net.maizegenetics.dna.read

Class FastqChunk

net.maizegenetics.dna.read.FastqChunk

public class FastqChunk

Hold Fastq single end Fastq file

Constructor Detail

FastqChunk

public FastqChunk(java.lang.String fastqFileS,
                  net.maizegenetics.dna.read.ReadUtils.ReadFormat format,
                  int startIndex,
                  int readNum)

Constructor, sample Fastq file, ignore those bad sequence at the beginning

Parameters:

fastqFileS -

format -

startIndex -

readNum -

FastqChunk

public FastqChunk(java.lang.String fastqFileS,
                  net.maizegenetics.dna.read.ReadUtils.ReadFormat format)

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

Parameters:

fastqFileS -

format -

FastqChunk

public FastqChunk(Read[] reads)

Method Detail

getPhredScale

public int getPhredScale()

Return phred score scale of the fastq, 33 or 64

Returns:

org.jetbrains.dokka.NodeRenderContent@71b1c884:

writeFastq

public void writeFastq(java.lang.String outputFileS,
                       net.maizegenetics.dna.read.ReadUtils.ReadFormat format)

Write Fastq file

Parameters:

outputFileS -

format -

writeFasta

public void writeFasta(java.lang.String outfileS)

getRead

public Read getRead(int index)

Return Fastq read

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@5309844:

getReadNum

public int getReadNum()

Return number of Fastq read

Returns:

org.jetbrains.dokka.NodeRenderContent@b35e8df: