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; }