kshakir f6d4b0aaf5 Using an embedded version of Picard for merging un-indexed bam files after scatter/gather instead of requiring the QScripts to specify the picard JAR. May do this for the GATK jar too. ... Fixed initialization of pending counts when using -startFromScratch so the count doesn't start at zero and end at -<#njobs>. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5483 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-21 18:20:01 +00:00
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BatchMerge.q	-ct x no longer includes coverage in the previous bin	2011-02-24 15:52:04 +00:00
FullCallingPipeline.q	Using an embedded version of Picard for merging un-indexed bam files after scatter/gather instead of requiring the QScripts to specify the picard JAR. May do this for the GATK jar too.	2011-03-21 18:20:01 +00:00
MultiFullCallingPipeline.scala	MFCP waits for other pipelines to finish by using the previous log file of one pipeline as virtual input to the next pipeline.	2011-02-25 17:51:01 +00:00
recalibrate.scala	Refactoring the qscript directory; oneoffs, playground, and core	2011-01-19 15:23:40 +00:00