org.broadinstitute.hellbender.utils.downsampling

Class DownsamplingMethod

java.lang.Object

org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod

All Implemented Interfaces:

java.io.Serializable

public final class DownsamplingMethod
extends java.lang.Object
implements java.io.Serializable

Describes the method for downsampling reads at a given locus.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static DownsampleType	DEFAULT_DOWNSAMPLING_TYPE Default type to use if no type is specified
static DownsamplingMethod	NONE Expresses no downsampling applied at all.
java.lang.Integer	toCoverage Actual downsampling target is specified as an integer number of reads.
java.lang.Double	toFraction Actual downsampling target is specified as a fraction of total available reads.
DownsampleType	type Type of downsampling to perform.

Constructor Summary

Constructors

Constructor and Description
DownsamplingMethod(DownsampleType type, java.lang.Integer toCoverage, java.lang.Double toFraction) If type is null, then DEFAULT_DOWNSAMPLING_TYPE will be used.

Method Summary

Modifier and Type	Method and Description
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

type

public final DownsampleType type

Type of downsampling to perform.

toCoverage

public final java.lang.Integer toCoverage

Actual downsampling target is specified as an integer number of reads. This field is null if no downsampling is to be done, or we are downsampling to a fraction.

toFraction

public final java.lang.Double toFraction

Actual downsampling target is specified as a fraction of total available reads. This field is null if no downsampling is to be done, or we are downsampling to coverage.

NONE

public static final DownsamplingMethod NONE

Expresses no downsampling applied at all.

DEFAULT_DOWNSAMPLING_TYPE

public static final DownsampleType DEFAULT_DOWNSAMPLING_TYPE

Default type to use if no type is specified

Constructor Detail

DownsamplingMethod

public DownsamplingMethod(DownsampleType type,
                          java.lang.Integer toCoverage,
                          java.lang.Double toFraction)

If type is null, then DEFAULT_DOWNSAMPLING_TYPE will be used. If type is not NONE, then either toFraction or toCoverage must be not null. At most one of toFraction or toCoverage can be specified. If specified, toCoverage must be > 0. If specified, toFraction must be >= 0.0 and <= 1.0

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object