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);