Uses of Class
com.milaboratory.core.io.sequence.PairedRead

Packages that use PairedRead

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

Uses of PairedRead in com.milaboratory.core

Methods in com.milaboratory.core with parameters of type PairedRead

Modifier and Type	Method and Description
Target[]	PairedEndReadsLayout.createTargets(PairedRead read)

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

Methods in com.milaboratory.core.io.sequence that return PairedRead

Modifier and Type	Method and Description
PairedRead	PairedReader.take()

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

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

Modifier and Type	Method and Description
PairedRead	RandomAccessPairedFastqReader.take()
PairedRead	RandomAccessPairedFastqReader.take(long recordNumber)

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

Modifier and Type	Method and Description
void	PairedFastqWriter.write(PairedRead read)

Uses of PairedRead in com.milaboratory.core.merger

Methods in com.milaboratory.core.merger that return PairedRead

Modifier and Type	Method and Description
PairedRead	PairedReadMergingResult.getOriginalRead()

Methods in com.milaboratory.core.merger with parameters of type PairedRead

Modifier and Type	Method and Description
PairedReadMergingResult	MismatchOnlyPairedReadMerger.merge(NSequenceWithQuality read1p, NSequenceWithQuality read2p, PairedRead pairedRead)
PairedReadMergingResult	MismatchOnlyPairedReadMerger.process(PairedRead pairedRead)

Constructors in com.milaboratory.core.merger with parameters of type PairedRead

Constructor and Description
PairedReadMergingResult(PairedRead originalRead) Constructor for failed merging result.
PairedReadMergingResult(PairedRead originalRead, NSequenceWithQuality overlappedSequence, int overlap, int errors, boolean reversed, int offset, MergerParameters.IdentityType identityType, double identity) Constructor for successful merging result.