Fix cactus_coverage default output
(doesn't affect outgroup trimming)
Don't skip last sequence chunk in repeatmasking

Closes #7.
Fix cactus_realign memory leak
Fixes to cactus realign from the nanopore branch.
Merge remote-tracking branch 'origin/development' into development
Fix to build.
Creating branch to represent my attempt at putting in EM for the
pairwise aligner.
Basic em tests now passing.
EM now working for large sequences.
Got restarts working.
Fixes
Merge branch 'em' into nanoporeHacks

Conflicts:
	bar/Makefile
	blast/Makefile
	blast/cactus_realign.c
	blast/cactus_realignTest.py