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 I believe this code has been out of date for awhile.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 |
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 |
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 |
ea70611 | Travis Abbott | 08 October 2012, 22:35:56 UTC | expose Vcf::Header->format_field_index this returns a mapping of format field IDs to their index | 08 October 2012, 22:45:42 UTC |
3515580 | Travis Abbott | 08 October 2012, 22:29:16 UTC | update gmt vcf rare-del-test to compute fet pvals in 1 shot instead of shelling out to R many times, we can just use apply() to do the calculation much faster | 08 October 2012, 22:45:41 UTC |
78c9665 | Kyung Kim | 08 October 2012, 21:47:19 UTC | Removed some useless log statements | 08 October 2012, 21:47:19 UTC |
32937a8 | apregier | 08 October 2012, 21:41:15 UTC | Merge branch 'my_annotation' into gb_master | 08 October 2012, 21:41:15 UTC |
281246b | apregier | 08 October 2012, 21:40:24 UTC | Clean up annotated vcf name in somatic variation" | 08 October 2012, 21:40:24 UTC |
e3cea63 | APipe Tester | 08 October 2012, 21:24:21 UTC | updated workflow submodule to e382ef3 | 08 October 2012, 21:24:21 UTC |
d80963f | nnutter | 08 October 2012, 21:11:25 UTC | revert change to mpileup options | 08 October 2012, 21:11:25 UTC |
50b324e | nnutter | 08 October 2012, 21:10:58 UTC | fix typo, remove my | 08 October 2012, 21:10:58 UTC |
1a64eb8 | Kyung Kim | 08 October 2012, 20:31:19 UTC | Update to get taxid from ncbi gi_taxid dmp file rather than taxonomy_db | 08 October 2012, 20:31:19 UTC |
41a74b2 | APipe Tester | 08 October 2012, 19:44:32 UTC | updated workflow submodule to 420f133 | 08 October 2012, 19:44:32 UTC |
79ae38d | Dan Koboldt | 08 October 2012, 19:41:32 UTC | Fix to enable v2.2.6 compatibility | 08 October 2012, 19:41:32 UTC |
27bbeb3 | Dan Koboldt | 08 October 2012, 19:34:50 UTC | Fix to enable v2.2.6 compatibility | 08 October 2012, 19:34:50 UTC |
1fc635c | Travis Abbott | 08 October 2012, 17:55:00 UTC | switch back to using VcfToBurdenMatrix in phenocorr accidentally commited a change that switched to the new version (CreateBurdenMatrix) while testing it | 08 October 2012, 17:55:00 UTC |
59e23a1 | Travis Abbott | 08 October 2012, 17:17:56 UTC | add gmt vcf create-burden-matrix | 08 October 2012, 17:18:29 UTC |
53db3dd | APipe Tester | 08 October 2012, 16:34:57 UTC | updated workflow submodule to d382a3e | 08 October 2012, 16:34:57 UTC |
b684062 | Eddie Belter | 08 October 2012, 15:48:30 UTC | Far and trimq2 ignores single fastqs from far | 08 October 2012, 15:48:38 UTC |
b96a6ab | APipe Tester | 08 October 2012, 15:48:18 UTC | updated jenkins submodule to 07c935a | 08 October 2012, 15:48:18 UTC |
49b994b | nnutter | 07 October 2012, 04:34:38 UTC | disable watch toggle button sooner to prevent multiple click events | 07 October 2012, 04:35:02 UTC |
e524504 | nnutter | 07 October 2012, 04:30:34 UTC | add role to project view | 07 October 2012, 04:35:02 UTC |
d42a7ae | Travis Abbott | 05 October 2012, 22:17:09 UTC | use parallel vep in phenocorr | 05 October 2012, 22:32:08 UTC |
ea967bf | Travis Abbott | 05 October 2012, 22:13:38 UTC | add parallel vep annotation to phenocorr | 05 October 2012, 22:32:07 UTC |
7fdb29e | Travis Abbott | 05 October 2012, 22:13:15 UTC | update Vep to allow input from stdin | 05 October 2012, 22:32:07 UTC |
4397f9c | Travis Abbott | 05 October 2012, 17:49:44 UTC | Let VEP headers store meta info lines (##) | 05 October 2012, 22:30:57 UTC |
3f5e20d | Eddie Belter | 05 October 2012, 22:15:09 UTC | SX: update trim by qual test | 05 October 2012, 22:15:13 UTC |
ed2d86a | nnutter | 05 October 2012, 22:12:50 UTC | override admin role status in test | 05 October 2012, 22:13:26 UTC |
e917101 | Eddie Belter | 05 October 2012, 22:12:57 UTC | CHANGELOG: Solexa - Add handling of multiple SX trimming/processing | 05 October 2012, 22:12:57 UTC |
e283f26 | Eddie Belter | 05 October 2012, 22:05:06 UTC | SX: Trim by qual on right end | 05 October 2012, 22:05:06 UTC |