general
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Man pages!


I would like to encorporate some domain-specific compression algorithm. Options
I know of:
  * G-SQZ (http://www.tgen.org/research/gsqueez.cfm) : not open source (i.e. not an option)
  * fqzcomp (http://seqanswers.com/forums/archive/index.php/t-6349.html)
  * DSRC (http://bioinformatics.oxfordjournals.org/cgi/content/short/27/6/860?rss=1) :
    Not yet available?
  * Invent my own.






program specific
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fastq-grep
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fastq-kmers
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fastq-match
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Specifying the score matrix, rather than using a hardcoded.

The implementation of the Smith-Waterman algorithm could be more efficient. We
might look to Phil Green's cross_match implementation for ideas.

An option to return the sequences that match past a certain threshold would be
useful.



fastq-uniq
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