:47:08 UTC | extract raw_input_for_chromosome code-deduplication: mburnett, gsanders | 06 September 2013, 22:26:06 UTC |
