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13 Commits (d496f2afdef81a5e6e86cb3b6548193cdc026e82)

Author SHA1 Message Date
kshakir 7f25019f37 Inprocess functions by default now log what output files they are running for. 
On -run cleaning up .done and .fail files for jobs that will be run.
Added detection to Firehose YAML generator shell script for (g)awk versions that ignore "\n" in patterns.
Removed obsolete mergeText and splitIntervals shell scripts.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4452 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-07 19:08:02 +00:00
depristo d841f260eb minor improvements to queue status 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4439 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 14:34:35 +00:00
kshakir 20b38b38f3 Updated from SnakeYAML 1.6 to 1.7. 
Added a pipeline java bean and YAML utility to serialize java beans.
Added a getFirehosePipelineYaml.sh that can pull firehose data into the pipeline yaml file format.
Updated the fullCallingPipeline.q to begin using the pipeline yaml file format for bams and reference.
More changes to come as this code gets tested out in the fullCallingPipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4329 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 19:47:49 +00:00
kshakir 1c94a73434 Fixed header generation when lines contain spaces. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4304 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 17:14:59 +00:00
kshakir 6dcbf04378 Added gsa-firehose2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4284 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 02:24:04 +00:00
depristo 8c16babe91 continuing improvements to the queueStatus helper script 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4261 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:04:59 +00:00
depristo 80e31df40d Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3965 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-07 12:36:28 +00:00
delangel be75b087ec a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype. 
b) Add "OG" annotation to genotypes. If Beagle changes genotypes, this annotation gets the original genotype call, to ease performance  comparisons. If not, this annotation gets an empty value.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3723 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-06 18:33:28 +00:00
kshakir 30cf78fdc0 Refactoring for a first version of scatter gather api with basic shell script implementations. 
Modified build script so that queue is cleaned during "ant clean".



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3611 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 18:39:20 +00:00
depristo a08c68362e Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1530 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 12:39:06 +00:00
depristo 5289230eb8 Version 0.2.1 (released) of the TableRecalibrator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 22:50:55 +00:00
aaron 056fcdc31c Adding a script for diff'ing the output of samtools and the GATK for the whole genome and each individual chromosome. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@882 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-02 21:19:39 +00:00
hanna 2ee2623926 Move non-java code out of playground. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@154 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 19:31:38 +00:00