com.milaboratory.core.merger

Class MismatchOnlyPairedReadMerger

java.lang.Object

com.milaboratory.core.merger.MismatchOnlyPairedReadMerger

All Implemented Interfaces:

cc.redberry.pipe.Processor<PairedRead,PairedReadMergingResult>, Serializable

public final class MismatchOnlyPairedReadMerger
extends Object
implements cc.redberry.pipe.Processor<PairedRead,PairedReadMergingResult>, Serializable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	MIN_SCORE_VALUE

Constructor Summary

Constructors

Constructor and Description
MismatchOnlyPairedReadMerger(int minOverlap, double minimalIdentity, int maxScoreValue, QualityMergingAlgorithm qualityMergingAlgorithm, PairedEndReadsLayout pairedEndReadsLayout) Creates paired-end reads merger.
MismatchOnlyPairedReadMerger(int minOverlap, double minimalIdentity, MergerParameters.IdentityType identityType, int maxScoreValue, QualityMergingAlgorithm qualityMergingAlgorithm, PairedEndReadsLayout pairedEndReadsLayout) Creates paired-end reads merger.
MismatchOnlyPairedReadMerger(MergerParameters parameters) Creates paired-end reads merger for Illumina (or other opposite reads) data.

Method Summary

Methods

Modifier and Type	Method and Description
static double	identity(MergerParameters.IdentityType identityType, NSequenceWithQuality seq1, int offset1, NSequenceWithQuality seq2, int offset2, int length)
PairedReadMergingResult	merge(NSequenceWithQuality read1p, NSequenceWithQuality read2p)
PairedReadMergingResult	merge(NSequenceWithQuality read1p, NSequenceWithQuality read2p, PairedRead pairedRead)
NSequenceWithQuality	overlap(NSequenceWithQuality seq1, NSequenceWithQuality seq2, int offset)
PairedReadMergingResult	process(PairedRead pairedRead)

Methods inherited from class java.lang.Object

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

Field Detail

MIN_SCORE_VALUE

public static final int MIN_SCORE_VALUE

See Also:

Constant Field Values

Constructor Detail

MismatchOnlyPairedReadMerger

public MismatchOnlyPairedReadMerger(MergerParameters parameters)

Creates paired-end reads merger for Illumina (or other opposite reads) data.

Parameters:

parameters - merger parameters

MismatchOnlyPairedReadMerger

public MismatchOnlyPairedReadMerger(int minOverlap,
                            double minimalIdentity,
                            int maxScoreValue,
                            QualityMergingAlgorithm qualityMergingAlgorithm,
                            PairedEndReadsLayout pairedEndReadsLayout)

Creates paired-end reads merger.

Parameters:

minOverlap - minimal number of nucleotide in overlap region

minimalIdentity - maximal allowed percent of mismatches in overlap region

maxScoreValue - maximal output quality score value

qualityMergingAlgorithm - algorithm to infer quality of merged reads from it's pairs

pairedEndReadsLayout - orientation of read pairs

MismatchOnlyPairedReadMerger

public MismatchOnlyPairedReadMerger(int minOverlap,
                            double minimalIdentity,
                            MergerParameters.IdentityType identityType,
                            int maxScoreValue,
                            QualityMergingAlgorithm qualityMergingAlgorithm,
                            PairedEndReadsLayout pairedEndReadsLayout)

Creates paired-end reads merger.

Parameters:

minOverlap - minimal number of nucleotide in overlap region

minimalIdentity - maximal allowed percent of mismatches in overlap region

identityType - identity type

maxScoreValue - maximal output quality score value

qualityMergingAlgorithm - algorithm to infer quality of merged reads from it's pairs

pairedEndReadsLayout - orientation of read pairs

Method Detail

merge

public PairedReadMergingResult merge(NSequenceWithQuality read1p,
                            NSequenceWithQuality read2p)

merge

public PairedReadMergingResult merge(NSequenceWithQuality read1p,
                            NSequenceWithQuality read2p,
                            PairedRead pairedRead)

identity

public static double identity(MergerParameters.IdentityType identityType,
              NSequenceWithQuality seq1,
              int offset1,
              NSequenceWithQuality seq2,
              int offset2,
              int length)

process

public PairedReadMergingResult process(PairedRead pairedRead)

Specified by:

process in interface cc.redberry.pipe.Processor<PairedRead,PairedReadMergingResult>

overlap

public NSequenceWithQuality overlap(NSequenceWithQuality seq1,
                           NSequenceWithQuality seq2,
                           int offset)

Parameters:

seq1 - sequence 1

seq2 - sequence 2

offset - position of first nucleotide of seq2 in seq1

Returns:

overlapped sequence