Package htsjdk.samtools.util

Class SolexaQualityConverter

java.lang.Object

htsjdk.samtools.util.SolexaQualityConverter

public class SolexaQualityConverter
extends Object

Optimized method for converting Solexa ASCII qualities into Phred scores. Pre-computes all values in order to eliminate repeated computation.

Field Summary

Fields

Modifier and Type	Field	Description
static final int	ILLUMINA_TO_PHRED_SUBTRAHEND	This value is removed from an Illumina 1.8 quality score to make it a Phred score
static final int	PHRED_ADDEND	This value is added to a Phred scord to make it printable ASCII
static final int	SOLEXA_ADDEND	This value is added to a Solexa quality score to make it printable ASCII

Method Summary

Modifier and Type	Method	Description
void	convertSolexa_1_3_QualityCharsToPhredBinary(byte[] solexaQuals)	Casava 1.3 stores phred-scaled qualities, but non-standard because they have 64 added to them rather than the standard 33.
void	convertSolexa_1_3_QualityCharsToPhredBinary(int offset, int length, byte[] solexaQuals)
void	convertSolexaQualityCharsToPhredBinary(byte[] solexaQuals)	Decodes an array of solexa quality ASCII chars into Phred numeric space.
void	convertSolexaQualityCharsToPhredChars(byte[] solexaQuals)	Decodes an array of solexa quality ASCII chars into Phred ASCII space.
static SolexaQualityConverter	getSingleton()
byte[]	getSolexaToPhredConversionTable()
byte	solexaCharToPhredBinary(byte solexaQuality)	Convert a solexa quality ASCII character into a phred score.

Methods inherited from class java.lang.Object

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

Field Details

SOLEXA_ADDEND

public static final int SOLEXA_ADDEND

This value is added to a Solexa quality score to make it printable ASCII

See Also:

• Constant Field Values

PHRED_ADDEND

public static final int PHRED_ADDEND

This value is added to a Phred scord to make it printable ASCII

See Also:

• Constant Field Values

ILLUMINA_TO_PHRED_SUBTRAHEND

public static final int ILLUMINA_TO_PHRED_SUBTRAHEND

This value is removed from an Illumina 1.8 quality score to make it a Phred score

See Also:

• Constant Field Values

Method Details

getSingleton

public static SolexaQualityConverter getSingleton()

solexaCharToPhredBinary

public byte solexaCharToPhredBinary(byte solexaQuality)

Convert a solexa quality ASCII character into a phred score.

getSolexaToPhredConversionTable

public byte[] getSolexaToPhredConversionTable()

Returns:

a byte array that can be indexed by Solexa ASCII quality, with value of corresponding Phred score. Elements 0-63 are invalid because Solexa qualities should all be >= 64. Do not modify this array!

convertSolexaQualityCharsToPhredBinary

public void convertSolexaQualityCharsToPhredBinary(byte[] solexaQuals)

Decodes an array of solexa quality ASCII chars into Phred numeric space. Decode in place in order to avoid extra object allocation.

convertSolexaQualityCharsToPhredChars

public void convertSolexaQualityCharsToPhredChars(byte[] solexaQuals)

Decodes an array of solexa quality ASCII chars into Phred ASCII space. Decode in place in order to avoid extra object allocation.

convertSolexa_1_3_QualityCharsToPhredBinary

public void convertSolexa_1_3_QualityCharsToPhredBinary(byte[] solexaQuals)

Casava 1.3 stores phred-scaled qualities, but non-standard because they have 64 added to them rather than the standard 33.

Parameters:

solexaQuals - qualities are converted in place.

convertSolexa_1_3_QualityCharsToPhredBinary

public void convertSolexa_1_3_QualityCharsToPhredBinary(int offset,
 int length,
 byte[] solexaQuals)