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;