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package artificialFastqGenerator;
import java.util.ArrayList;
import java.util.logging.Level;
import java.util.logging.Logger;
/**
* An instance of this class can be used to create new Nucleobase and Read objects.
*
* Copyright (C) 2012 The Institute of Cancer Research (ICR).
*
* This file is part of ArtificialFastqGenerator v1.0.0.
*
* ArtificialFastqGenerator is free software: you can redistribute it and/or modify it under the terms of the GNU General
* Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU Public License along with this
* program. If not, see <http://www.gnu.org/licenses/>
*
* Authour's contact email: Matthew.Frampton@icr.ac.uk
*/
public class NucleobaseAndReadFactory {
private long numNucleobasesCreated;
private long numReadsCreated;
private int xCoordinate;
private int yCoordinate;
private int readLength;
private QualityScoreAndErrorGenerator qualityScoreAndErrorGenerator;
private Logger logger;
/**
* Initialises a new NucleobaseAndReadFactory object.
*
* @param startingXCoord - the starting X coordinate.
* @param startingYCoord - the starting Y coordinate.
* @param readLength - the lenght of each read.
* @param useRealQualityScores - true if using quality scores from an existing fastq file, else false.
* @param simulateErrorInRead - true if simulating error in reads, else false.
* @param fastq1ForQualityScoresPath - the 1st fastq file whose quality scores are used.
* @param fastq2ForQualityScoresPath - the 2nd fastq file whose quality scores are used.
*/
public NucleobaseAndReadFactory(int startingXCoord, int startingYCoord, int readLength, boolean useRealQualityScores,
boolean simulateErrorInRead, String fastq1ForQualityScoresPath, String fastq2ForQualityScoresPath) {
numNucleobasesCreated = 0;
numReadsCreated = 0;
xCoordinate = startingXCoord;
yCoordinate = startingYCoord;
this.readLength = readLength;
qualityScoreAndErrorGenerator = new QualityScoreAndErrorGenerator(readLength,useRealQualityScores,
simulateErrorInRead,fastq1ForQualityScoresPath,fastq2ForQualityScoresPath);
logger = Main.logger;
}
/**
* Update the x and y coordinates.
*/
private void updateXAndYCoords() {
if (xCoordinate == 20100) {
xCoordinate = 1000;
yCoordinate = yCoordinate + 1;
} else {
xCoordinate = xCoordinate + 1;}
}
/**
* Create a Nucleobase object.
*
* @param genotype - the nucleobase's genotype.
* @return newNucleobase - a new nucleobase object.
*/
public Nucleobase createNucleobase(char genotype) {
numNucleobasesCreated = numNucleobasesCreated + 1;
Nucleobase newNucleobase = new Nucleobase(genotype,numNucleobasesCreated,0);
return newNucleobase;
}
/**
* Create a pair of reads.
*
* @param leftEndSequence - the sequence of nucleobases for the left read.
* @param rightEndSequence - the sequence of nucleobases for the right read.
*/
public void createPairedEndReads(ArrayList<Nucleobase> leftEndSequence, ArrayList<Nucleobase> rightEndSequence) {
updateXAndYCoords();
Read leftRead = createRead(leftEndSequence, null, true);
Read rightRead = createRead(rightEndSequence, leftRead, false);
leftRead.setPairedEndRead(rightRead);
}
/**
* Create a new Read object.
*
* @param nucleobases - the sequence of nucleobases for the read.
* @param pairedEndRead - the other read with which this read forms a pair.
* @return newRead - a new Read object.
*/
private Read createRead(ArrayList<Nucleobase> nucleobases, Read pairedEndRead, boolean isLeft) {
numReadsCreated = numReadsCreated + 1;
ArrayList<char[]> qualityScoresAndGenotypesRead = qualityScoreAndErrorGenerator.getQualityScoresAndGenotypesRead(isLeft, nucleobases);
char[] encodedQualityScores = qualityScoresAndGenotypesRead.get(0);
char[] genotypesThatAreRead = qualityScoresAndGenotypesRead.get(1);
Read newRead = new Read(nucleobases,numReadsCreated,pairedEndRead,isLeft,encodedQualityScores,genotypesThatAreRead,xCoordinate,yCoordinate);
return newRead;
}
/**
* Get the number of nucleobases that have been created.
*
* @return numNucleobasesCreated - the number of Nucleobase objects that have been created so far.
*/
public long getNumNucleobasesCreated() {
return numNucleobasesCreated;
}
/**
* Get the number of reads that have been created.
*
* @return numReadsCreated - the number of Read objects that have been created so far.
*/
public long getNumReadsCreated() {
return numReadsCreated;
}
/**
* Get the number of base call errors that have been simulated.
*
* @return numBaseCallErrors - the number of base call errors that have been simulated.
*/
public long getNumBaseCallErrors() {
return qualityScoreAndErrorGenerator.getNumBaseCallErrors();
}
/**
* Get the number of ACGT nucleobases that have been called.
*
* @return numACGTBasesCalled - the number of ACGT nucleobases that have been called.
*/
public long getNumACGTBasesCalled() {
return qualityScoreAndErrorGenerator.getNumACGTBasesCalled();
}
/**
* Log the overall error statistics.
*/
public void logOverallErrorStats() {
long totalBaseCalls = numReadsCreated * (long) readLength;
logger.log(Level.INFO,"# reads=" + numReadsCreated);
logger.log(Level.INFO,"# nucleobase calls=" + totalBaseCalls);
logger.log(Level.INFO,"# ACGT nucleobase calls=" + qualityScoreAndErrorGenerator.getNumACGTBasesCalled());
logger.log(Level.INFO,"# ACGT call errors=" + qualityScoreAndErrorGenerator.getNumBaseCallErrors());
}
/**
* Reset fields ready to process a new chromosome.
*/
public void resetFieldsForNewChromosome() {
numNucleobasesCreated = 0;
numReadsCreated = 0;
qualityScoreAndErrorGenerator.resetNumBaseCallErrors();
}
}
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