working on genotype caller

So far, this adds code written for a different purpose and contains a
half-assed attempt at 'pileup'.
WIP
Merge branch 'master' into genotyper
compilable 'decompose' function

Function that breaks a read into pieces useful for genotype calling.
Don't expect it to work just yet.
WIP
WIP
Merge branch 'master' into genotyper
finish reorg

This moves Pileup into the new Bam folder, adds some pieces of an old
Pileup lookalike into it, cleans up around it all and silences some
compiler warnings.
newtype 'Qual' for improved documentation
WIP
restructuring of pileup logic

Introduced appropriate state monad, a handful of primitives, and an
outline of the code.  Doesn't even compile so far.
completed pileup

The pileup function compiles and does something; we actually get
separate piles out of a stream.  So far, it's completely untested,
though.
some convenience functions
Merge branch 'septools' into genotyper
fixed an oops
some cleanup
WIP
Merge branch 'master' into genotyper

Conflicts:
	Bio/Bam.hs
	Bio/Bam/Raw.hs
	biohazard.cabal
	tools/biohazard-tools.cabal
WIP
added simple indel calling

Also adds arithmetic with quality scores to Bio.Util; addition in log
space should come in handy once in a while.