e37365a | Chris Miller | 30 July 2013, 21:06:50 UTC | fix warning message | 30 July 2013, 21:07:02 UTC |
804e1f1 | Feiyu Du | 30 July 2013, 18:49:46 UTC | skip ./. as . | 30 July 2013, 18:49:46 UTC |
1fd1dbb | Jason Walker | 30 July 2013, 17:58:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 30 July 2013, 17:58:03 UTC |
6f2bfa3 | Jason Walker | 30 July 2013, 17:57:47 UTC | PerLaneTophat will now use 12 threads | 30 July 2013, 17:57:47 UTC |
8ec4c19 | Eddie Belter | 30 July 2013, 17:48:38 UTC | GM: import/export metadata uses utility test compare_ok | 30 July 2013, 17:48:38 UTC |
cdeb30d | Eddie Belter | 30 July 2013, 17:48:11 UTC | GM: update output for import metadata | 30 July 2013, 17:48:11 UTC |
6c7abaf | APipe Tester | 30 July 2013, 17:00:28 UTC | Updated `gmt` tab completion. | 30 July 2013, 17:00:28 UTC |
d8b9129 | APipe Tester | 30 July 2013, 16:59:07 UTC | Updated `genome` tab completion. | 30 July 2013, 16:59:07 UTC |
21effcf | APipe Tester | 30 July 2013, 16:56:47 UTC | Updated class browser cache. | 30 July 2013, 16:56:47 UTC |
af0d527 | Scott Smith | 30 July 2013, 16:50:19 UTC | moved CopyCat to a top-level namespace | 30 July 2013, 16:50:19 UTC |
6afd833 | Scott Smith | 30 July 2013, 16:45:13 UTC | moved Sciclone to the top level of gmt | 30 July 2013, 16:45:13 UTC |
dbc686a | Scott Smith | 30 July 2013, 16:18:48 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 30 July 2013, 16:18:48 UTC |
69e7134 | Scott Smith | 30 July 2013, 16:18:29 UTC | updated sciclone to use github | 30 July 2013, 16:18:29 UTC |
e966f79 | Chris Miller | 29 July 2013, 21:45:34 UTC | bug where tumor/normal segments didn't get input | 29 July 2013, 21:46:04 UTC |
ae75af0 | APipe Tester | 29 July 2013, 21:13:08 UTC | updated jenkins submodule to e7c9b43 | 29 July 2013, 21:13:08 UTC |
2014c5d | Gabriel Sanderson | 29 July 2013, 21:07:16 UTC | Merge branch 'fpmakebed' into gb_master | 29 July 2013, 21:07:16 UTC |
eb72a8f | Gabriel Sanderson | 24 July 2013, 22:05:16 UTC | CHANGELOG: Fix for the Candidate March 2013 Reference Alignment processing profile. The FalsePositiveVcf filter will now function properly in the reference alignment pipeline as written by this processing profile. Filter: Do not remove existing vcfs if it is a file and not a symlink. FalsePositiveVcf and VarFilterSnv: Refactor out get_samples_from_header for code re-use. Now function either on snvs.hq (in vcf format) or snvs.vcf.gz to play nicely with refalign and PC respectively. Still pretty hacky. FalsePositiveVcf VarFilterSnv Filter: added _check_native_file_counts_vcf to the Filter.pm base class for validating output that involves vcf headers. | 29 July 2013, 21:02:27 UTC |
3f99e58 | APipe Tester | 29 July 2013, 20:42:33 UTC | Updated `genome` tab completion. | 29 July 2013, 20:42:33 UTC |
230db6a | APipe Tester | 29 July 2013, 20:40:19 UTC | Updated class browser cache. | 29 July 2013, 20:40:19 UTC |
91687db | Scott Smith | 29 July 2013, 20:30:28 UTC | updated genome model export metadata and its test case | 29 July 2013, 20:30:28 UTC |
251b608 | Scott Smith | 29 July 2013, 20:27:45 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 29 July 2013, 20:27:45 UTC |
fe8a784 | APipe Tester | 29 July 2013, 19:56:41 UTC | updated ur submodule to 1943110 | 29 July 2013, 19:56:41 UTC |
0153589 | Kyung Kim | 29 July 2013, 19:09:36 UTC | Update to remove taxonomy sql db use .. will instead get taxid from text file | 29 July 2013, 19:09:36 UTC |
2808ef5 | APipe Tester | 26 July 2013, 21:12:38 UTC | Updated `gmt` tab completion. | 26 July 2013, 21:13:01 UTC |
abcf62d | APipe Tester | 26 July 2013, 21:11:37 UTC | Updated `genome` tab completion. | 26 July 2013, 21:13:01 UTC |
2e74043 | APipe Tester | 26 July 2013, 21:07:50 UTC | Updated class browser cache. | 26 July 2013, 21:13:01 UTC |
72cc9e8 | APipe Tester | 26 July 2013, 21:06:59 UTC | updated jenkins submodule to 0506c50 | 26 July 2013, 21:06:59 UTC |
321e1d7 | Yang Li | 26 July 2013, 20:58:27 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 26 July 2013, 20:58:27 UTC |
eb3508b | APipe Tester | 26 July 2013, 20:44:09 UTC | updated workflow submodule to b066a0b | 26 July 2013, 20:44:09 UTC |
a321a3d | APipe Tester | 26 July 2013, 18:31:00 UTC | updated jenkins submodule to 7b1aad7 | 26 July 2013, 18:31:00 UTC |
df58764 | Scott Smith | 26 July 2013, 18:19:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 26 July 2013, 18:19:30 UTC |
dc0b762 | APipe Tester | 26 July 2013, 18:19:00 UTC | updated jenkins submodule to f2bce79 | 26 July 2013, 18:19:00 UTC |
dd3632a | Scott Smith | 26 July 2013, 18:14:32 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 26 July 2013, 18:14:32 UTC |
6682970 | APipe Tester | 26 July 2013, 17:07:04 UTC | updated jenkins submodule to ae76eff | 26 July 2013, 17:07:04 UTC |
c53095a | APipe Tester | 26 July 2013, 17:01:36 UTC | updated jenkins submodule to 573ffcc | 26 July 2013, 17:01:36 UTC |
89df26f | APipe Tester | 26 July 2013, 16:37:20 UTC | updated jenkins submodule to 08bfa85 | 26 July 2013, 16:37:20 UTC |
e18ea70 | Scott Smith | 26 July 2013, 16:15:03 UTC | added test case for UpdateInputsFromModelGroup | 26 July 2013, 16:15:03 UTC |
c4a259b | Yang Li | 26 July 2013, 16:04:52 UTC | Fixed double counting logic error | 26 July 2013, 16:04:52 UTC |
ef611e8 | Anthony Brummett | 26 July 2013, 14:27:58 UTC | When asking for user's input, always read from the terminal When commands are used in shell pipelines, is likely not readable as the source for the user's input | 26 July 2013, 14:27:58 UTC |
f14c3c2 | Dave Larson | 26 July 2013, 14:12:55 UTC | Increase requested memory resources for ProcessValidation command. It seems to need quite a bit in its currrent implementation. | 26 July 2013, 14:12:55 UTC |
17cf6a2 | APipe Tester | 26 July 2013, 11:32:38 UTC | Updated `gmt` tab completion. | 26 July 2013, 11:32:38 UTC |
94f553d | APipe Tester | 26 July 2013, 11:31:42 UTC | Updated `genome` tab completion. | 26 July 2013, 11:31:42 UTC |
1f5769f | APipe Tester | 26 July 2013, 11:29:50 UTC | Updated class browser cache. | 26 July 2013, 11:29:50 UTC |
379d8f5 | APipe Tester | 26 July 2013, 03:25:38 UTC | updated jenkins submodule to e808181 | 26 July 2013, 03:25:38 UTC |
1cd6a54 | Scott Smith | 25 July 2013, 23:20:39 UTC | fix liftover, rename svold to bedpe, and ensure that chr is chopped back off of chromosome names | 25 July 2013, 23:21:08 UTC |
fec1eec | Obi Griffith | 25 July 2013, 22:55:33 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 July 2013, 22:55:33 UTC |
5c5cfdb | APipe Tester | 25 July 2013, 22:38:49 UTC | Updated `genome` tab completion. | 25 July 2013, 22:38:49 UTC |
f416b8c | APipe Tester | 25 July 2013, 22:37:07 UTC | Updated class browser cache. | 25 July 2013, 22:37:07 UTC |
be9480b | Scott Smith | 25 July 2013, 22:31:39 UTC | update tool to sync one model group's inputs from another | 25 July 2013, 22:31:54 UTC |
34504ac | APipe Tester | 25 July 2013, 21:17:44 UTC | Updated `genome` tab completion. | 25 July 2013, 21:17:44 UTC |
4afda7e | APipe Tester | 25 July 2013, 21:16:09 UTC | Updated class browser cache. | 25 July 2013, 21:16:09 UTC |
ce3d8f7 | Scott Smith | 25 July 2013, 20:53:13 UTC | tool to bulk update clinseq models from another group of models | 25 July 2013, 21:10:12 UTC |
3136ae6 | APipe Tester | 25 July 2013, 20:46:29 UTC | Updated `genome` tab completion. | 25 July 2013, 20:46:29 UTC |
9534fdb | APipe Tester | 25 July 2013, 20:44:35 UTC | Updated class browser cache. | 25 July 2013, 20:44:35 UTC |
dba9cf1 | Scott Smith | 25 July 2013, 20:36:08 UTC | add an importer to match the exporter for model metadata | 25 July 2013, 20:36:56 UTC |
3d97240 | Scott Smith | 25 July 2013, 19:39:27 UTC | add an importer to match the exporter for model metadata | 25 July 2013, 20:36:55 UTC |
6c9663c | Thomas Mooney | 25 July 2013, 14:51:08 UTC | update clinseq test data again | 25 July 2013, 14:51:08 UTC |
c4fa85a | Dave Larson | 25 July 2013, 03:42:08 UTC | slightly better caching of Fasta info. Probably better ways to do this. | 25 July 2013, 13:53:02 UTC |
92b800f | Dave Larson | 24 July 2013, 22:25:35 UTC | updated test to cover some of new functionality | 25 July 2013, 13:53:01 UTC |
45aec16 | Dave Larson | 24 July 2013, 22:25:10 UTC | bugfixes uncovered during building of test cases | 25 July 2013, 13:53:00 UTC |
3b34108 | Dave Larson | 24 July 2013, 15:47:05 UTC | add some functionality to Genome::File::Fasta to get chromosome lists etc. Needs work and tests. | 25 July 2013, 13:52:58 UTC |
f7d4c67 | APipe Tester | 24 July 2013, 21:43:49 UTC | Updated `gmt` tab completion. | 24 July 2013, 21:44:01 UTC |
d0a11c3 | APipe Tester | 24 July 2013, 21:42:57 UTC | Updated `genome` tab completion. | 24 July 2013, 21:44:00 UTC |
8a49d9a | APipe Tester | 24 July 2013, 21:41:04 UTC | Updated class browser cache. | 24 July 2013, 21:44:00 UTC |
e77bba4 | Anthony Brummett | 24 July 2013, 21:40:27 UTC | Try to detect filesystem problems with FileMux-type datasources These data sources now require that the directory containing the data files must exist and be readable. This should catch cases where there's a broken symlink, archived allocation or NFS problem. | 24 July 2013, 21:43:23 UTC |
5a8b670 | Yang Li | 24 July 2013, 21:32:10 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 24 July 2013, 21:32:10 UTC |
507a5f9 | Dave Larson | 24 July 2013, 20:11:33 UTC | fix sample name regex as in import-variants | 24 July 2013, 20:11:40 UTC |
bf5858f | Yang Li | 24 July 2013, 19:59:19 UTC | Fixed threshold value types from Int to Float. Added hint regarding window size | 24 July 2013, 19:59:19 UTC |
e2d17dc | Yang Li | 24 July 2013, 19:41:21 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 24 July 2013, 19:41:21 UTC |
3e015df | Eddie Belter | 24 July 2013, 18:58:41 UTC | InstData Gatk: add get base recal to base recal bam result | 24 July 2013, 19:01:56 UTC |
a670e80 | Eddie Belter | 24 July 2013, 18:57:27 UTC | InstData Gatk: idel realigner only uses indel vcfs | 24 July 2013, 19:01:55 UTC |
bb985fa | Eddie Belter | 24 July 2013, 18:56:58 UTC | InstData Gatk: still link snvs vcf if there is not an indel result for known sites | 24 July 2013, 19:01:55 UTC |
2cf464d | Eddie Belter | 23 July 2013, 16:55:23 UTC | InstData GATK: show display name for known sites | 24 July 2013, 19:01:54 UTC |
f51a44d | Anthony Brummett | 24 July 2013, 13:51:01 UTC | avoid a 'used once' warning | 24 July 2013, 13:52:23 UTC |
42df5fc | Anthony Brummett | 23 July 2013, 22:34:44 UTC | improve efficiency when accept_reference_IUB_codes is in use Validate the option once in the validator method Create a sub to transform the reference once before the annotator loop starts and call it in the loop. | 24 July 2013, 13:52:22 UTC |
c009672 | Anthony Brummett | 23 July 2013, 22:14:26 UTC | simplify delegating to the appropriate annotator method | 24 July 2013, 13:52:22 UTC |
a08cd1c | Anthony Brummett | 23 July 2013, 22:13:06 UTC | lc() and validate the annotation_filter param in the validate method | 24 July 2013, 13:52:21 UTC |
abe6ef8 | Anthony Brummett | 23 July 2013, 20:32:20 UTC | extract method for the main annotation loop | 24 July 2013, 13:52:21 UTC |
5f058b7 | Anthony Brummett | 23 July 2013, 20:11:46 UTC | extract method to create the annotator object | 24 July 2013, 13:52:20 UTC |
daf32a8 | Anthony Brummett | 23 July 2013, 20:06:33 UTC | remove useless benchmarking around annotation setup There's nothing to benchmark other than the time to open the variant input file. If we want to add instrumentation to that, then we'll add it in later | 24 July 2013, 13:52:20 UTC |
f7f58e8 | Anthony Brummett | 23 July 2013, 20:03:14 UTC | Move the data caching check into the validation method Also removed the now-useless benchmaking around the now-removed caching | 24 July 2013, 13:52:19 UTC |
bf3b3cc | Anthony Brummett | 23 July 2013, 19:58:40 UTC | build param checking moved into validation method | 24 July 2013, 13:52:19 UTC |
7406609 | Anthony Brummett | 23 July 2013, 19:55:43 UTC | extract method to close the report filehandle the temp_output_file name needs to be saved between the call to _setup_report_fh and _close_report_fh | 24 July 2013, 13:52:18 UTC |
8da90ef | Anthony Brummett | 23 July 2013, 19:45:58 UTC | remove unused variable | 24 July 2013, 13:52:18 UTC |
2abc6db | Anthony Brummett | 23 July 2013, 19:44:47 UTC | extract method to set up the report/output filehandle | 24 July 2013, 13:52:17 UTC |
5800b85 | Anthony Brummett | 23 July 2013, 19:19:22 UTC | extract method for creating the variant reader iterator | 24 July 2013, 13:52:17 UTC |
c7f3202 | Anthony Brummett | 23 July 2013, 19:15:53 UTC | extract method for the start log message | 24 July 2013, 13:52:16 UTC |
861bb8a | Anthony Brummett | 23 July 2013, 18:54:14 UTC | Call the method instead of remembering the value | 24 July 2013, 13:52:16 UTC |
1837b8a | Anthony Brummett | 23 July 2013, 18:47:37 UTC | Other comments/code in execute() indicate this param is deprecated | 24 July 2013, 13:52:15 UTC |
8f86f94 | Anthony Brummett | 23 July 2013, 21:37:11 UTC | Extract pre-execution parameter validation to its own method | 24 July 2013, 13:52:15 UTC |
1c3d1ea | Thomas Mooney | 24 July 2013, 13:39:56 UTC | Give life to the --target-regions option. | 24 July 2013, 13:39:56 UTC |
011f934 | Nathan Nutter | 24 July 2013, 03:05:14 UTC | updated expected (duplicated) workflow output | 24 July 2013, 03:05:14 UTC |
53b80c6 | Nathan Nutter | 23 July 2013, 22:22:00 UTC | we use gtmp not tmp since tmp is double counted | 24 July 2013, 02:37:50 UTC |
b1b8472 | Scott Smith | 24 July 2013, 02:26:20 UTC | sciClone bmm and vendor/r-cran-normt3 update | 24 July 2013, 02:26:49 UTC |
599310d | Gabriel Sanderson | 23 July 2013, 22:40:25 UTC | Merge branch 'master' into gb_master | 23 July 2013, 22:40:25 UTC |
7432e89 | Gabriel Sanderson | 23 July 2013, 22:25:36 UTC | SamtoolsToBed now tries to get DP from the sample column if it cannot find it in INFO if the input is a vcf. | 23 July 2013, 22:39:42 UTC |
ddfaa83 | Thomas Mooney | 23 July 2013, 22:34:52 UTC | Use alignment result accessor to get BAM file regardless of input model type. (whole_rmdup_bam_file was the old ref-align specific way to get at these) | 23 July 2013, 22:34:52 UTC |
961c8ff | APipe Tester | 23 July 2013, 20:06:51 UTC | updated ur submodule to 834d6c2 | 23 July 2013, 20:06:51 UTC |
d355de6 | Nathan Nutter | 23 July 2013, 19:58:35 UTC | remove unnecessary files | 23 July 2013, 19:58:46 UTC |
64f13e6 | Eddie Belter | 23 July 2013, 19:32:58 UTC | Sample Import Manager: update expected values for launch command in test | 23 July 2013, 19:32:58 UTC |