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Build # 225

Build Type

push

travis-ci

Committed by lbergelson

Commit Message

improve the handling GATKTool optionally required arguments
GATKTool now instantiates appropriate argument collections based on the value of requiresReads, requieresReference, and requiresIntervals
these use the standard argument parsing system and show up in help instead of being a special case
Features/variants are still handled specially because they are handled differently
added Optional/Required versions of these and Feature/Variant argument collections

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