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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org/broadinstitute/sting/queue	Updated Queue GATK generation to reflect -B and -I changes.	2010-08-25 22:17:36 +00:00
BaseTransitionTableCalculator.scala	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
HelloWorld.scala	support for scala walkers	2009-08-28 00:15:01 +00:00
ScalaCountLoci.scala	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00