| 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 |
| 7aa5d2c | Kyung Kim | 10 October 2012, 19:19:28 UTC | Remove virome repeatmasker remove files tool .. not needed anymore | 10 October 2012, 19:19:28 UTC |
| b7b00b0 | Kyung Kim | 10 October 2012, 19:14:56 UTC | Removed virome repeat masker remove files event which was merged with another event | 10 October 2012, 19:14:56 UTC |
| 0a9656f | Ben Oberkfell | 10 October 2012, 18:49:21 UTC | CHANGELOG: Merge in changes to allow querying from Postgres using the GENOME_QUERY_POSTGRES variable Merge branch 'gms-pg-query' | 10 October 2012, 18:49:54 UTC |
| f3ef01a | Thomas Mooney | 10 October 2012, 17:51:41 UTC | DV2 dispatcher: write logs to the parent workflow's log directory. CHANGELOG: The logs for variant detection will now appear in the build's log directory rather than alongside the output under "/variants". | 10 October 2012, 17:51:41 UTC |
| 13a574a | nnutter | 10 October 2012, 17:29:05 UTC | rename resource to break caching | 10 October 2012, 17:29:49 UTC |
| d77e80d | nnutter | 10 October 2012, 17:24:29 UTC | add project ID to the part request | 10 October 2012, 17:29:49 UTC |
| 47eb8bc | Malachi Griffith | 10 October 2012, 17:24:26 UTC | Fixed StrelkaToBed off-by-one error, updated test results, moved test inputs and results to testsuite/data | 10 October 2012, 17:24:26 UTC |
| e62665e | Nathan Dees | 10 October 2012, 17:09:16 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 October 2012, 17:09:16 UTC |
| f16ddf9 | Nathan Dees | 10 October 2012, 17:09:05 UTC | added zscore pvalue tool for testing Ts before Cs | 10 October 2012, 17:09:05 UTC |
| ec36e4b | nnutter | 09 October 2012, 22:26:41 UTC | allow note header and body to be set when abandoning | 10 October 2012, 17:05:22 UTC |
| 595e9ff | Beifang Niu | 10 October 2012, 16:44:37 UTC | Add dGene match feature | 10 October 2012, 16:44:37 UTC |
| d885297 | apregier | 10 October 2012, 16:41:53 UTC | Merge branch 'fireteam' into gb_master | 10 October 2012, 16:41:53 UTC |
| 2ea2d56 | apregier | 10 October 2012, 16:41:25 UTC | Update clin-seq summarize-builds test data | 10 October 2012, 16:41:25 UTC |
| 3ba913c | Nathan Dees | 10 October 2012, 16:04:03 UTC | first iteration of a p-value for sequence in window before a C->T | 10 October 2012, 16:04:03 UTC |
| f93b2ab | Malachi Griffith | 10 October 2012, 15:32:28 UTC | Added simple code testing module | 10 October 2012, 15:32:28 UTC |
| e8702e6 | Malachi Griffith | 10 October 2012, 15:31:35 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 October 2012, 15:31:35 UTC |
| a68c26f | Malachi Griffith | 10 October 2012, 15:31:11 UTC | Minor updates | 10 October 2012, 15:31:11 UTC |
| 4baccbd | Jason Walker | 09 October 2012, 14:25:35 UTC | Add a none option to skip coverage | 10 October 2012, 14:05:17 UTC |
| 585444d | Dave Larson | 10 October 2012, 02:54:21 UTC | add some code to display genomic control and standard error | 10 October 2012, 02:54:29 UTC |
| 97b623b | dmorton | 09 October 2012, 23:00:13 UTC | gmb view now shows logs of running steps | 09 October 2012, 23:01:01 UTC |
| fbeb75b | apregier | 09 October 2012, 22:54:37 UTC | Merge branch 'fireteam' into gb_master | 09 October 2012, 22:54:37 UTC |
| f8d67a0 | apregier | 09 October 2012, 21:46:00 UTC | Parameter to specify which dbsnp info fields to annotate in the vcf This new parameter on the somatic variation processing profile should be a string in the form expected by the --info-fields parameter of joinx vcf-annotate | 09 October 2012, 21:50:47 UTC |
| 096d204 | apregier | 09 October 2012, 21:44:47 UTC | Joinx vcf-annotate handles --no-info correctly | 09 October 2012, 21:50:47 UTC |
| da7a59d | Ian Ferguson | 09 October 2012, 21:28:27 UTC | Updated ErrorRate in GMT/BioSamtools/ErrorRate.pm Updated the version of the ErrorRate C utility used by Genome::Model::Tools::BioSamtools::ErrorRate. The C utility had a bug that incorrectly parsed SAM flags set to 0. | 09 October 2012, 21:28:27 UTC |
| 6c2e59a | Mark Burnett | 09 October 2012, 20:19:57 UTC | Revert all statsd client code. This reverts commits: 6c614a5541335a9886f57d6b2c136938c52a5888 3709183628244f00805ce7e95aca1fb938067491 ede989d6c7c47d4842bce499450c2bbc6ffb68bc 8285ce9c889cd2412c06fedefc7964d7f7dd6b66 80c40f6d23b561f781184c312ba775240997c858 f679cd1b1942e9c2dc735e8ebc6ac253a54e61ac Must wait until perl 5.8 dependency is installed. | 09 October 2012, 20:19:57 UTC |
| 80961cb | Adam Coffman | 09 October 2012, 19:23:52 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 October 2012, 19:23:52 UTC |
| 5e97dc8 | Adam Coffman | 09 October 2012, 19:23:47 UTC | update sam to fastq to work with picard versions 1.77 and newer | 09 October 2012, 19:23:47 UTC |
| c333e37 | Travis Abbott | 09 October 2012, 18:53:14 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 October 2012, 18:53:14 UTC |
| f51ea4a | Travis Abbott | 09 October 2012, 18:52:39 UTC | update RareDelTest to work with Workflow (making things inputs/outputs) | 09 October 2012, 18:52:39 UTC |
| b7f7af7 | Dave Larson | 09 October 2012, 18:30:40 UTC | forgot to take into account interface changes | 09 October 2012, 18:30:40 UTC |
| 4f75edd | Dave Larson | 09 October 2012, 18:17:18 UTC | minor refactor of clinical correlation filtering and addition of support for missing and filtered genotype rate filtering. | 09 October 2012, 18:17:25 UTC |
| 4545924 | Dan Koboldt | 09 October 2012, 17:52:29 UTC | Merge branch 'master' of git+ssh://git/srv/git/genome | 09 October 2012, 17:52:29 UTC |
| fa65a4e | Dan Koboldt | 09 October 2012, 17:52:18 UTC | Update to rare del table generation | 09 October 2012, 17:52:18 UTC |
| f679cd1 | Mark Burnett | 09 October 2012, 17:48:15 UTC | Fix failing Bsmap test due to botched commit revert. | 09 October 2012, 17:50:22 UTC |
| de08cf6 | Travis Abbott | 09 October 2012, 17:36:20 UTC | make add_filter method for Vep::Reader | 09 October 2012, 17:36:20 UTC |
| 1480940 | apregier | 09 October 2012, 17:17:58 UTC | Merge branch 'fireteam' into gb_master | 09 October 2012, 17:17:58 UTC |
| 60eef91 | apregier | 09 October 2012, 17:17:20 UTC | Fix Sniper sorting problem | 09 October 2012, 17:17:33 UTC |
| c2b0429 | Mark Burnett | 09 October 2012, 15:57:51 UTC | Revert "Add instrumentation to Sys::lock_resource" This reverts commit 5206d70a5b05f6d26cd8427b0f9676b0336762c3. This commit breaks build tests, because Net::Statsd is not available to perl 5.8 on many machines. | 09 October 2012, 15:57:51 UTC |
| 914b0c0 | Kyung Kim | 09 October 2012, 15:16:26 UTC | Clean up | 09 October 2012, 15:16:26 UTC |
| 80c40f6 | Mark Burnett | 08 October 2012, 21:05:13 UTC | Attempt to instrument bwa infer insert size failure rate | 09 October 2012, 13:51:19 UTC |
| 8285ce9 | Mark Burnett | 08 October 2012, 21:03:14 UTC | Collect genome model build start times (per build) | 09 October 2012, 13:51:18 UTC |
| 5206d70 | Mark Burnett | 08 October 2012, 21:01:39 UTC | Add instrumentation to Sys::lock_resource | 09 October 2012, 13:51:18 UTC |
| ede989d | Mark Burnett | 08 October 2012, 20:59:56 UTC | Save AlignmentResult read_count in statsd | 09 October 2012, 13:51:18 UTC |
| 3709183 | Mark Burnett | 08 October 2012, 20:58:55 UTC | Add timing and counts to disk allocation | 09 October 2012, 13:51:17 UTC |
| 6c614a5 | Mark Burnett | 08 October 2012, 18:27:54 UTC | Add prototype statsd client. It is likely that this interface will be changed significantly. | 09 October 2012, 13:51:17 UTC |
| b4712c7 | Travis Abbott | 09 October 2012, 01:21:27 UTC | explicitly include Genom::File::Vcf::Reader | 09 October 2012, 01:21:27 UTC |
| fa4d5f3 | Travis Abbott | 09 October 2012, 01:06:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 October 2012, 01:06:30 UTC |
| a3a0b23 | Travis Abbott | 09 October 2012, 01:04:49 UTC | implement G/File/Vcf/Reader->add_filter This allows the user to supply a coderef that takes an entry and returns a bool indicating whether or not we want to return the entry. In order for the Reader to return an entry, it has to pass all user supplied filters. | 09 October 2012, 01:04:49 UTC |
| ed08f99 | Obi Griffith | 09 October 2012, 00:56:50 UTC | created tool for identifying which caller is responsible for each snv/indel in final bed files | 09 October 2012, 00:56:50 UTC |
| 79efbd0 | Travis Abbott | 09 October 2012, 00:31:30 UTC | fix compile error in Genome::Vcf::Entry | 09 October 2012, 00:32:05 UTC |
| 595b820 | APipe Tester | 08 October 2012, 23:30:23 UTC | updated workflow submodule to f6acdea | 08 October 2012, 23:30:23 UTC |
| 0e781cd | Travis Abbott | 08 October 2012, 22:57:13 UTC | change column naming in RareDelTest fisher_p_value -> fet_p_value to match previous results | 08 October 2012, 22:57:13 UTC |
