cleaned up merge conflict junk
fixed log issues
fixed merge issue
Merge branch 'master' into blin
improved error counts
options
refactor for pier2
merge with blin changes
merge w/ blin, split off hmmparse
improved error message in hmm hit parsing
merge with gcclassif-dev; fixed merge conflicts
Merge branch 'master' of https://github.com/bylin/nealelab-scripts
Merge branch 'master' into blin
add support for reverse order