| 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 |
| 7640656 | apregier | 28 September 2012, 18:07:06 UTC | Add max_mem_gb param option for allpaths | 03 October 2012, 21:56:34 UTC |
| 0610077 | Anthony Brummett | 03 October 2012, 21:52:43 UTC | When determining a sire configuration module from a hostname, convert - to _ so it will be a valid Perl module name | 03 October 2012, 21:52:43 UTC |
| 78c758e | nnutter | 03 October 2012, 21:04:15 UTC | assign (un)archive to a job group | 03 October 2012, 21:07:01 UTC |
| dd0e5cb | Thomas Mooney | 03 October 2012, 20:20:40 UTC | Go back to using $model->real_input_properties so input names are displayed. | 03 October 2012, 20:20:40 UTC |
| 1eda1c4 | Thomas Mooney | 03 October 2012, 20:12:30 UTC | Use the $self-> calling convention for subroutines. | 03 October 2012, 20:12:30 UTC |
| 4961c22 | Thomas Mooney | 03 October 2012, 20:07:58 UTC | Use empty spacer when right-justifying names. Otherwise names one less than the desired length would end up left rather than right aligned. | 03 October 2012, 20:07:58 UTC |
| f02d364 | nnutter | 03 October 2012, 17:21:57 UTC | fix typo | 03 October 2012, 17:22:20 UTC |
| 0208d9d | Malachi Griffith | 03 October 2012, 16:49:00 UTC | Fix read counting bug in clinseq summarize-svs | 03 October 2012, 16:49:00 UTC |
| 1b3a0c4 | Charles Lu | 03 October 2012, 16:41:43 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 03 October 2012, 16:41:43 UTC |
| 2f79e8f | Charles Lu | 03 October 2012, 16:41:40 UTC | new R function to do pooled-burden test | 03 October 2012, 16:41:40 UTC |
| b533f93 | Nathan Nutter | 03 October 2012, 16:32:53 UTC | change a couple of copy-pasted blocks to use cached reference | 03 October 2012, 16:33:48 UTC |
| 5f58fd3 | Nathan Nutter | 03 October 2012, 16:24:13 UTC | get mm9 reference object and used cached path | 03 October 2012, 16:33:47 UTC |
| 4f4c990 | Nathan Nutter | 03 October 2012, 16:23:34 UTC | change a bunch of copy-pasted blocks to use cached reference | 03 October 2012, 16:33:25 UTC |
| f625a97 | Charles Lu | 03 October 2012, 15:51:43 UTC | added =cut POD directive to properly end POD section. | 03 October 2012, 15:51:43 UTC |
| 08206ff | APipe Tester | 03 October 2012, 14:07:16 UTC | updated workflow submodule to 6380275 | 03 October 2012, 14:07:16 UTC |
| c844517 | APipe Tester | 03 October 2012, 13:43:25 UTC | updated jenkins submodule to 1cba942 | 03 October 2012, 13:43:25 UTC |
| 5a23c98 | Travis Abbott | 02 October 2012, 23:11:54 UTC | add is_sample_filtered to Vcf::Entry | 02 October 2012, 23:12:09 UTC |
| 686ca0c | APipe Tester | 02 October 2012, 21:56:49 UTC | updated workflow submodule to c9c7838 | 02 October 2012, 21:56:49 UTC |
| e2fad5c | Travis Abbott | 02 October 2012, 21:40:26 UTC | make sure gene list in burden test summary has no dups | 02 October 2012, 21:43:03 UTC |
| 5ebd81f | Travis Abbott | 02 October 2012, 18:19:34 UTC | include all gene annotation in plots | 02 October 2012, 21:43:03 UTC |
| 66d50ad | Travis Abbott | 02 October 2012, 18:19:04 UTC | add peek to Vep::Reader | 02 October 2012, 21:43:03 UTC |
| c251f74 | Travis Abbott | 02 October 2012, 18:18:40 UTC | don't use UR for Vcf Entries | 02 October 2012, 21:43:02 UTC |
| 259f15f | Adam Coffman | 02 October 2012, 20:49:00 UTC | add picard 1.77 as an available version | 02 October 2012, 20:49:00 UTC |
| 6f3ca38 | Adam Coffman | 02 October 2012, 20:35:32 UTC | fall back on all_sequences.fa if all_sequences.bowtie is not present | 02 October 2012, 20:35:32 UTC |
| ea19296 | Adam Coffman | 02 October 2012, 20:28:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 02 October 2012, 20:28:30 UTC |
| 5a76fba | Adam Coffman | 02 October 2012, 20:27:11 UTC | Change gmt convert bed-to-annotation to use up to date algorithm Command will now take an input specifying which version of the annotator to use | 02 October 2012, 20:27:11 UTC |
| 72ec59c | Kyung Kim | 02 October 2012, 20:26:44 UTC | update output and create summary file | 02 October 2012, 20:26:44 UTC |
| 05a68ed | Thomas Mooney | 02 October 2012, 18:50:26 UTC | Provide for skipping NovoRealign if there were no SVs from Breakdancer. | 02 October 2012, 18:50:26 UTC |
| 32d5e02 | Nathan Dees | 02 October 2012, 15:42:21 UTC | removed default build 36 ref. added "SV_Contigs" to model names. | 02 October 2012, 15:42:21 UTC |
| 93b5112 | Nathan Dees | 02 October 2012, 15:40:09 UTC | fixed a scoping issue | 02 October 2012, 15:40:09 UTC |
| f0b02ea | Nathan Dees | 02 October 2012, 15:20:45 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 02 October 2012, 15:20:45 UTC |
