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https://github.com/genome/genome
23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
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
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