Wrote script to turn fasta into fastq
Added in STAR alignment
Made rRNA removal optional. (I think there might be too many darn options at this point...)
fixed some filename inconsistancy bugs
silly syntax issue, forgot to check last time
modified the equalization so that the case of no reverse reads won't be an issue
modified to take in 0 as number of entries and not die
trying to make everything work with empty read files; problems with
conflation of 0 and undef in perl.
don't want to delete files, because renaming is a pain; instead cp -l