htsjdk.samtools.cram.structure

Class SubstitutionMatrix

java.lang.Object

htsjdk.samtools.cram.structure.SubstitutionMatrix

public class SubstitutionMatrix
extends java.lang.Object

Substitution matrix, used to represent base substitutions for reference-based CRAM compression. The matrix is stored internally in two forms; the packed/encoded form used for serialization, and an expanded in-memory form used for fast bi-directional interconversion between bases and substitution codes during read and write. This implementation allows both upper and lower case versions of a given reference base to be substituted with the same (upper case) substitute base (except for 'N', which is only handled for upper case) although it does not *generate* substitutions for lower case reference bases.

Field Summary

Fields

Modifier and Type	Field and Description
static int	BASES_SIZE

Constructor Summary

Constructors

Constructor and Description
SubstitutionMatrix(byte[] matrix) Create a SubstitutionMatrix from a serialized byte array
SubstitutionMatrix(java.util.List<CRAMCompressionRecord> records) Create a SubstitutionMatrix given a list of CramCompressionRecord

Method Summary

Modifier and Type	Method and Description
byte	base(byte refBase, byte code) Given a reference base and a substitution code, return the corresponding substitution base.
byte	code(byte refBase, byte readBase) Given a reference base and a read base, find the corresponding substitution code
byte[]	getEncodedMatrix() Return this substitution matrix as a byte array in a form suitable for serialization.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

BASES_SIZE

public static final int BASES_SIZE

Constructor Detail

SubstitutionMatrix

public SubstitutionMatrix(java.util.List<CRAMCompressionRecord> records)

Create a SubstitutionMatrix given a list of CramCompressionRecord

Parameters:

records - array of CramCompressionRecord with Substitutions

SubstitutionMatrix

public SubstitutionMatrix(byte[] matrix)

Create a SubstitutionMatrix from a serialized byte array

Parameters:

matrix - serialized substitution matrix from a CRAM stream

Method Detail

code

public byte code(byte refBase,
                 byte readBase)

Given a reference base and a read base, find the corresponding substitution code

Parameters:

refBase - reference base being substituted

readBase - read base to substitute for the reference base

Returns:

code to be used for this refBase/readBase pair

base

public byte base(byte refBase,
                 byte code)

Given a reference base and a substitution code, return the corresponding substitution base.

Parameters:

refBase - reference base being substituted

code - substitution code

Returns:

base to be substituted for this (refBase, code) pair

getEncodedMatrix

public byte[] getEncodedMatrix()

Return this substitution matrix as a byte array in a form suitable for serialization.

Returns:

the encoded matrix in serialized form

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object