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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qscript	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
src/org/broadinstitute/sting	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
test/org/broadinstitute/sting/queue	While generating YAML now warning and skipping TSV rows that don't have all values.	2011-02-25 20:50:03 +00:00