A hacked up version of cactus just for adding cactus_realign for the
nanopore pipeline.
Removing pinches and cacti dependency
Removing 3edge connected dependency.
Format realign
Lots of fixes to cactus_realign + the addition of a mode to allow
posterior probs to be output.
Merge branch 'em' into nanoporeHacks

Conflicts:
	bar/Makefile
	blast/Makefile
	blast/cactus_realign.c
	blast/cactus_realignTest.py
Merge branch 'em' into nanoporeHacks
Merge branch 'em2' into nanoporeHacks
Merge branch 'em2' into nanoporeHacks
Merge branch 'em2' into nanoporeHacks
Merge branch 'em2' into nanoporeHacks
New features.
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