org.broadinstitute.hellbender.cmdline.argumentcollections

Class RequiredReadInputArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection

org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReadInputArgumentCollection

All Implemented Interfaces:

java.io.Serializable

public final class RequiredReadInputArgumentCollection
extends ReadInputArgumentCollection

An 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.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<java.lang.String>	readFilesNames

Fields inherited from class org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection

readIndices, readValidationStringency

Constructor Summary

Constructors

Constructor and Description
RequiredReadInputArgumentCollection()

Method Summary

Modifier and Type	Method and Description
java.util.List<java.io.File>	getReadFiles() Get the list of BAM/SAM/CRAM files specified at the command line
java.util.List<java.lang.String>	getReadFilesNames() Get the list of BAM/SAM/CRAM filenames specified at the command line
java.util.List<java.nio.file.Path>	getReadPaths() Get the list of BAM/SAM/CRAM files specified at the command line.

Methods inherited from class org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection

getReadIndexPaths, getReadValidationStringency

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

readFilesNames

@Argument(fullName="input",
          shortName="I",
          doc="BAM/SAM/CRAM file containing reads",
          optional=false,
          common=true)
public java.util.List<java.lang.String> readFilesNames

Constructor Detail

RequiredReadInputArgumentCollection

public RequiredReadInputArgumentCollection()

Method Detail

getReadFiles

public java.util.List<java.io.File> getReadFiles()

Description copied from class: ReadInputArgumentCollection

Get the list of BAM/SAM/CRAM files specified at the command line

Specified by:

getReadFiles in class ReadInputArgumentCollection

getReadPaths

public java.util.List<java.nio.file.Path> getReadPaths()

Description copied from class: ReadInputArgumentCollection

Get the list of BAM/SAM/CRAM files specified at the command line. Paths are the preferred format, as this can handle both local disk and NIO direct access to cloud storage.

Specified by:

getReadPaths in class ReadInputArgumentCollection

getReadFilesNames

public java.util.List<java.lang.String> getReadFilesNames()

Description copied from class: ReadInputArgumentCollection

Get the list of BAM/SAM/CRAM filenames specified at the command line

Specified by:

getReadFilesNames in class ReadInputArgumentCollection