4f775810871daffb3d5e7a564253481a2bb88ede,java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java,HaplotypeScore,getHaplotypeFromRead,#ExtendedPileupElement#number#,163

Before Change


            if ( baseOffset >= read.getReadLength() )
                break;

            haplotypeBases[i] = read.getReadBases()[baseOffset];
            baseQualities[i] = (double)read.getBaseQualities()[baseOffset];
        }

After Change


        double[] baseQualities = new double[contextSize];
        Arrays.fill(baseQualities,0.0);

        final byte[] readBases = read.getReadBases();
        final byte[] readQuals = read.getBaseQualities();
        for (int i = 0; i < contextSize; i++ ) {
            int baseOffset = i + baseOffsetStart;