Package org.broadinstitute.hellbender.utils.clipping

Enum Class ClippingRepresentation

java.lang.Object

java.lang.Enum<ClippingRepresentation>

org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation

All Implemented Interfaces:

Serializable, Comparable<ClippingRepresentation>, Constable

public enum ClippingRepresentation
extends Enum<ClippingRepresentation>

How should we represent a clipped bases in a read?

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
HARDCLIP_BASES	WARNING: THIS OPTION IS STILL UNDER DEVELOPMENT AND IS NOT SUPPORTED.
REVERT_SOFTCLIPPED_BASES	Turn all soft-clipped bases into matches
SOFTCLIP_BASES	Change the read's cigar string to soft clip (S, see sam-spec) away the bases.
WRITE_NS	Clipped bases are changed to Ns
WRITE_NS_Q0S	Clipped bases are change to have both an N base and a Q0 quality score
WRITE_Q0S	Clipped bases are changed to have Q0 quality score

Method Summary

Modifier and Type	Method	Description
static ClippingRepresentation	valueOf(String name)	Returns the enum constant of this class with the specified name.
static ClippingRepresentation[]	values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

WRITE_NS

public static final ClippingRepresentation WRITE_NS

Clipped bases are changed to Ns

WRITE_Q0S

public static final ClippingRepresentation WRITE_Q0S

Clipped bases are changed to have Q0 quality score

WRITE_NS_Q0S

public static final ClippingRepresentation WRITE_NS_Q0S

Clipped bases are change to have both an N base and a Q0 quality score

SOFTCLIP_BASES

public static final ClippingRepresentation SOFTCLIP_BASES

Change the read's cigar string to soft clip (S, see sam-spec) away the bases. Note that this can only be applied to cases where the clipped bases occur at the start or end of a read.

HARDCLIP_BASES

public static final ClippingRepresentation HARDCLIP_BASES

WARNING: THIS OPTION IS STILL UNDER DEVELOPMENT AND IS NOT SUPPORTED. Change the read's cigar string to hard clip (H, see sam-spec) away the bases. Hard clipping, unlike soft clipping, actually removes bases from the read, reducing the resulting file's size but introducing an irrevesible (i.e., lossy) operation. Note that this can only be applied to cases where the clipped bases occur at the start or end of a read.

REVERT_SOFTCLIPPED_BASES

public static final ClippingRepresentation REVERT_SOFTCLIPPED_BASES

Turn all soft-clipped bases into matches

Method Details

values

public static ClippingRepresentation[] values()

Returns an array containing the constants of this enum class, in the order they are declared.

Returns:

an array containing the constants of this enum class, in the order they are declared

valueOf

public static ClippingRepresentation valueOf(String name)

Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum class has no constant with the specified name

NullPointerException - if the argument is null