Package org.broadinstitute.hellbender.cmdline
package org.broadinstitute.hellbender.cmdline
-
ClassDescriptionAdapter shim/alternate GATK entry point for use by GATK tests to run tools in command line argument validation mode.Abstract class to facilitate writing command-line programs.A shim to make use of try-with-resources for tool shutdownWhen a tool is removed from GATK (after having been tagged with @DeprecatedFeature for a suitable period), an entry should be added to this list to issue a message when the user tries to run that tool.Created by davidben on 11/30/15.This class is a static helper for implementing 'mode arguments' by tools.Base class for all Picard tools.Adapter shim for use within GATK to run Picard tools.A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.Program group for use with internal test CommandLinePrograms only.