Merge pull request #2 from mitenjain/ian_dev

Ian dev
Adding in emission training to the em code!
Increasing the number of EM iterations to be sure.
Merge remote-tracking branch 'origin/master'
fixed channel plot PNG bug that happens on R without proper PNG support
new relative density plot in coverage
new version of pipeline that treats folders in the read folder as different read types to be analyzed separately
new version that separates into read types. Designed to blast if user has a local blast installation, and not blast otherwise
finished adding AbstractUnmappedMetaAnalysis. Introduced multiple ways of analyzing unmapped reads, as well as re-introducing blasting them
added muscle script to new scripts/ folder
committing things so i can rebase
rebased
fixing conflicts