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
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TraverseTest.sh	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
TraverseTestProf.sh	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
buildRODs.sh	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
calcCallerMD5s.csh	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!	2009-09-04 12:39:06 +00:00
getFirehosePipelineYaml.sh	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00
makeResources.sh	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
mergeText.sh	Fixed header generation when lines contain spaces.	2010-09-17 17:14:59 +00:00
queueStatus.csh	Added gsa-firehose2	2010-09-15 02:24:04 +00:00
readStatsDiff.sh	Adding a script for diff'ing the output of samtools and the GATK for the whole genome and each individual chromosome.	2009-06-02 21:19:39 +00:00
runbeagle.sh	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.	2010-07-06 18:33:28 +00:00
splitIntervals.sh	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00