net.maizegenetics.pangenome.hapCalling

Class FastqcolToFastaConverter

net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter

public class FastqcolToFastaConverter

Constructor Detail

FastqcolToFastaConverter

public FastqcolToFastaConverter(@NotNull
                                java.io.File inDir,
                                @NotNull
                                java.io.File outDir,
                                int nthreads,
                                @NotNull
                                java.lang.String inExt,
                                @NotNull
                                java.lang.String outExt,
                                boolean removeAdapter,
                                boolean expandReads)

Method Detail

getValidFiles

public java.io.File[] getValidFiles()

getMyLogger

@NotNull
public NonExistentClass getMyLogger()

convertAllFiles

@NotNull
public NonExistentClass convertAllFiles()

Set up multithreading and hand out files to each thread

countFiles

@NotNull
public NonExistentClass countFiles(@NotNull
                                            kotlinx.coroutines.CoroutineScope $receiver)

load file indices to channel

launchProcessor

@NotNull
public NonExistentClass launchProcessor(@NotNull
                                                 kotlinx.coroutines.CoroutineScope $receiver,
                                                 int id,
                                                 @NotNull
                                                 kotlinx.coroutines.channels.ReceiveChannel<java.lang.Integer> channel)

Call converter function on each file

convertFile

public void convertFile(@NotNull
                        java.io.File file)

Write a fasta or a fastq file from the given FASTQCOL input file

lineToFasta

@NotNull
public java.lang.String lineToFasta(@NotNull
                                             java.lang.String line,
                                             @NotNull
                                             java.lang.String sampleName,
                                             int counter)

Given a string in FASTQCOL format and associated metadata, return a string in fasta format FASTQCOL is really a csv file with four columns:

1. number of reads with the sequence,

2. quality scores (integers, separated by spaces),

3. base sequence,

4. position of illumina adapter (0 if no adapter is present)

Parameters: line: the input string, in FASTQCOL format sampleName: the name of the original file, minus extensions counter: the row number of this line in the original file

Returns: a fasta-formatted string

lineToFastq

@NotNull
public java.lang.String lineToFastq(@NotNull
                                             java.lang.String line,
                                             @NotNull
                                             java.lang.String sampleName,
                                             int counter)

Given a string in FASTQCOL format and associated metadata, return a string in fastq format Parameters: line: the input string, in FASTQCOL format sampleName: the name of the original file, minus extensions counter: the row number of this line in the original file

Returns: a fastq-formatted string

getOutDir

@NotNull
public java.io.File getOutDir()

getNthreads

public int getNthreads()

getInExt

@NotNull
public java.lang.String getInExt()

getOutExt

@NotNull
public java.lang.String getOutExt()

getRemoveAdapter

public boolean getRemoveAdapter()

getExpandReads

public boolean getExpandReads()