org.dishevelled.bio.tools

Class BinFastqQualityScores

java.lang.Object

org.dishevelled.bio.tools.BinFastqQualityScores

All Implemented Interfaces:

Callable<Integer>

public final class BinFastqQualityScores
extends Object
implements Callable<Integer>

Bin quality scores from files in FASTQ format.

Since:

2.2

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
BinFastqQualityScores(Path inputFastqPath, File outputFastqFile) Bin quality scores from files in FASTQ format.

Method Summary

Modifier and Type	Method and Description
(package private) static String	bin(String quality) Bin the specified quality scores per Illumina technical note, "Reducing Whole-Genome Data Storage Footprint."
(package private) static int	binQualityScore(int qualityScore) Bin the specified quality score per Illumina technical note, "Reducing Whole-Genome Data Storage Footprint."
Integer	call()
static void	main(String[] args) Main.

Methods inherited from class java.lang.Object

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

Constructor Detail

BinFastqQualityScores

public BinFastqQualityScores(Path inputFastqPath,
                             File outputFastqFile)

Bin quality scores from files in FASTQ format.

Parameters:

inputFastqPath - input FASTQ path, if any

outputFastqFile - output FASTQ file, if any

Method Detail

call

public Integer call()
             throws Exception

Specified by:

call in interface Callable<Integer>

Throws:

Exception

bin

static String bin(String quality)

Bin the specified quality scores per Illumina technical note, "Reducing Whole-Genome Data Storage Footprint."

Parameters:

quality - quality scores to bin

Returns:

the specified quality scores binned per Illumina technical note

binQualityScore

static int binQualityScore(int qualityScore)

Bin the specified quality score per Illumina technical note, "Reducing Whole-Genome Data Storage Footprint."

Parameters:

qualityScore - quality score to bin

Returns:

the specified quality score binned per Illumina technical note

main

public static void main(String[] args)

Main.

Parameters:

args - command line args