private static double getConsensusScoreWithFunction1(Read sequence, Consensus consensus) {
		double score = 0;
		// takes into account that S + c(endgap) scores 0;
		for (int col = sequence.getOffset(); col < sequence.getOffset() + sequence.getLength(); col++) {
			if (col >= 0 && col < consensus.getSymbols().size()) {
				Metasymbol sym = consensus.getSymbols().get(col);
				char c = sequence.sequence.get(col-sequence.getOffset());
				if (!sym.symbols.contains(c)) {
					score+=1;
				}
			}
			
		}
		return score;
	}