129 lines
4.6 KiB
Java
129 lines
4.6 KiB
Java
/*
|
|
* The Broad Institute
|
|
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
|
|
* This software and its documentation are copyright 2009 by the
|
|
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
|
|
*
|
|
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
|
|
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
|
|
*/
|
|
package edu.mit.broad.picard.illumina;
|
|
|
|
/**
|
|
* Holds all the Bustard-level data we need (so far) about an individual read.
|
|
*
|
|
* @author Kathleen Tibbetts
|
|
*/
|
|
public class BustardReadData {
|
|
|
|
private static final String PADDING ="00000";
|
|
|
|
final private String machineName;
|
|
final private int runNumber;
|
|
final private int laneNumber;
|
|
final private int tileNumber;
|
|
final private String firstReadSequence;
|
|
final private String firstReadQualities;
|
|
final private String secondReadSequence;
|
|
final private String secondReadQualities;
|
|
final private boolean pf;
|
|
final private double intensities[][];
|
|
final private int xCoordinate;
|
|
final private int yCoordinate;
|
|
private final SolexaQualityConverter converter = new SolexaQualityConverter();
|
|
|
|
|
|
/**
|
|
* Constructor that takes everything to populate this object
|
|
*
|
|
* @param machineName
|
|
* @param runNumber
|
|
* @param laneNumber
|
|
* @param tileNumber
|
|
* @param firstReadSequence
|
|
* @param firstReadQualities
|
|
* @param secondReadSequence
|
|
* @param secondReadQualities
|
|
* @param pf
|
|
* @param intensities
|
|
* @param xCoordinate
|
|
* @param yCoordinate
|
|
*/
|
|
public BustardReadData(String machineName, int runNumber, int laneNumber, int tileNumber,
|
|
String firstReadSequence, String firstReadQualities,
|
|
String secondReadSequence, String secondReadQualities,
|
|
boolean pf, double[][] intensities, int xCoordinate, int yCoordinate ) {
|
|
|
|
this.machineName = machineName;
|
|
this.runNumber = runNumber;
|
|
this.laneNumber = laneNumber;
|
|
this.tileNumber = tileNumber;
|
|
this.firstReadSequence = firstReadSequence;
|
|
this.firstReadQualities = firstReadQualities;
|
|
this.secondReadSequence = secondReadSequence;
|
|
this.secondReadQualities = secondReadQualities;
|
|
this.pf = pf;
|
|
this.intensities = intensities;
|
|
this.xCoordinate = xCoordinate;
|
|
this.yCoordinate = yCoordinate;
|
|
}
|
|
|
|
// TODO: Finalize read name -- ask Tim
|
|
/**
|
|
* Composes a name for this read from its values
|
|
*
|
|
* @return the read name
|
|
*/
|
|
public String getReadName() {
|
|
return this.machineName + ":" + this.laneNumber + ":" + this.tileNumber +
|
|
":" + this.xCoordinate + ":" + this.yCoordinate;
|
|
}
|
|
|
|
/**
|
|
* Gets Phred-style qualitites for the first read
|
|
*
|
|
* @return the String of qualities
|
|
*/
|
|
public String getFirstReadPhredQualities() {
|
|
return decodeSolexaQualitiesToPhred(getFirstReadQualities());
|
|
}
|
|
|
|
/**
|
|
* Gets Phred-style qualitites for the second read
|
|
*
|
|
* @return the String of qualities
|
|
*/
|
|
public String getSecondReadPhredQualities() {
|
|
return decodeSolexaQualitiesToPhred(getSecondReadQualities());
|
|
}
|
|
|
|
/**
|
|
* Converts a string of Solexa qualities to a Phred-style quality String
|
|
*
|
|
* @param qualities the Solexa qualities to decode
|
|
* @return the String of Phred qualities
|
|
*/
|
|
private String decodeSolexaQualitiesToPhred(String qualities) {
|
|
StringBuilder sb = new StringBuilder();
|
|
for (char c : qualities.toCharArray()) {
|
|
// Quality char is phred score + 33
|
|
sb.append((char)(converter.solexaToPhred((byte)c)+33));
|
|
}
|
|
return sb.toString();
|
|
}
|
|
|
|
public String getMachineName() { return machineName; }
|
|
public int getRunNumber() { return runNumber; }
|
|
public int getLaneNumber() { return laneNumber; }
|
|
public int getTileNumber() { return tileNumber; }
|
|
public String getFirstReadSequence() { return firstReadSequence; }
|
|
public String getFirstReadQualities() { return firstReadQualities; }
|
|
public String getSecondReadSequence() { return secondReadSequence; }
|
|
public String getSecondReadQualities() { return secondReadQualities; }
|
|
public double[][] getIntensities() { return intensities; }
|
|
public boolean isPf() { return pf; }
|
|
public int getXCoordinate() { return xCoordinate; }
|
|
public int getYCoordinate() { return yCoordinate; }
|
|
|
|
}
|