127 lines
4.1 KiB
Java
Executable File
127 lines
4.1 KiB
Java
Executable File
package org.broadinstitute.sting.utils;
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import net.sf.samtools.SAMUtils;
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/**
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* QualityUtils is a static class (no instantiation allowed!) with some utility methods for manipulating
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* quality scores.
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*
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* @author Kiran Garimella
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*/
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public class QualityUtils {
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public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE;
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public final static double ERROR_RATE_OF_MAX_QUAL_SCORE = qualToErrorProbRaw(MAX_QUAL_SCORE);
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public final static double MIN_REASONABLE_ERROR = 0.0001;
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public final static byte MAX_REASONABLE_Q_SCORE = 40;
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public final static byte MIN_USABLE_Q_SCORE = 6;
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public final static int MAPPING_QUALITY_UNAVAILABLE = 255;
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private static double qualToErrorProbCache[] = new double[256];
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static {
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for (int i = 0; i < 256; i++) qualToErrorProbCache[i] = qualToErrorProbRaw(i);
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}
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/**
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* Private constructor. No instantiating this class!
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*/
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private QualityUtils() {}
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/**
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* Convert a quality score to a probability. This is the Phred-style
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* conversion, *not* the Illumina-style conversion (though asymptotically, they're the same).
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*
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* @param qual a quality score (0-40)
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* @return a probability (0.0-1.0)
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*/
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static public double qualToProb(byte qual) {
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return 1.0 - qualToErrorProb(qual);
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}
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static public double qualToProb(double qual) {
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return 1.0 - Math.pow(10.0, qual/(-10.0));
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}
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/**
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* Convert a quality score to a probability of error. This is the Phred-style
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* conversion, *not* the Illumina-style conversion (though asymptotically, they're the same).
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*
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* @param qual a quality score (0 - 255)
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* @return a probability (0.0 - 1.0)
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*/
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static private double qualToErrorProbRaw(int qual) {
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return Math.pow(10.0, ((double) qual)/-10.0);
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}
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static public double qualToErrorProb(byte qual) {
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return qualToErrorProbCache[(int)qual & 0xff]; // Map: 127 -> 127; -128 -> 128; -1 -> 255; etc.
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}
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static public double[] qualArrayToLog10ErrorProb(byte[] quals) {
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double[] returnArray = new double[quals.length];
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for( int iii = 0; iii < quals.length; iii++ ) {
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returnArray[iii] = ((double) quals[iii])/-10.0;
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}
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return returnArray;
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}
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/**
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* Convert a probability to a quality score. Note, this is capped at Q40.
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*
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* @param prob a probability (0.0-1.0)
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* @return a quality score (0-40)
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*/
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static public byte probToQual(double prob) {
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return probToQual(prob, MIN_REASONABLE_ERROR);
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//return (byte) Math.round(-10.0*Math.log10(1.0 - prob + 0.0001));
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}
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/**
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* Convert a probability to a quality score. Note, this is capped at a quality score which is determined by _eps_.
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*
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* @param prob a probability (0.0-1.0)
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* @param eps min probabilty allowed (0.0-1.0)
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* @return a quality score (0-255)
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*/
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static public byte probToQual(double prob, double eps) {
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double lp = Math.round(-10.0*Math.log10(1.0 - prob + eps));
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byte b = boundQual((int)lp);
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//System.out.printf("LP is %f, byte is %d%n", lp, b);
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return b;
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}
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static public double phredScaleCorrectRate(double trueRate) {
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return phredScaleErrorRate(1-trueRate);
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}
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static public double phredScaleErrorRate(double errorRate) {
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return Math.abs(-10.0*Math.log10(errorRate));
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}
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static public double lodToPhredScaleErrorRate(double lod) {
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return phredScaleErrorRate(1.0 / (Math.pow(10.0, lod) + 1.0));
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}
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/**
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* Return a quality score, capped at max qual.
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*
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* @param qual the uncapped quality score
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* @return the capped quality score
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*/
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static public byte boundQual(int qual) {
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return boundQual(qual, MAX_QUAL_SCORE);
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}
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/**
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* Returns an integer quality score bounded by 1 - maxQual.
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*
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* @param qual
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* @param maxQual
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* @return
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*/
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static public byte boundQual(int qual, byte maxQual) {
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//return (byte) Math.min(qual, maxQual);
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return (byte) Math.max(Math.min(qual, maxQual), 1);
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}
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}
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