127 lines
4.3 KiB
Java
Executable File
127 lines
4.3 KiB
Java
Executable File
package org.broadinstitute.sting.utils;
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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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/**
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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 - Math.pow(10.0, ((double) qual)/-10.0);
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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 (byte) Math.round(-10.0*Math.log10(1.0 - prob + 0.0001));
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}
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/**
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* Compress a base and a probability into a single byte so that it can be output in a SAMRecord's SQ field.
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* Note: the highest probability this function can encode is 64%, so this function should only never be used on the best base hypothesis.
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* Another note: the probability encoded here gets rounded to the nearest 1%.
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*
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* @param baseIndex the base index
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* @param prob the base probability
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* @return a byte containing the index and the probability
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*/
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static public byte baseAndProbToCompressedQuality(int baseIndex, double prob) {
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byte compressedQual = 0;
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compressedQual = (byte) baseIndex;
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byte cprob = (byte) (100.0*prob);
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byte qualmask = (byte) 252;
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compressedQual += ((cprob << 2) & qualmask);
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return compressedQual;
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}
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/**
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* From a compressed base, extract the base index (0:A, 1:C, 2:G, 3:T)
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*
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* @param compressedQual the compressed quality score, as returned by baseAndProbToCompressedQuality
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* @return base index
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*/
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static public int compressedQualityToBaseIndex(byte compressedQual) {
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return (int) (compressedQual & 0x3);
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}
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/**
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* From a compressed base, extract the base probability
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*
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* @param compressedQual the compressed quality score, as returned by baseAndProbToCompressedQuality
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* @return the probability
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*/
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static public double compressedQualityToProb(byte compressedQual) {
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// Because java natives are signed, extra care must be taken to avoid
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// shifting a 1 into the sign bit in the implicit promotion of 2 to an int.
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int x2 = ((int) compressedQual) & 0xff;
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x2 = (x2 >>> 2);
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return ((double) x2)/100.0;
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}
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/**
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* Return the complement of a base index.
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*
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* @param baseIndex the base index (0:A, 1:C, 2:G, 3:T)
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* @return the complementary base index
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*/
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static public byte complement(int baseIndex) {
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switch (baseIndex) {
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case 0: return 3; // a -> t
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case 1: return 2; // c -> g
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case 2: return 1; // g -> c
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case 3: return 0; // t -> a
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default: return -1; // wtf?
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}
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}
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/**
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* Return the complement of a compressed quality
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*
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* @param compressedQual the compressed quality score (as returned by baseAndProbToCompressedQuality)
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* @return the complementary compressed quality
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*/
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static public byte complementCompressedQuality(byte compressedQual) {
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int baseIndex = compressedQualityToBaseIndex(compressedQual);
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double prob = compressedQualityToProb(compressedQual);
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return baseAndProbToCompressedQuality(complement(baseIndex), prob);
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}
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/**
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* Return the reverse complement of a byte array of compressed qualities
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*
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* @param compressedQuals a byte array of compressed quality scores
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* @return the reverse complement of the byte array
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*/
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static public byte[] reverseComplementCompressedQualityArray(byte[] compressedQuals) {
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byte[] rcCompressedQuals = new byte[compressedQuals.length];
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for (int pos = 0; pos < compressedQuals.length; pos++) {
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rcCompressedQuals[compressedQuals.length - pos - 1] = complementCompressedQuality(compressedQuals[pos]);
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}
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return rcCompressedQuals;
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}
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}
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