several bug fixes
Added function to build an sqlite database from blast hits (not currently being used because everything is in a MySQL sb)

I also made some corrections to the ORF coordinates
get_orf_coords modified to be able to find stop codon for ORFs with frameshifts
Modified to combine the coordinates if there are multiple hits to the same subject seq

I also had to modify orf_inetgrity to look for frameshifts
Modified the loops so that hits are combined for each subject sequence BEFORE determining if they are overlapping
Modified to optionally use a GTF file to convert between gene_ids and contig names
Rewritten to loop through all tree files in a folder and all 4 Selaginella species

I've also added an optional GTF file to convert between gene_ids and contig names
Rewritten to update info in db rather than outputting sequences

It has also been modified to group sequences that are adjacent in the tree even if they are
paraphyletic
Added info about the R library to use to the output
Modified to work with unnested features (CDS without exons or genes)
Added option to print sequence lengths instead of cumulative lengths
Added parse_GTF function and added some error checking to flatten_GTF
Modified to consider adjacent paraphyletic sequences to be redundant.

It also now uses ORF info from the db to translate between gene_id names and sequence names
Added line to print tasks to STDOUT in addition to executing them
Added option to remove ALL blueleaf sequences (KRAUS, MOEL, UNC and WILD)
Added code to add default log names when pipeline is run on all BLUELEAF sepcies
first commit
Reorganized so that adding info from TAIR is a done by a function that is specified with the TAIR option
Added function to add sequence data to db