Refactored to work with a SQLite database of blast results
first commit
Fixed a bug that was preventing CDS features from being written to the GTF

This is because the write statement was nested in the "if strand == '-'" block
Refactored database building to speed it up

Moved database construction to Heathpy, where it was rewritten to be less robust but faster

I also changed the naming of the database files (so they keep the original extension, with ",db"/".inx" added after)

I also added a default tree for cases where there isn't one in the tree file. This tree
won't have any of the taxa in it so there won't be any groups, but it prevents the program from crashing
removed an extraneous print statement that was added for debugging purposes
Refactored to work with MySQL rather than sqlite
changed the naming of the sequence index file so it will be xxx.fa.inx rather than xxx.inx
Adds additional columns when printing cumulative lengths for contig number and filename

This means a lot less messing around in R before printing cumulative lengths
Refactored to work with MySQL database rather than sqlite
Changing some of the filenames and adding code to remove sequences after calculating consensus sequences