org.broadinstitute.hellbender.cmdline.argumentcollections

Class ReadInputArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

OptionalReadInputArgumentCollection, RequiredReadInputArgumentCollection

public abstract class ReadInputArgumentCollection
extends java.lang.Object
implements java.io.Serializable

An abstract argument collection for use with tools that accept input files containing reads (eg., BAM/SAM/CRAM files).

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.List<java.lang.String>	readIndices
protected htsjdk.samtools.ValidationStringency	readValidationStringency

Constructor Summary

Constructors

Constructor and Description
ReadInputArgumentCollection()

Method Summary

Modifier and Type	Method and Description
abstract java.util.List<java.io.File>	getReadFiles() Get the list of BAM/SAM/CRAM files specified at the command line
abstract 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>	getReadIndexPaths()
abstract java.util.List<java.nio.file.Path>	getReadPaths() Get the list of BAM/SAM/CRAM files specified at the command line.
htsjdk.samtools.ValidationStringency	getReadValidationStringency() Get the read validation stringency specified at the command line, or the default value if none was specified at the command line.

Methods inherited from class java.lang.Object

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

Field Detail

readValidationStringency

@Argument(fullName="read-validation-stringency",
          shortName="VS",
          doc="Validation stringency for all SAM/BAM/CRAM/SRA files read by this program.  The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.",
          common=true,
          optional=true)
protected htsjdk.samtools.ValidationStringency readValidationStringency

readIndices

@Argument(fullName="read-index",
          shortName="read-index",
          doc="Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.",
          common=true,
          optional=true)
protected java.util.List<java.lang.String> readIndices

Constructor Detail

ReadInputArgumentCollection

public ReadInputArgumentCollection()

Method Detail

getReadPaths

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

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.

getReadIndexPaths

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

Returns:

The list of indices to be used with the read inputs, or null if none were specified and the indices should be inferred automatically. If explicit indices are specified, they must be specified for all read inputs, and are assumed to be in the same order as the read inputs.

getReadFiles

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

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

getReadFilesNames

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

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

getReadValidationStringency

public htsjdk.samtools.ValidationStringency getReadValidationStringency()

Get the read validation stringency specified at the command line, or the default value if none was specified at the command line.