kshakir 0105e8d063 Updated Queue GATK generation to reflect -B and -I changes. ... To add support for "-I:tumor tumor.bam", the GATK argument import_file (-I) is now generated as a List of NamedFile objects. Could not get sugar working 100%. To activate sugar import the gatk package. This effectively adds a new method to java.io.File called toNamedFile. When adding a file to the list call countReads.import_file :+= myJavaFile.toNamedFile See scala/qscript/examples for actual examples. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4122 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-25 22:17:36 +00:00
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qscript	Updated Queue GATK generation to reflect -B and -I changes.	2010-08-25 22:17:36 +00:00
src	Updated Queue GATK generation to reflect -B and -I changes.	2010-08-25 22:17:36 +00:00
test/org/broadinstitute/sting/queue/util	Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).	2010-08-11 21:58:26 +00:00