added new tool w/ rough framework
everythin in place, but untested
wrap around coordinates outside length

Forgot that some reads align *completely* outside the canonical region,
fixed that.  Also wrap around mate positions, even though their
semantics isn't completely clear where we split entries.
fix map quality

At least in the easy cases, where there are only two alignments reported
which conincide after coordinate normalization, we can "fix" mapq by
assigning 37 to it.
manpage and usage information
bump version number
added Myers' Aligner
bump version numbers
silence some warnings
add convenience functions
Merge branch 'master' into genotyper

Conflicts:
	Bio/Bam.hs
	Bio/Bam/Raw.hs
	biohazard.cabal
	tools/biohazard-tools.cabal