public byte getPhred(double position) {
int basePosition = (int) position;
for (AlignmentBlock block : getAlignmentBlocks()) {
if (block.contains(basePosition)) {
int offset = basePosition - block.getStart();
byte score = block.getQuality(offset);
return score;
}
}
return 0;
}
public byte getBase(double position) {
int basePosition = (int) position;
for (AlignmentBlock block : getAlignmentBlocks()) {
if (block.contains(basePosition)) {
int offset = basePosition - block.getStart();
byte base = block.getBases()[offset];
return base;
}
}
return 0;
}