2 Link against quip so we can run these tools on quip/fastq/bam/sam with one
5 Make a website for fastq-tools.
11 Specifying the score matrix, rather than using a hardcoded.
13 The implementation of the Smith-Waterman algorithm could be more efficient. We
14 might look to Phil Green's cross_match implementation for ideas.
16 An option to return the sequences that match past a certain threshold would be