org.broadinstitute.hellbender.utils.bwa

Enum BwaMemIndex.Algorithm

java.lang.Object

java.lang.Enum<BwaMemIndex.Algorithm>

org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.Algorithm

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<BwaMemIndex.Algorithm>

Enclosing class:

BwaMemIndex

public static enum BwaMemIndex.Algorithm
extends java.lang.Enum<BwaMemIndex.Algorithm>

Indexing algorithms supported by Bwa.

Enum Constant Summary

Enum Constants

Enum Constant and Description
AUTO Chooses the most appropriate algorithm based on characteristic of the reference.
IS Linear-time algorithm for constructing suffix array.
RB2 The Ropebwt2 algorithm.

Method Summary

Modifier and Type	Method and Description
java.lang.String	toBwaName() The string name use by the Bwa command line to denote that algorithm.
static BwaMemIndex.Algorithm	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static BwaMemIndex.Algorithm[]	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

AUTO

public static final BwaMemIndex.Algorithm AUTO

Chooses the most appropriate algorithm based on characteristic of the reference. For references shorter than 2Gbases it will use IS whereas for larger reference it will employ RB2.

IS

public static final BwaMemIndex.Algorithm IS

Linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB. IS is the default algorithm due to its simplicity. The current codes for IS algorithm are reimplemented by Yuta Mori.

See Also:

"http://bio-bwa.sourceforge.net/bwa.shtml"

RB2

public static final BwaMemIndex.Algorithm RB2

The Ropebwt2 algorithm.

See Also:

"https://arxiv.org/pdf/1406.0426.pdf"

Method Detail

values

public static BwaMemIndex.Algorithm[] 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 (BwaMemIndex.Algorithm c : BwaMemIndex.Algorithm.values())
    System.out.println(c);

Returns:

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

valueOf

public static BwaMemIndex.Algorithm 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

toBwaName

public java.lang.String toBwaName()

The string name use by the Bwa command line to denote that algorithm.

Returns:

never null and unique across algorithms.