Classes and Subpackages of org.broadinstitute.gatk.utils.commandline

org.broadinstitute.gatk.utils.commandline.ArgumentDefinition
org.broadinstitute.gatk.utils.commandline.ArgumentDefinitionGroup
org.broadinstitute.gatk.utils.commandline.ArgumentDefinitions
org.broadinstitute.gatk.utils.commandline.ArgumentException
org.broadinstitute.gatk.utils.commandline.ArgumentMatch
org.broadinstitute.gatk.utils.commandline.ArgumentMatchFileSource
org.broadinstitute.gatk.utils.commandline.ArgumentMatchFileValue
org.broadinstitute.gatk.utils.commandline.ArgumentMatchSite
org.broadinstitute.gatk.utils.commandline.ArgumentMatchSiteUnitTest
org.broadinstitute.gatk.utils.commandline.ArgumentMatchSource
org.broadinstitute.gatk.utils.commandline.ArgumentMatchSourceUnitTest
org.broadinstitute.gatk.utils.commandline.ArgumentMatchStringValue
org.broadinstitute.gatk.utils.commandline.ArgumentMatchValue
org.broadinstitute.gatk.utils.commandline.ArgumentMatches
org.broadinstitute.gatk.utils.commandline.ArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram$ATDTestOutputArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram$OutputNotRequiredNoDefaultSamArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram$OutputNotRequiredNoDefaultStreamArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram$OutputNotRequiredNoDefaultVcfArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram$OutputNotRequiredSamArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram$OutputNotRequiredStreamArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram$OutputNotRequiredVcfArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram$OutputRequiredSamArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram$OutputRequiredStreamArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptorUnitTest$ATDTestCommandLineProgram$OutputRequiredVcfArgumentSource
org.broadinstitute.gatk.utils.commandline.ArgumentValueOutOfRangeException
org.broadinstitute.gatk.utils.commandline.ArgumentsAreMutuallyExclusiveException
org.broadinstitute.gatk.utils.commandline.CommandLineProgram
org.broadinstitute.gatk.utils.commandline.CommandLineUtils
org.broadinstitute.gatk.utils.commandline.CompoundArgumentTypeDescriptor
org.broadinstitute.gatk.utils.commandline.DefinitionMatcher
org.broadinstitute.gatk.utils.commandline.Gatherer
org.broadinstitute.gatk.utils.commandline.IntervalArgumentCollection
org.broadinstitute.gatk.utils.commandline.IntervalBinding
org.broadinstitute.gatk.utils.commandline.IntervalBindingArgumentTypeDescriptor
org.broadinstitute.gatk.utils.commandline.InvalidArgumentException
org.broadinstitute.gatk.utils.commandline.InvalidArgumentIntegrationTest
org.broadinstitute.gatk.utils.commandline.InvalidArgumentValueException
org.broadinstitute.gatk.utils.commandline.LoggingIntegrationTest
org.broadinstitute.gatk.utils.commandline.LoggingIntegrationTest$LoggingTestProvider
org.broadinstitute.gatk.utils.commandline.MissingArgumentException
org.broadinstitute.gatk.utils.commandline.MissingArgumentValueException
org.broadinstitute.gatk.utils.commandline.MultiplexArgumentTypeDescriptor
org.broadinstitute.gatk.utils.commandline.ParsedArgs
org.broadinstitute.gatk.utils.commandline.ParsedListArgs
org.broadinstitute.gatk.utils.commandline.ParsingEngine
org.broadinstitute.gatk.utils.commandline.ParsingEngineArgumentFiles
org.broadinstitute.gatk.utils.commandline.ParsingEngineArgumentProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$AllLociArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$AnalysisTypeArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$ArgumentCollectionProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$BaseArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$BooleanArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$CamelCaseArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$DefaultValueArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$DerivedArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$DuplicateLongNameProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$DuplicateShortNameProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$EnumArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$InputFileArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$IntegerListArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$ListRodBindingArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$MultiCharShortNameArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$MultiValueArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$MultipleArgumentCollectionProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$MutuallyExclusiveArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$NoArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$NumericRangeArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$OptionalRodBindingArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$PackageProtectedArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$PrimitiveArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$RequiredArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$ShortNameOnlyRodBindingArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$SingleRodBindingArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$UnrequiredArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$UntypedListArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$ValidatingArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$VariantContextRodBindingArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingEngineUnitTest$VariedTypeArgProvider
org.broadinstitute.gatk.utils.commandline.ParsingMethod
org.broadinstitute.gatk.utils.commandline.RodBinding
org.broadinstitute.gatk.utils.commandline.RodBindingArgumentTypeDescriptor
org.broadinstitute.gatk.utils.commandline.RodBindingCollection
org.broadinstitute.gatk.utils.commandline.RodBindingCollectionArgumentTypeDescriptor
org.broadinstitute.gatk.utils.commandline.RodBindingCollectionUnitTest
org.broadinstitute.gatk.utils.commandline.RodBindingCollectionUnitTest$RodBindingCollectionArgProvider
org.broadinstitute.gatk.utils.commandline.RodBindingUnitTest
org.broadinstitute.gatk.utils.commandline.SimpleArgumentTypeDescriptor
org.broadinstitute.gatk.utils.commandline.Tags
org.broadinstitute.gatk.utils.commandline.TooManyValuesForArgumentException
org.broadinstitute.gatk.utils.commandline.UnknownEnumeratedValueException
org.broadinstitute.gatk.utils.commandline.UnmatchedArgumentException

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All Classes in org.broadinstitute.gatk.utils.commandline