| b84fdb2 | Eddie Belter | 24 October 2012, 16:30:16 UTC | Solexa: update gettign default results | 24 October 2012, 16:30:24 UTC |
| 1963ac6 | dmorton | 24 October 2012, 15:36:49 UTC | Enhance 'genome model build status' Now shows model id in addition to model name. Now has color option for statuses. | 24 October 2012, 15:40:17 UTC |
| eb6a1e0 | dmorton | 24 October 2012, 15:33:46 UTC | Make Genome::Command::ColorMixin And update Genome::Command::Viewer subclasses to use it. | 24 October 2012, 15:40:16 UTC |
| 279ece2 | Thomas Mooney | 24 October 2012, 13:35:16 UTC | Fix typo in maize reference build id | 24 October 2012, 13:35:16 UTC |
| eb8f1ad | Thomas Mooney | 24 October 2012, 13:34:49 UTC | Add plink pp to AQID genotype processing. | 24 October 2012, 13:34:49 UTC |
| 9bb7f48 | APipe Tester | 23 October 2012, 22:38:52 UTC | updated ur submodule to 18cd780 | 23 October 2012, 22:38:52 UTC |
| a1e2a21 | Anthony Brummett | 23 October 2012, 22:30:49 UTC | new command for reading a FastQ file and guessing what the quality score encoding is | 23 October 2012, 22:30:49 UTC |
| daef4e9 | Thomas Mooney | 23 October 2012, 20:27:08 UTC | Replace joinx syscall with call to gmt tool. | 23 October 2012, 20:27:08 UTC |
| 1b31b20 | Thomas Mooney | 23 October 2012, 20:10:39 UTC | Merge branch 'master' of ssh://git/srv/git/genome :( | 23 October 2012, 20:10:39 UTC |
| 4c0448d | Thomas Mooney | 23 October 2012, 20:07:45 UTC | First version of new command to process validation variants for review. This is based on `gmt validation process-somatic-validation`, but located for future inclusion in the SomaticValidation pipeline itself. | 23 October 2012, 20:07:45 UTC |
| bb10792 | Thomas Mooney | 23 October 2012, 19:56:12 UTC | Rethrow errors getting processing in AQID. | 23 October 2012, 19:56:12 UTC |
| fcb09b6 | Mark Burnett | 22 October 2012, 20:05:23 UTC | Reinstate statsd client code. | 23 October 2012, 19:47:15 UTC |
| cb10ed2 | Brian Derickson | 23 October 2012, 19:08:59 UTC | cosmetic changes | 23 October 2012, 19:08:59 UTC |
| f4c2593 | Brian Derickson | 23 October 2012, 19:05:51 UTC | fix for allocations with IDs that contain spaces | 23 October 2012, 19:05:57 UTC |
| 94d9e27 | Kyung Kim | 23 October 2012, 18:05:06 UTC | remove existing log file before running genome::sys->open_file_for_writing | 23 October 2012, 18:05:06 UTC |
| 78e32a6 | APipe Tester | 23 October 2012, 16:28:37 UTC | updated workflow submodule to cba0eaa | 23 October 2012, 16:28:37 UTC |
| 3778509 | Brian Derickson | 23 October 2012, 16:19:10 UTC | CHANGELOG: build unarchive command now parallel and fault tolerant Previously this command would unarchive each allocation serially and would stop at the first failure per build. It now unarchives all allocations per build in parallel and reports errors as they occur and in a summary report immediately before the command exits. | 23 October 2012, 16:22:14 UTC |
| d8410ec | Brian Derickson | 22 October 2012, 19:43:37 UTC | Added wait_for_lsf_job_ids to Genome::Sys This method takes a list of LSF job ids and waits for all of them to finish before returning. Return value is a hash of job_id => status pairs. Also added test to cover this addition, though it will not be run as part of the automated test suite because it requires LSF jobs to be scheduled which can hang for a number of reasons. | 23 October 2012, 16:22:13 UTC |
| 10c14cf | Kyung Kim | 23 October 2012, 15:40:13 UTC | bug fix .. remove existing parse output file to prevent it from crashing when using g::sys->open_file_for_writing to write new parse file during re-runs | 23 October 2012, 15:40:13 UTC |
| e0b6662 | APipe Tester | 23 October 2012, 02:37:47 UTC | updated workflow submodule to dc6b73c | 23 October 2012, 02:37:47 UTC |
| f9fc45c | Travis Abbott | 22 October 2012, 21:23:32 UTC | consider all genes in which a variant is deleterious The rare/deleterious test previously only used the most severe gene. | 22 October 2012, 21:25:04 UTC |
| 4f4aa3d | Nathan Nutter | 19 October 2012, 21:51:09 UTC | update submodule pointer: genome-snapshot-deps | 19 October 2012, 21:51:09 UTC |
| 8069ca8 | Nathan Nutter | 19 October 2012, 21:43:26 UTC | improve check_inputs, especially relating to segmented bams - check if bam_file is defined earlier - check if bam_file exists earlier - remove nested conditionals that are not needed due to earlier checks - check if segment is defined instead of just true | 19 October 2012, 21:50:07 UTC |
| 50249b3 | Brian Derickson | 19 October 2012, 19:00:53 UTC | fixed null in-clause warning In Genome::Model::Build::ReferenceAlignment->merged_alignment_result, should only attempt to get merged alignment results if any software result users that point to the current build are found. If none are found, just return immediately. Before this change, a Genome::InstrumentData::AlignmentResult::Merged->get(undef) was performed, which emitted a warning and always returned nothing. | 19 October 2012, 19:03:38 UTC |
| 4a67fbf | Charles Lu | 19 October 2012, 17:44:06 UTC | updated the telomere script, added documentation | 19 October 2012, 17:44:06 UTC |
| f903bde | Scott Smith | 18 October 2012, 21:25:21 UTC | tMerge branch 'master' of ssh://git/srv/git/genome | 18 October 2012, 21:25:21 UTC |
| 92d2e04 | Scott Smith | 18 October 2012, 21:25:07 UTC | updated model group bridges to refer to the group as "group", and updated the lister to be less confusing | 18 October 2012, 21:25:07 UTC |
| c53d290 | apregier | 18 October 2012, 21:10:11 UTC | Merge branch 'vep' into gb_master | 18 October 2012, 21:10:11 UTC |
| 336bba6 | apregier | 18 October 2012, 19:57:44 UTC | Update path to download vep cache | 18 October 2012, 19:57:44 UTC |
| 227df48 | apregier | 18 October 2012, 19:38:36 UTC | If using sift,condel, or polyphen with vep, the full cache will be used | 18 October 2012, 19:48:10 UTC |
| 30e1a2f | Chris Miller | 15 October 2012, 15:08:23 UTC | adding indel readcounts | 18 October 2012, 18:28:23 UTC |
| 9d79077 | Thomas Mooney | 18 October 2012, 18:03:07 UTC | Use more direct accessor name when defining previously defined variant input. | 18 October 2012, 18:03:07 UTC |
| 944c093 | Adam Coffman | 18 October 2012, 18:00:33 UTC | ensure package and class name match - rt 86914 | 18 October 2012, 18:00:33 UTC |
| c5bfb9e | APipe Tester | 17 October 2012, 21:48:22 UTC | updated ur submodule to bb913e1 | 17 October 2012, 21:48:22 UTC |
| cb27f29 | Thomas Mooney | 17 October 2012, 19:52:12 UTC | Grab the callback script from our module's directory. | 17 October 2012, 19:52:12 UTC |
| 9b3f575 | apregier | 17 October 2012, 19:35:21 UTC | Merge branch 'fireteam' into gb_master | 17 October 2012, 19:35:21 UTC |
| 7551b99 | apregier | 17 October 2012, 19:34:49 UTC | Add new version of allpaths | 17 October 2012, 19:34:49 UTC |
| 948e093 | APipe Tester | 17 October 2012, 18:30:31 UTC | updated ur submodule to 535e2ad | 17 October 2012, 18:30:31 UTC |
| c2711d8 | Brian Derickson | 17 October 2012, 18:23:43 UTC | fixed recursive directory read/write check in Genome/Sys | 17 October 2012, 18:23:48 UTC |
| 0947a3c | Gabriel Sanderson | 17 October 2012, 18:17:28 UTC | Roll this back until I figure out build diffs Revert "CHANGELOG: DV2 vcf combinations now maintain multiple columns per sample." This reverts commit 22d4005511f83a645ef8e150ae6bc0059cde3449. | 17 October 2012, 18:17:28 UTC |
| 31cb43d | Ben Oberkfell | 17 October 2012, 18:15:50 UTC | Merge branch 'master' of git:/srv/git/genome | 17 October 2012, 18:15:50 UTC |
| d13a960 | Ben Oberkfell | 17 October 2012, 18:15:32 UTC | dont print this debug line. | 17 October 2012, 18:15:32 UTC |
| b6b56a8 | nnutter | 17 October 2012, 16:19:11 UTC | infer paired end status if this is read group segment | 17 October 2012, 16:19:35 UTC |
| f68732f | nnutter | 17 October 2012, 16:16:21 UTC | check that $bam_file is set | 17 October 2012, 16:19:34 UTC |
| 1024284 | nnutter | 12 October 2012, 19:09:22 UTC | fix uninitialized value $unarchived_count | 17 October 2012, 16:19:34 UTC |
| af8726a | Jasreet Hundal | 17 October 2012, 14:41:17 UTC | Alias commands added from Genome::InstrumentData::Solexa | 17 October 2012, 14:41:17 UTC |
| 66c8a40 | Thomas Mooney | 17 October 2012, 13:58:17 UTC | Increase PhenotypeCorrelation memory limit to 8GB. 4GB was too low to complete one of the R scripts on a WGS dataset. | 17 October 2012, 13:58:17 UTC |
| 5e1ee34 | Gabriel Sanderson | 16 October 2012, 22:37:38 UTC | Merge branch 'tcga' into gb_master | 16 October 2012, 22:37:38 UTC |
| 22d4005 | Gabriel Sanderson | 12 October 2012, 20:00:18 UTC | CHANGELOG: DV2 vcf combinations now maintain multiple columns per sample. There is now one column per detector with fields from that detector as well as one "consensus" column that joinx creates for a final answer for that sample. Incremented vcf version so that new files will be generated. | 16 October 2012, 21:28:06 UTC |
| bb9b9c3 | apregier | 16 October 2012, 21:19:51 UTC | Merge branch 'music' into gb_master | 16 October 2012, 21:19:51 UTC |
| f4b4a40 | apregier | 16 October 2012, 21:19:09 UTC | Add doc to review-file-dir on music model | 16 October 2012, 21:19:23 UTC |
| 089c19b | apregier | 16 October 2012, 21:06:53 UTC | Music model can include a variant black list to exclude from the validation list | 16 October 2012, 21:19:22 UTC |
| 2756b41 | Adam Coffman | 16 October 2012, 20:54:21 UTC | suppress stack trace for duplicate name error messages on model creation rt 86892 | 16 October 2012, 20:54:21 UTC |
| d3d565f | Eddie Belter | 16 October 2012, 20:25:19 UTC | SX: make base a command v1 so subcommands show | 16 October 2012, 20:25:19 UTC |
| 05e472d | Thomas Mooney | 16 October 2012, 20:17:34 UTC | Merge branch 'master' of ssh://git/srv/git/genome :( | 16 October 2012, 20:17:34 UTC |
| 2926b77 | APipe Tester | 16 October 2012, 20:16:49 UTC | updated workflow submodule to 301757e | 16 October 2012, 20:16:49 UTC |
| 546c04e | Thomas Mooney | 16 October 2012, 20:15:27 UTC | Update SomaticVariation inputs in preparation for supporting RnaSeq as inputs. | 16 October 2012, 20:15:27 UTC |
| fecbc0a | Ben Oberkfell | 16 October 2012, 20:13:41 UTC | fixes for postgres in UR | 16 October 2012, 20:13:41 UTC |
| b7342b5 | Ben Oberkfell | 16 October 2012, 20:12:35 UTC | Merge branch 'master' of git:/srv/git/genome Conflicts: lib/perl/Genome/Model/MutationalSignificance.pm lib/perl/Genome/Model/MutationalSignificance/Command/CompileValidationList.pm | 16 October 2012, 20:12:35 UTC |
| 6eb2e29 | Ben Oberkfell | 16 October 2012, 20:08:09 UTC | properly query postgres but write to both | 16 October 2012, 20:08:47 UTC |
| 473b7c7 | Ben Oberkfell | 15 October 2012, 06:00:14 UTC | further fixes for querying postgres & properly syncing | 16 October 2012, 20:08:46 UTC |
| 12c093e | apregier | 12 October 2012, 22:53:44 UTC | Respect filter_previously_discovered_variants even for non-software result runs of identify-previously-discovered-variants | 16 October 2012, 20:08:46 UTC |
| 75a38c6 | Scott Smith | 12 October 2012, 22:25:23 UTC | added Gary to the author list on Genome.pm | 16 October 2012, 20:08:46 UTC |
| 4848d4a | Scott Smith | 12 October 2012, 22:19:42 UTC | added Mark Burnett, David Morton, and Obi Griffith | 16 October 2012, 20:08:46 UTC |
| 322798f | Jason Walker | 12 October 2012, 21:39:28 UTC | Revert the value_class_name to Genome::Model::ReferenceAlignment for tumor and normal models in SomaticVariation. The value_class_name is used when inputs are defined. Another solution will be reaquired so Genome::Model::RnaSeq is a valid model class. | 16 October 2012, 20:08:45 UTC |
| d523094 | Travis Abbott | 12 October 2012, 20:40:04 UTC | fix typo in variable reference | 16 October 2012, 20:08:45 UTC |
| 896ea1d | Jason Walker | 12 October 2012, 20:03:22 UTC | Update the tumor_model and normal_model accessors in SomaticVariation to find any Model regardless of subclass | 16 October 2012, 20:08:45 UTC |
| 4f8ed12 | Travis Abbott | 12 October 2012, 19:53:47 UTC | Change VcfToVariantMatrix to write to many tmpfiles previously, this command would write partial output, compute more, read in the previous output, append to it in memory, and write it all back out again. That leads to O(n^2) complexity in the number of data chunks. If we instead write out each chunk to a temp file, then merge at the end, we get O(n). | 16 October 2012, 20:08:45 UTC |
| 4f18376 | apregier | 12 October 2012, 19:45:21 UTC | CHANGELOG Music model allows user to specify black-list of gene ids that should be excluded from validation list | 16 October 2012, 20:08:45 UTC |
| c9b3ec9 | APipe Tester | 12 October 2012, 19:19:54 UTC | updated workflow submodule to c3b7c03 | 16 October 2012, 20:08:44 UTC |
| da1141a | Malachi Griffith | 12 October 2012, 18:19:30 UTC | Added build level checks for intrument data in clinseq update-analyis code | 16 October 2012, 20:08:44 UTC |
| 5e95322 | Chris Miller | 12 October 2012, 17:59:16 UTC | added non-reference option | 16 October 2012, 20:08:44 UTC |
| 2b589ee | Kyung Kim | 12 October 2012, 15:40:37 UTC | update to move report file creation to base | 16 October 2012, 20:08:44 UTC |
| 2aedb04 | apregier | 25 September 2012, 21:25:18 UTC | Add ROI list to be included in validation | 16 October 2012, 20:08:43 UTC |
| d098c36 | Jason Walker | 12 October 2012, 14:35:39 UTC | CHANGELOG: RNA-seq BAMs are now acceptable inputs to SomaticVariation. | 16 October 2012, 20:08:43 UTC |
| 63fd8df | APipe Tester | 12 October 2012, 02:18:56 UTC | updated workflow submodule to f8d15b1 | 16 October 2012, 20:08:43 UTC |
| cb5e21f | Cyriac Kandoth | 11 October 2012, 22:53:59 UTC | 4 column ROI files can now be used with annotation-format | 16 October 2012, 20:08:43 UTC |
| 0cab229 | Kyung Kim | 11 October 2012, 22:11:36 UTC | Moved taxon db accessor to base class | 16 October 2012, 20:08:42 UTC |
| 8114cb3 | Gabriel Sanderson | 11 October 2012, 21:01:57 UTC | Remove unnecessary vcf generation code in combines. I believe this code has been out of date for awhile. And it passes unit tests and builds look fine. The real combined vcf generation should happen in Genome::Model::Tools::DetectVariants2::Result::Vcf::Combine | 16 October 2012, 20:08:42 UTC |
| ca92410 | nnutter | 11 October 2012, 20:20:33 UTC | update data_directory test to only care about allocation_path portion | 16 October 2012, 20:08:42 UTC |
| 8e261bd | nnutter | 11 October 2012, 18:30:08 UTC | update submodule pointers | 16 October 2012, 20:08:42 UTC |
| deebdbe | Travis Abbott | 09 October 2012, 18:52:39 UTC | update RareDelTest to work with Workflow (making things inputs/outputs) | 16 October 2012, 20:08:41 UTC |
| 35d38c6 | Travis Abbott | 09 October 2012, 17:36:20 UTC | make add_filter method for Vep::Reader | 16 October 2012, 20:08:41 UTC |
| 151f1b7 | Eddie Belter | 16 October 2012, 20:03:53 UTC | SX: rm save reader input files | 16 October 2012, 20:03:53 UTC |
| 73f73e2 | Eddie Belter | 16 October 2012, 20:01:32 UTC | SX: validate uses __meta__ instead of get class object | 16 October 2012, 20:01:32 UTC |
| 09db2fa | Eddie Belter | 15 October 2012, 18:04:17 UTC | SX: rm "base" from any command line ops. Mostly in tests | 16 October 2012, 19:44:54 UTC |
| e259ee4 | Eddie Belter | 08 October 2012, 18:30:11 UTC | SX Rename: now uses _create_evaluator instead of _eval_seqs | 16 October 2012, 19:44:53 UTC |
| 528f394 | Eddie Belter | 08 October 2012, 18:20:56 UTC | SX Base: move evalutor creation before opening inputs and outputs | 16 October 2012, 19:44:53 UTC |
| 23ec3b0 | Eddie Belter | 08 October 2012, 18:11:54 UTC | SX Trim: update to use _create_evaluator | 16 October 2012, 19:44:53 UTC |
| d862b0e | Eddie Belter | 08 October 2012, 17:53:06 UTC | SX Filter Base: rename _create_sequence_evaluator to _create_evaluator | 16 October 2012, 19:44:52 UTC |
| 2c667b2 | Eddie Belter | 08 October 2012, 17:51:54 UTC | SX Base: change _eval_seqs to _create_evaluator to return anon sub to eval seqs | 16 October 2012, 19:44:52 UTC |
| 486ae54 | Eddie Belter | 08 October 2012, 17:45:12 UTC | SX Filter: rm use and named block | 16 October 2012, 19:44:51 UTC |
| aa6cb84 | Eddie Belter | 08 October 2012, 17:39:00 UTC | SX Fitler: can return sequence evaluator | 16 October 2012, 19:44:51 UTC |
| 6453088 | Eddie Belter | 16 October 2012, 19:40:00 UTC | SX: update save reader files | 16 October 2012, 19:41:36 UTC |
| d89b69c | Eddie Belter | 16 October 2012, 19:39:30 UTC | SX: update euler cmd display name | 16 October 2012, 19:41:36 UTC |
| d8b0d52 | Eddie Belter | 16 October 2012, 19:07:17 UTC | SX: mv save_files property from quake and euler to ext cmd base | 16 October 2012, 19:41:35 UTC |
| cff47cf | Eddie Belter | 16 October 2012, 19:06:04 UTC | SX: add cmd display name to trimmers quake and euler ec | 16 October 2012, 19:41:35 UTC |
| af6bdce | Eddie Belter | 15 October 2012, 22:34:39 UTC | SX: mv saving reader output from base to ext cmd base | 16 October 2012, 19:41:34 UTC |
| e46a502 | Eddie Belter | 15 October 2012, 22:31:30 UTC | SX: convert eurler and quake to ext cmd base | 16 October 2012, 19:41:34 UTC |
| d5e5054 | Eddie Belter | 15 October 2012, 22:28:07 UTC | SX: euler and quake - update class names | 16 October 2012, 19:41:33 UTC |
