Package org.broadinstitute.hellbender.cmdline.argumentcollections
package org.broadinstitute.hellbender.cmdline.argumentcollections
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ClassDescriptionIntended to be used as an @ArgumentCollection for specifying intervals at the command line.An argument collection for use with tools that mark optical duplicates.Class that defines the variant arguments used for a MultiVariantWalker.An argument collection for use with tools that mark optical duplicates.An argument collection for use with tools that accept zero or more input files containing Feature records (eg., BED files, hapmap files, etc.).An interval argument class that allows -L to be specified but does not require it.An argument collection for use with tools that accept zero or more input files containing reads (eg., BAM/SAM/CRAM files).An argument collection for use with tools that optionally accept a reference file as input.An ArgumentCollection with an optional output argument, and utility methods for printing String output to it To use this class add an @ArgumentCollection variable to your tool like so:An argument collection for use with tools that accept zero or more input files containing VariantContext records (eg., VCF files).An abstract argument collection for use with tools that accept input files containing reads (eg., BAM/SAM/CRAM files).An abstract ArgumentCollection for specifying a reference sequence fileAn argument collection for use with tools that accept one or more input files containing Feature records (eg., BED files, hapmap files, etc.), and require at least one such input.An ArgumentCollection that requires one or more intervals be specified with -L at the command lineAn argument collection for use with tools that accept one or more input files containing reads (eg., BAM/SAM/CRAM files), and require at least one such input.An argument collection for use with tools that require a reference file as input.An argument collection for use with tools that accept one or more input files containing VariantContext records (eg., VCF files), and require at least one such input.interface for argument collections that control how sequence dictionary validation should be handleddoesn't provide a configuration argument, and always returns false, useful for tools that do not want to perform sequence dictionary validation, like alignersmost tools will want to use this, it defaults to performing sequence dictionary validation but provides the option to disable it