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
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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	Inprocess functions by default now log what output files they are running for.	2010-10-07 19:08:02 +00:00
makeResources.sh	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
queueStatus.csh	minor improvements to queue status	2010-10-06 14:34:35 +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