public final class MismatchOnlyPairedReadMerger extends Object implements cc.redberry.pipe.Processor<PairedRead,PairedReadMergingResult>, Serializable
| Modifier and Type | Field and Description |
|---|---|
static int |
MIN_SCORE_VALUE |
| 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.
|
| 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) |
public static final int MIN_SCORE_VALUE
public MismatchOnlyPairedReadMerger(MergerParameters parameters)
parameters - merger parameterspublic MismatchOnlyPairedReadMerger(int minOverlap,
double minimalIdentity,
int maxScoreValue,
QualityMergingAlgorithm qualityMergingAlgorithm,
PairedEndReadsLayout pairedEndReadsLayout)
minOverlap - minimal number of nucleotide in overlap regionminimalIdentity - maximal allowed percent of mismatches in overlap regionmaxScoreValue - maximal output quality score valuequalityMergingAlgorithm - algorithm to infer quality of merged reads from it's pairspairedEndReadsLayout - orientation of read pairspublic MismatchOnlyPairedReadMerger(int minOverlap,
double minimalIdentity,
MergerParameters.IdentityType identityType,
int maxScoreValue,
QualityMergingAlgorithm qualityMergingAlgorithm,
PairedEndReadsLayout pairedEndReadsLayout)
minOverlap - minimal number of nucleotide in overlap regionminimalIdentity - maximal allowed percent of mismatches in overlap regionidentityType - identity typemaxScoreValue - maximal output quality score valuequalityMergingAlgorithm - algorithm to infer quality of merged reads from it's pairspairedEndReadsLayout - orientation of read pairspublic PairedReadMergingResult merge(NSequenceWithQuality read1p, NSequenceWithQuality read2p)
public PairedReadMergingResult merge(NSequenceWithQuality read1p, NSequenceWithQuality read2p, PairedRead pairedRead)
public static double identity(MergerParameters.IdentityType identityType, NSequenceWithQuality seq1, int offset1, NSequenceWithQuality seq2, int offset2, int length)
public PairedReadMergingResult process(PairedRead pairedRead)
process in interface cc.redberry.pipe.Processor<PairedRead,PairedReadMergingResult>public NSequenceWithQuality overlap(NSequenceWithQuality seq1, NSequenceWithQuality seq2, int offset)
seq1 - sequence 1seq2 - sequence 2offset - position of first nucleotide of seq2 in seq1Copyright © 2018. All rights reserved.