uni.bielefeld.cmg.sparkhit.io

Class FastqUnitBuffer

java.lang.Object

uni.bielefeld.cmg.sparkhit.io.FastqUnitBuffer

All Implemented Interfaces:

NGSfileUnitBuffer

public class FastqUnitBuffer
extends java.lang.Object
implements NGSfileUnitBuffer

Returns an object for buffering Fastq files. Providing Fastq unit buffer for multi-thread Fastq input stream. This class is used in local mode only. For cluster mode, Spark "textFile" function is used to access input Fastq file.

See Also:

Field Summary

Fields

Modifier and Type	Field and Description
java.io.BufferedReader	inputBufferedReader
readInfo[]	reads

Constructor Summary

Constructors

Constructor and Description
FastqUnitBuffer(java.io.BufferedReader inputBufferedReader) A constructor that sets input BufferedReader for buffering input Fastq files.
FastqUnitBuffer(java.io.BufferedReader inputBufferedReader, int unitCount) This constructor is deprecated

Method Summary

Methods

Modifier and Type	Method and Description
void	addReadUnit(readInfo read, int unitsMark) This method adds a read into the Fastq unit buffer.
void	loadBufferedFastq() This method loads 1000 fastq units into buffer for streaming fastq reads.
readInfo	nextUnit() This method provides a thread safe access point for loading Fastq reads.

Methods inherited from class java.lang.Object

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

Field Detail

reads

public readInfo[] reads

inputBufferedReader

public java.io.BufferedReader inputBufferedReader

Constructor Detail

FastqUnitBuffer

public FastqUnitBuffer(java.io.BufferedReader inputBufferedReader)

A constructor that sets input BufferedReader for buffering input Fastq files.

Parameters:

inputBufferedReader - Java BufferedReader.

FastqUnitBuffer

public FastqUnitBuffer(java.io.BufferedReader inputBufferedReader,
               int unitCount)

This constructor is deprecated

Parameters:

inputBufferedReader -

unitCount -

Method Detail

loadBufferedFastq

public void loadBufferedFastq()

This method loads 1000 fastq units into buffer for streaming fastq reads. Each fastq unit is a four line string providing essential information for a sequencing unit.

addReadUnit

public void addReadUnit(readInfo read,
               int unitsMark)

This method adds a read into the Fastq unit buffer.

Specified by:

addReadUnit in interface NGSfileUnitBuffer

Parameters:

read - readInfo a type of data structure class describing a sequencing read.

unitsMark - the count of buffered Fastq units.

nextUnit

public readInfo nextUnit()

This method provides a thread safe access point for loading Fastq reads.

Returns:

readInfo a type of data structure class describing a sequencing read