6bb864da2a7941caaebb0de351cb488164b69a7c,java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java,MinimumNQSCovariate,getValue,#SAMRecord#number#,49
Before Change
int maxIndex = Math.min(offset + windowReach, read.getBaseQualities().length - 1);
for ( int iii = minIndex; iii < maxIndex; iii++ ) {
if( read.getBaseQualities()[iii] < minQual ) {
minQual = read.getBaseQualities()[iii];
}
}
return minQual;
After Change
public final Comparable getValue( final SAMRecord read, final int offset ) {
// Loop over the list of base quality scores in the window and find the minimum
byte[] quals = read.getBaseQualities();
int minQual = quals[offset];
int minIndex = Math.max(offset - windowReach, 0);
int maxIndex = Math.min(offset + windowReach, quals.length - 1);