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Merged bug fix from Stable into Unstable

This commit is contained in:
Menachem Fromer 2012-01-27 16:03:16 -05:00
parent f7ac1f4a69 a9671b73ca
commit 0e17cbbce9
1 changed files with 5 additions and 5 deletions
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10
public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
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@ -17,7 +17,7 @@ public class QualityUtils {
private static double qualToErrorProbCache[] = new double[256]; private static double qualToErrorProbCache[] = new double[256];
static { static {
for (int i = 0; i < 256; i++) qualToErrorProbCache[i] = qualToErrorProbRaw((byte)i); for (int i = 0; i < 256; i++) qualToErrorProbCache[i] = qualToErrorProbRaw(i);
} }
/** /**
@ -44,15 +44,15 @@ public class QualityUtils {
* Convert a quality score to a probability of error. This is the Phred-style * Convert a quality score to a probability of error. This is the Phred-style
* conversion, *not* the Illumina-style conversion (though asymptotically, they're the same). * conversion, *not* the Illumina-style conversion (though asymptotically, they're the same).
* *
* @param qual a quality score (0-40) * @param qual a quality score (0 - 255)
* @return a probability (0.0-1.0) * @return a probability (0.0 - 1.0)
*/ */
static public double qualToErrorProbRaw(byte qual) { static private double qualToErrorProbRaw(int qual) {
return Math.pow(10.0, ((double) qual)/-10.0); return Math.pow(10.0, ((double) qual)/-10.0);
} }
static public double qualToErrorProb(byte qual) { static public double qualToErrorProb(byte qual) {
return qualToErrorProbCache[qual]; return qualToErrorProbCache[(int)qual & 0xff]; // Map: 127 -> 127; -128 -> 128; -1 -> 255; etc.
} }
/** /**