| 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 |
| 9b8776a | Eddie Belter | 15 October 2012, 22:26:09 UTC | SX: mv euler and quake to trim dir | 16 October 2012, 19:41:32 UTC |
| f4d5b03 | Adam Coffman | 16 October 2012, 18:35:36 UTC | force symlink creation over existing destination | 16 October 2012, 18:35:36 UTC |
| a05bc35 | Travis Abbott | 16 October 2012, 17:34:38 UTC | do FET for genes with rare+deleterious variants | 16 October 2012, 17:36:42 UTC |
| ed4453c | Travis Abbott | 16 October 2012, 17:33:36 UTC | update RareDel{Test,Table} so they can be run by workflow make params inputs/output, etc | 16 October 2012, 17:36:42 UTC |
| bf63954 | Thomas Mooney | 16 October 2012, 16:22:16 UTC | Update default RNASeq processing profile (RT#86846) | 16 October 2012, 16:22:16 UTC |
| 5daf177 | Thomas Mooney | 16 October 2012, 16:11:28 UTC | Allow incompatible references for RNASeq instrument data that will be aligned. | 16 October 2012, 16:11:28 UTC |
| 6ddb387 | Brian Derickson | 15 October 2012, 22:30:13 UTC | archiving now checks file permissions before attempting to archive | 15 October 2012, 22:30:19 UTC |
| 5342de1 | Brian Derickson | 15 October 2012, 22:29:52 UTC | added new method to Genome::Sys, recursively_validate_directory_for_read_write_access, that recursively checks that all files in a directory are readable and writable | 15 October 2012, 22:30:18 UTC |
| cda533a | apregier | 15 October 2012, 18:42:35 UTC | Merge branch 'my_annotation' into gb_master | 15 October 2012, 18:42:35 UTC |
| 1196ad3 | apregier | 15 October 2012, 18:40:57 UTC | Sort gold2geno bed file before joinx intersect | 15 October 2012, 18:41:11 UTC |
| 135cbd8 | Brian Derickson | 15 October 2012, 18:12:52 UTC | updated is_archived method on build, now checks all allocations instead of just its data directory | 15 October 2012, 18:13:14 UTC |
| 26d8306 | Malachi Griffith | 15 October 2012, 17:49:54 UTC | Minor update to clinseq to allow samples combined from multiple individuals by use of --force | 15 October 2012, 17:49:54 UTC |
| 87eb4f3 | apregier | 15 October 2012, 14:53:27 UTC | Merge branch 'music' into gb_master | 15 October 2012, 14:53:27 UTC |
| cf448a8 | apregier | 15 October 2012, 14:52:29 UTC | Music model accepts additional variant lists to include in validation | 15 October 2012, 14:52:29 UTC |
| 9418daf | Cyriac Kandoth | 15 October 2012, 12:37:29 UTC | Fix chrom bounds exception, and add option to print reading frames | 15 October 2012, 12:37:29 UTC |
| 85f66fa | apregier | 13 October 2012, 02:33:50 UTC | Merge branch 'music' into gb_master | 13 October 2012, 02:33:50 UTC |
| 32482ef | apregier | 12 October 2012, 22:53:44 UTC | Respect filter_previously_discovered_variants even for non-software result runs of identify-previously-discovered-variants | 13 October 2012, 02:33:03 UTC |
| 321abad | Scott Smith | 12 October 2012, 22:25:23 UTC | added Gary to the author list on Genome.pm | 12 October 2012, 22:25:23 UTC |
| cc95713 | Scott Smith | 12 October 2012, 22:19:55 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 October 2012, 22:19:55 UTC |
| 0f1105d | Scott Smith | 12 October 2012, 22:19:42 UTC | added Mark Burnett, David Morton, and Obi Griffith | 12 October 2012, 22:19:42 UTC |
| 6fde969 | 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. | 12 October 2012, 21:39:36 UTC |
| 6990e8a | Travis Abbott | 12 October 2012, 20:40:04 UTC | fix typo in variable reference | 12 October 2012, 20:40:30 UTC |
| ed8c9cb | 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 | 12 October 2012, 20:03:31 UTC |
| 54f3df9 | Travis Abbott | 12 October 2012, 19:55:34 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 October 2012, 19:55:34 UTC |
| 78eb0fb | 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). | 12 October 2012, 19:53:47 UTC |
| 48c4ba4 | apregier | 12 October 2012, 19:45:51 UTC | Merge branch 'music' into gb_master | 12 October 2012, 19:45:51 UTC |
| dc92972 | 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 | 12 October 2012, 19:45:32 UTC |
| 55838ca | APipe Tester | 12 October 2012, 19:19:54 UTC | updated workflow submodule to c3b7c03 | 12 October 2012, 19:19:54 UTC |
| 7c49c7b | Malachi Griffith | 12 October 2012, 18:20:01 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 October 2012, 18:20:01 UTC |
| 9ff5e8a | Malachi Griffith | 12 October 2012, 18:19:30 UTC | Added build level checks for intrument data in clinseq update-analyis code | 12 October 2012, 18:19:30 UTC |
| 28f1ee6 | Chris Miller | 12 October 2012, 17:59:16 UTC | added non-reference option | 12 October 2012, 17:59:32 UTC |
| e7ba1e1 | Travis Abbott | 12 October 2012, 16:14:24 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 October 2012, 16:14:24 UTC |
| aa03582 | Kyung Kim | 12 October 2012, 15:40:37 UTC | update to move report file creation to base | 12 October 2012, 15:40:37 UTC |
| 27ddcc6 | apregier | 12 October 2012, 14:41:08 UTC | Merge branch 'music' into gb_master | 12 October 2012, 14:41:08 UTC |
| badf64a | apregier | 25 September 2012, 21:25:18 UTC | Add ROI list to be included in validation | 12 October 2012, 14:39:30 UTC |
| 4b8e042 | Jason Walker | 12 October 2012, 14:35:39 UTC | CHANGELOG: RNA-seq BAMs are now acceptable inputs to SomaticVariation. | 12 October 2012, 14:36:03 UTC |
| 9ff1a67 | APipe Tester | 12 October 2012, 02:18:56 UTC | updated workflow submodule to f8d15b1 | 12 October 2012, 02:18:56 UTC |
| bf01b62 | Cyriac Kandoth | 11 October 2012, 22:53:59 UTC | 4 column ROI files can now be used with annotation-format | 11 October 2012, 22:53:59 UTC |
| 0baf43d | Kyung Kim | 11 October 2012, 22:11:41 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 11 October 2012, 22:11:41 UTC |
| 8ec297f | Kyung Kim | 11 October 2012, 22:11:36 UTC | Moved taxon db accessor to base class | 11 October 2012, 22:11:36 UTC |
| 9687c96 | Gabriel Sanderson | 11 October 2012, 21:03:31 UTC | Merge branch 'tcga' into gb_master | 11 October 2012, 21:03:31 UTC |
| 95b2ccd | 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 | 11 October 2012, 21:03:19 UTC |
| 3e38301 | nnutter | 11 October 2012, 20:20:33 UTC | update data_directory test to only care about allocation_path portion | 11 October 2012, 20:21:06 UTC |
| 56d2787 | nnutter | 11 October 2012, 18:30:08 UTC | update submodule pointers | 11 October 2012, 20:21:05 UTC |
| 95fb381 | Ben Oberkfell | 11 October 2012, 20:09:51 UTC | Merge branch 'master' of git:/srv/git/genome | 11 October 2012, 20:09:51 UTC |
| c3321b1 | Ben Oberkfell | 11 October 2012, 20:09:44 UTC | CHANGELOG: fix race condition related to canceling operations in the middle of an oracle sync | 11 October 2012, 20:09:44 UTC |
| b348ae8 | apregier | 11 October 2012, 18:58:13 UTC | Merge branch 'fireteam' into gb_master | 11 October 2012, 18:58:13 UTC |
| 6682f24 | apregier | 11 October 2012, 18:57:11 UTC | Sort imported dbsnp vcf the same way as pipeline vcfs are sorted | 11 October 2012, 18:57:29 UTC |
| b6baa74 | Ian Ferguson | 11 October 2012, 18:38:06 UTC | Updated version of ErrorRate C util Updated Genome::Model::Tools::BioSamTools::ErrorRate.pm to point to the latest version of the ErrorRate C utility. | 11 October 2012, 18:38:06 UTC |
| 1f3e827 | APipe Tester | 11 October 2012, 15:39:06 UTC | updated workflow submodule to 6d2e351 | 11 October 2012, 15:39:06 UTC |
| 4a9ee3e | Jim Weible | 11 October 2012, 15:31:17 UTC | skip dumping the structure | 11 October 2012, 15:31:17 UTC |
| 166530e | Kyung Kim | 11 October 2012, 15:21:14 UTC | removed virome-event cd-hit remove files workflow event | 11 October 2012, 15:21:14 UTC |
| 92a75b8 | Malachi Griffith | 11 October 2012, 00:41:46 UTC | Reintroduce use of previously discovered variants into default clin-seq processing steps | 11 October 2012, 00:41:46 UTC |
| 161364e | Obi Griffith | 11 October 2012, 00:13:24 UTC | removed samtools (used just as a prefilter for and thus redundant with sniper) | 11 October 2012, 00:13:24 UTC |
| add9d91 | Dave Larson | 10 October 2012, 21:05:12 UTC | add rs id to test to double check implementation. Still vulnerable to changes to clinical correlation | 10 October 2012, 21:05:12 UTC |
| 9cd0f56 | Dave Larson | 10 October 2012, 19:23:31 UTC | fix to handle presence of rsID in variant names | 10 October 2012, 21:03:11 UTC |
| b162b70 | Kyung Kim | 10 October 2012, 21:02:34 UTC | Update to avoid parsing through entire gi_taxid dmp file when no more taxids are sought for | 10 October 2012, 21:02:34 UTC |
| b5a1b82 | nnutter | 10 October 2012, 20:47:07 UTC | only pass body_text if it is defined | 10 October 2012, 20:47:17 UTC |
| 47d06da | Malachi Griffith | 10 October 2012, 19:49:13 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 October 2012, 19:49:13 UTC |
| 6542e14 | Malachi Griffith | 10 October 2012, 19:48:59 UTC | Update strelka test results | 10 October 2012, 19:48:59 UTC |
