| 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 |
| 0b9522a | nnutter | 05 October 2012, 21:37:15 UTC | Merge branch 'watched_projects' | 05 October 2012, 21:37:15 UTC |
| dc61fd7 | nnutter | 05 October 2012, 21:26:49 UTC | add watch/unwatch button to project page CHANGELOG: Instead of showing all projects you have created in the project sidebar we now only show projects that you have explicitly requested to watch. You can (un)watch projects by going to the project page and clicking the (un)watch button in the upper right. Or alternatively by using the `genome project watch` (or unwatch) commands. | 05 October 2012, 21:36:58 UTC |
| 6e6c2a6 | nnutter | 05 October 2012, 21:26:21 UTC | add project part ID as row ID attribute | 05 October 2012, 21:36:58 UTC |
| 78c6b8b | nnutter | 05 October 2012, 21:25:23 UTC | add span with ID projectID | 05 October 2012, 21:36:57 UTC |
| b313b79 | nnutter | 05 October 2012, 21:24:48 UTC | add spans with IDs hiddenAuthUser and hiddenAuthUserID | 05 October 2012, 21:36:57 UTC |
| 85ec2f6 | nnutter | 05 October 2012, 21:22:51 UTC | allow single REST delete by parameters not just ID | 05 October 2012, 21:36:57 UTC |
| 8ec5e70 | nnutter | 05 October 2012, 21:21:44 UTC | add user ID to whoami page | 05 October 2012, 21:36:56 UTC |
| c32c0cf | nnutter | 05 October 2012, 17:35:50 UTC | switch project sidebar to use watchers | 05 October 2012, 21:36:56 UTC |
| e926893 | nnutter | 05 October 2012, 17:34:56 UTC | add watch and unwatch commands for projects | 05 October 2012, 21:36:56 UTC |
| f0f99c8 | nnutter | 05 October 2012, 17:34:11 UTC | add watcher concept to projects | 05 October 2012, 21:36:55 UTC |
| 9ccc78b | apregier | 05 October 2012, 20:49:47 UTC | Merge branch 'my_annotation' into gb_master | 05 October 2012, 20:49:47 UTC |
| ec070ad | apregier | 05 October 2012, 20:49:13 UTC | Update varscan version and test data for VarscanSomatic. Better test data will follow shortly | 05 October 2012, 20:49:26 UTC |
| be12bd9 | apregier | 05 October 2012, 13:42:23 UTC | Clean up varscan validation test | 05 October 2012, 20:49:26 UTC |
| 8cd0491 | Eddie Belter | 05 October 2012, 19:58:15 UTC | SX: trim is command tree | 05 October 2012, 19:58:15 UTC |
| eefa442 | apregier | 05 October 2012, 19:32:43 UTC | Merge branch 'vep' into gb_master | 05 October 2012, 19:32:43 UTC |
| c1e817f | apregier | 05 October 2012, 19:30:48 UTC | Fix problems with vep cache | 05 October 2012, 19:31:16 UTC |
| 75496a6 | Kyung Kim | 05 October 2012, 18:03:09 UTC | Update name of taxononmy db | 05 October 2012, 18:03:09 UTC |
| 0b1ecb3 | nnutter | 05 October 2012, 13:48:00 UTC | prevent crash if result is missing v2 metrics | 05 October 2012, 13:48:00 UTC |
| 02cace1 | nnutter | 05 October 2012, 13:46:59 UTC | add # to header line | 05 October 2012, 13:46:59 UTC |
| 196e507 | Travis Abbott | 05 October 2012, 05:17:03 UTC | add gmt tabix list-chromosomes (tabix -l) | 05 October 2012, 05:18:13 UTC |
| 8e0c89c | Travis Abbott | 05 October 2012, 05:15:54 UTC | When it comes to VCF parsing, we need to be lazy let's not parse out sample data unless we're actually asked for it. | 05 October 2012, 05:18:13 UTC |
| 151a69d | Travis Abbott | 05 October 2012, 05:15:20 UTC | remove debugging print statements | 05 October 2012, 05:18:12 UTC |
| 026d16c | Travis Abbott | 05 October 2012, 05:14:12 UTC | fix handling of empty EXTRA fields in Vep files | 05 October 2012, 05:18:12 UTC |
| c8531a1 | Travis Abbott | 03 October 2012, 19:40:09 UTC | add num-cores option to BurdenAnalysis | 05 October 2012, 05:18:12 UTC |
| 37cfec7 | Malachi Griffith | 05 October 2012, 01:36:00 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 October 2012, 01:36:00 UTC |
| b1cbab9 | Malachi Griffith | 05 October 2012, 01:34:31 UTC | Change model input to build input and other cosmetic changes to clinseq clonality analysis | 05 October 2012, 01:34:31 UTC |
| 9f85424 | Ben Oberkfell | 04 October 2012, 22:27:40 UTC | restore varscan module and fix validation test | 04 October 2012, 22:27:40 UTC |
| 0b6fa1f | apregier | 04 October 2012, 21:10:42 UTC | Merge branch 'copy' into gb_master | 04 October 2012, 21:10:42 UTC |
| 54ce64d | apregier | 04 October 2012, 20:22:09 UTC | Add annotate vcf step to somatic variation pipeline | 04 October 2012, 21:02:42 UTC |
| b813ef2 | apregier | 28 September 2012, 19:18:13 UTC | Add a parameter to somatic variation to specify whether to filter previously discovered variants | 04 October 2012, 21:02:41 UTC |
| 3e9e035 | Beifang Niu | 04 October 2012, 21:01:56 UTC | fixed the binomial test error | 04 October 2012, 21:01:56 UTC |
| cc9421f | Beifang Niu | 04 October 2012, 20:22:35 UTC | First write of new proximity module | 04 October 2012, 20:22:35 UTC |
| 9f103be | Dan Koboldt | 04 October 2012, 20:01:24 UTC | Trying to take server version of Varscan.pm | 04 October 2012, 20:01:24 UTC |
| 2629fe8 | Dan Koboldt | 04 October 2012, 19:58:59 UTC | My change to VarScan.pm | 04 October 2012, 19:58:59 UTC |
| 233adb0 | nnutter | 04 October 2012, 19:01:46 UTC | re-enable cuffcompare | 04 October 2012, 19:01:46 UTC |
| e6e1b76 | Jason Walker | 04 October 2012, 18:13:19 UTC | Update the env variable for the cuffcompare test case | 04 October 2012, 18:13:29 UTC |
| d76f606 | nnutter | 04 October 2012, 17:46:41 UTC | disable cuffcompare test | 04 October 2012, 17:47:03 UTC |
| 474b1cb | APipe Tester | 04 October 2012, 17:40:33 UTC | updated workflow submodule to 422ee19 | 04 October 2012, 17:40:33 UTC |
| 91cd372 | nnutter | 04 October 2012, 03:32:33 UTC | fix for map not returning words | 04 October 2012, 03:32:33 UTC |
| b6b3b8d | nnutter | 04 October 2012, 03:31:38 UTC | probably don't want a use above here | 04 October 2012, 03:31:38 UTC |
| e399afd | apregier | 03 October 2012, 21:57:20 UTC | Merge branch 'allpaths' into gb_master | 03 October 2012, 21:57:20 UTC |
| 0e54fb6 | apregier | 28 September 2012, 18:07:29 UTC | Set max_mem_gb for allpaths builds | 03 October 2012, 21:56:34 UTC |
