HistogramGenerator addRead(final GATKRead read) {
final byte[] quals =
(useOriginalQualities
? ReadUtils.getOriginalBaseQualities(read)
: read.getBaseQualities());
if (quals == null) {
return this;
}
final int length = quals.length;
final boolean isReverseStrand = read.isReverseStrand();
ensureArraysBigEnough(length + 1);
for (int i = 0; i < length; ++i) {
final int cycle = isReverseStrand ? length - i : i + 1;
if (read.isPaired() && read.isSecondOfPair()) {
secondReadTotalsByCycle[cycle] += quals[i];
secondReadCountsByCycle[cycle] += 1;
} else {
firstReadTotalsByCycle[cycle] += quals[i];
firstReadCountsByCycle[cycle] += 1;
}
}
return this;
}
