This is a simple implementation of a BLAST postprocessing
tool that realigns the sequences using quality adjusted
alignment (i.e. accounting for quality values in the sequences).

Note that the actual implementation of the quality-adjusted
alignment is in the "bio" library, specifically in the file
	http://malde.org/~ketil/bio/Bio/Alignment/QAlign.hs

You will need:

1. a working Haskell compiler, preferably GHC
2. the "bio" library installed, available as 
	http://malde.org/~ketil/bio
   (Use darcs to download it, follow instructions to
    install it.)

Now, you should be able to

	ghc --make -O2 src/PostN.hs -o postn

To use it, you will need:

	a blast database file (db.seq)
	a blast query file (query.seq)
	the query quality values (query.qual)
	the blastn results in XML format (blast.xml)

You should then be able to do:

	./postn -s query.seq query.qual db.seq blast.xml 

which will print one line per alignment, with fields:

	query seq, db seq, blast idents, blast bits, blast evalue
	smith-waterman bits, quality adjusted bits, s-w length, qual adj length

You can also replace -s by -l in the command line, which will output the
complete alignments.

This is a conceptual prototype only, exepect a more polished interface
if it develops into a more production oriented tool :-)

Mail me (ketil at malde dot org) with any questions or problems!