Added in hmm plots.
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
mistake
also a mistake
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
changed pipeline.sh back to not have submodule blast
bug fixes
more fixes to blast
final bug fixes
merging everything together
merging v2