54 lines
1.8 KiB
Java
Executable File
54 lines
1.8 KiB
Java
Executable File
package org.broadinstitute.sting.utils;
|
|
|
|
/**
|
|
* QualityUtils is a static class (no instantiation allowed!) with some utility methods for manipulating
|
|
* quality scores.
|
|
*
|
|
* @author Kiran Garimella
|
|
*/
|
|
public class QualityUtils {
|
|
/**
|
|
* Private constructor. No instantiating this class!
|
|
*/
|
|
private QualityUtils() {}
|
|
|
|
/**
|
|
* Convert a quality score to a probability. This is the Phred-style
|
|
* conversion, *not* the Illumina-style conversion (though asymptotically, they're the same).
|
|
*
|
|
* @param qual a quality score (0-40)
|
|
* @return a probability (0.0-1.0)
|
|
*/
|
|
static public double qualToProb(byte qual) {
|
|
return 1.0 - Math.pow(10.0, ((double) qual)/-10.0);
|
|
}
|
|
|
|
/**
|
|
* Convert a probability to a quality score. Note, this is capped at Q40.
|
|
*
|
|
* @param prob a probability (0.0-1.0)
|
|
* @return a quality score (0-40)
|
|
*/
|
|
static public byte probToQual(double prob) {
|
|
return (byte) Math.round(-10.0*Math.log10(1.0 - prob + 0.0001));
|
|
}
|
|
|
|
/**
|
|
* Compress a base and a probability into a single byte so that it can be output in a SAMRecord's SQ field.
|
|
* Note: the highest probability this function can encode is 64%, so this function should only never be used on the best base hypothesis.
|
|
* Another note: the probability encoded here gets rounded to the nearest 1%.
|
|
*
|
|
* @param baseIndex the base index
|
|
* @param prob the base probability
|
|
* @return a byte containing the index and the probability
|
|
*/
|
|
static public byte baseAndProbToCompressedQuality(int baseIndex, double prob) {
|
|
byte compressedQual = (byte) baseIndex;
|
|
byte cprob = (byte) (100.0*prob);
|
|
byte qualmask = (byte) 252;
|
|
compressedQual += ((cprob << 2) & qualmask);
|
|
|
|
return compressedQual;
|
|
}
|
|
}
|