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gatk-3.8/public/java/src/org/broadinstitute/sting/commandline
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Mauricio Carneiro e2d41f0282 Turning @Output required to false 
By default all output is assigned to stdout if a -o is not provided. Technically this makes @Output a not required parameter, and the documentation is misleading because it's reading from the annotation.
GSA-820 #resolve
 		2013-03-05 17:26:16 -05:00
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Advanced.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Argument.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentCollection.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentDefinition.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentDefinitionGroup.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentDefinitions.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentException.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentIOType.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatch.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchFileValue.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchSite.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchSource.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchSourceType.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchStringValue.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchValue.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatches.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentSource.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentTypeDescriptor.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ClassType.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
CommandLineProgram.java Added an option to print out the version string 2013-02-15 12:42:59 -05:00
CommandLineUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
EnumerationArgumentDefault.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Gather.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Gatherer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Hidden.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Input.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
IntervalArgumentCollection.java Last manual license update (hopefully) 2013-01-18 16:13:07 -05:00
IntervalBinding.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MissingArgumentValueException.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Output.java Turning @Output required to false 2013-03-05 17:26:16 -05:00
ParsedArgs.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ParsedListArgs.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ParsingEngine.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
ParsingEngineArgumentFiles.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ParsingEngineArgumentProvider.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ParsingMethod.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
RodBinding.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Tags.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00