uni.bielefeld.cmg.sparkhit.pipeline

Class SparkPipe

java.lang.Object

uni.bielefeld.cmg.sparkhit.pipeline.SparkPipe

All Implemented Interfaces:

java.io.Serializable

public class SparkPipe
extends java.lang.Object
implements java.io.Serializable

Returns an object for running the Sparkhit-recruiter pipeline. This is the main pipeline for fragment recruitment.

See Also:

, Serialized Form

Constructor Summary

Constructors

Constructor and Description
SparkPipe()

Method Summary

Methods

Modifier and Type	Method and Description
RefStructBuilder	loadReference() This method builds the reference index.
void	setMatrix(ScoreMatrix mat) This method sets the scoring matrix for sequence alignment.
void	setParam(DefaultParam param) This method sets the input parameters.
void	setStruct(RefStructBuilder ref) This method sets the reference builder object.
void	spark() This method runs the Sparkhit pipeline using Spark RDD operations.
void	sparkFastqToLine() This method transforms fastq format to line-based format.
void	sparkLineFile() reading line based fastq data

Methods inherited from class java.lang.Object

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

Constructor Detail

SparkPipe

public SparkPipe()

Method Detail

loadReference

public RefStructBuilder loadReference()

This method builds the reference index.

Returns:

the reference index.

sparkFastqToLine

public void sparkFastqToLine()

This method transforms fastq format to line-based format.

sparkLineFile

public void sparkLineFile()

reading line based fastq data

spark

public void spark()

This method runs the Sparkhit pipeline using Spark RDD operations.

setParam

public void setParam(DefaultParam param)

This method sets the input parameters.

Parameters:

param - DefaultParam.

setStruct

public void setStruct(RefStructBuilder ref)

This method sets the reference builder object.

Parameters:

ref - RefStructBuilder.

setMatrix

public void setMatrix(ScoreMatrix mat)

This method sets the scoring matrix for sequence alignment.

Parameters:

mat - ScoreMatrix.