net.maizegenetics.dna.read

Class PEFastqChunk

net.maizegenetics.dna.read.PEFastqChunk

public class PEFastqChunk

Hold PE Fastq file. Providing merging function

Constructor Detail

PEFastqChunk

public PEFastqChunk(java.lang.String fastqR1FileS,
                    java.lang.String fastqR2FileS,
                    net.maizegenetics.dna.read.ReadUtils.ReadFormat format,
                    int startIndex,
                    int readNum)

Constructor to sample PE Fastq files, ignore those bad sequence at the beginning

Parameters:

fastqR1FileS -

fastqR2FileS -

format -

startIndex -

readNum -

PEFastqChunk

public PEFastqChunk(java.lang.String fastqR1FileS,
                    java.lang.String fastqR2FileS,
                    net.maizegenetics.dna.read.ReadUtils.ReadFormat format)

Constructor to read in whole PE Fastq files, fastq file should be small for test

Parameters:

fastqR1FileS -

fastqR2FileS -

format -

Method Detail

getPhredScale

public int getPhredScale()

Return phred score scale of the fastq, 33 or 64

Returns:

org.jetbrains.dokka.NodeRenderContent@3e0749a7:

getPERead

public PERead getPERead(int index)

Return PE read

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@5f32d1ab:

getPEReadNum

public int getPEReadNum()

Return number of PE read

Returns:

org.jetbrains.dokka.NodeRenderContent@19bb113:

merge

public void merge(boolean ifPrintAlignment)

Merge PE to Pcontig

Parameters:

ifPrintAlignment -

writePEFastq

public void writePEFastq(java.lang.String fastqR1FileS,
                         java.lang.String fastqR2FileS,
                         net.maizegenetics.dna.read.ReadUtils.ReadFormat format)

Write original PE sequence

Parameters:

fastqR1FileS -

fastqR2FileS -

format -

writeMergedPEFastq

public void writeMergedPEFastq(java.lang.String fastqR1FileS,
                               java.lang.String fastqR2FileS,
                               java.lang.String fastqContigFileS,
                               net.maizegenetics.dna.read.ReadUtils.ReadFormat format)

Write PE read and Pcontig read, when there is a Pcontig, PE read will not be output

Parameters:

fastqR1FileS -

fastqR2FileS -

fastqContigFileS -

format -