public class SolexaQualityConverter extends Object
Modifier and Type | Field | Description |
---|---|---|
static int |
ILLUMINA_TO_PHRED_SUBTRAHEND |
This value is removed from an Illumina 1.8 quality score to make it a Phred score
|
static int |
PHRED_ADDEND |
This value is added to a Phred scord to make it printable ASCII
|
static int |
SOLEXA_ADDEND |
This value is added to a Solexa quality score to make it printable ASCII
|
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.
|
public static final int SOLEXA_ADDEND
public static final int PHRED_ADDEND
public static final int ILLUMINA_TO_PHRED_SUBTRAHEND
public static SolexaQualityConverter getSingleton()
public byte solexaCharToPhredBinary(byte solexaQuality)
public byte[] getSolexaToPhredConversionTable()
public void convertSolexaQualityCharsToPhredBinary(byte[] solexaQuals)
public void convertSolexaQualityCharsToPhredChars(byte[] solexaQuals)
public void convertSolexa_1_3_QualityCharsToPhredBinary(byte[] solexaQuals)
solexaQuals
- qualities are converted in place.public void convertSolexa_1_3_QualityCharsToPhredBinary(int offset, int length, byte[] solexaQuals)