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gatk-3.8/scala/qscript/examples
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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
..
ExampleCountReads.scala Updated Queue GATK generation to reflect -B and -I changes. 2010-08-25 22:17:36 +00:00
ExampleUnifiedGenotyper.scala Updated Queue GATK generation to reflect -B and -I changes. 2010-08-25 22:17:36 +00:00