Uses of Class
com.milaboratory.core.io.sequence.fastq.QualityFormat

Packages that use QualityFormat

Package	Description
com.milaboratory.core.io.sequence
com.milaboratory.core.io.sequence.fastq
com.milaboratory.core.sequence

Uses of QualityFormat in com.milaboratory.core.io.sequence

Methods in com.milaboratory.core.io.sequence with parameters of type QualityFormat

Modifier and Type	Method and Description
static SingleReadLazy	SingleReadLazy.create(QualityFormat format, long id, byte[] buffer, int descriptionFrom, short dataOffset, short qualityOffset, short dataLength, short descriptionLength, boolean replaceWildcards)

Uses of QualityFormat in com.milaboratory.core.io.sequence.fastq

Fields in com.milaboratory.core.io.sequence.fastq declared as QualityFormat

Modifier and Type	Field and Description
static QualityFormat	SingleFastqReader.DEFAULT_QUALITY_FORMAT If FastqReader fails to guess file format, this value will be used by default.

Methods in com.milaboratory.core.io.sequence.fastq that return QualityFormat

Modifier and Type	Method and Description
static QualityFormat	QualityFormat.fromName(String name)
QualityFormat	SingleFastqReader.getQualityFormat()
static QualityFormat	QualityFormat.valueOf(String name) Returns the enum constant of this type with the specified name.
static QualityFormat[]	QualityFormat.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in com.milaboratory.core.io.sequence.fastq with parameters of type QualityFormat

Modifier and Type	Method and Description
SingleRead	FastqRecordsReader.createRead(long id, QualityFormat format)

Constructors in com.milaboratory.core.io.sequence.fastq with parameters of type QualityFormat

Constructor and Description
PairedFastqReader(File file1, File file2, QualityFormat format, CompressionType ct)
PairedFastqReader(File file1, File file2, QualityFormat format, CompressionType ct, boolean replaceWildcards, boolean lazyReads)
PairedFastqReader(InputStream stream1, InputStream stream2, QualityFormat format, CompressionType ct, boolean guessQualityFormat, int bufferSize, boolean replaceWildcards, boolean lazyReads)
PairedFastqReader(String fileName1, String fileName2, QualityFormat format, CompressionType ct)
PairedFastqReader(String fileName1, String fileName2, QualityFormat format, CompressionType ct, boolean replaceWildcards, boolean lazyReads)
PairedFastqWriter(String file1, String file2, QualityFormat qualityFormat, CompressionType ct)
SingleFastqReader(File file, QualityFormat format, CompressionType ct) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(InputStream stream, QualityFormat format, CompressionType ct) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(InputStream stream, QualityFormat format, CompressionType ct, boolean guessQualityFormat, int bufferSize, boolean replaceWildcards, boolean lazyReads) Creates a SingleFastqReader stream from a FASTQ files with single-end read data
SingleFastqReader(String file, QualityFormat format, CompressionType ct) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqWriter(File file, QualityFormat qualityFormat, CompressionType ct)
SingleFastqWriter(OutputStream outputStream, QualityFormat qualityFormat, CompressionType ct)
SingleFastqWriter(OutputStream outputStream, QualityFormat qualityFormat, CompressionType ct, int bufferSize)
SingleFastqWriter(String fileName, QualityFormat qualityFormat, CompressionType ct)

Uses of QualityFormat in com.milaboratory.core.sequence

Methods in com.milaboratory.core.sequence with parameters of type QualityFormat

Modifier and Type	Method and Description
static SequenceQuality	SequenceQuality.create(QualityFormat format, byte[] data, boolean check) Factory method for the SequenceQualityPhred object.
static SequenceQuality	SequenceQuality.create(QualityFormat format, byte[] data, int from, int length, boolean check) Factory method for the SequenceQualityPhred object.
byte[]	SequenceQuality.encode(QualityFormat format) Encodes current quality line with given format.
void	SequenceQuality.encodeTo(QualityFormat format, byte[] buffer, int offset) Encodes current quality line with given offset.

Constructors in com.milaboratory.core.sequence with parameters of type QualityFormat

Constructor and Description
SequenceQuality(String string, QualityFormat format) Creates a phred sequence quality from a string formatted with corresponding offset.