org.broadinstitute.hellbender.utils.clipping

Enum ClippingRepresentation

java.lang.Object

java.lang.Enum<ClippingRepresentation>

org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<ClippingRepresentation>

public enum ClippingRepresentation
extends java.lang.Enum<ClippingRepresentation>

How should we represent a clipped bases in a read?

Enum Constant Summary

Enum Constants

Enum Constant and 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 and Description
static ClippingRepresentation	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static ClippingRepresentation[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

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 Detail

values

public static ClippingRepresentation[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (ClippingRepresentation c : ClippingRepresentation.values())
    System.out.println(c);

Returns:

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

valueOf

public static ClippingRepresentation valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (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:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null