Merged ContigSplitter and MasterGlue using a call to MultiDir.sh
Currently works

Bugs:
Adds an extra empty folder
Intermediate outputs are stored in wrong folder
Same as previous but committed correctly

Working program

Known bugs:
Intermediate files stored incorrectly
ContigSplitter creates extra empty folder for contigs

Next iteration:
Replace MultiDir.sh with python while loop
Replaced the bash script 'Multidir.sh' with python.

Known bugs:
None

Up next:
Replace Glimmer cshell scripts with python
Move scripts to second hard drive and make available to everyone
Working to remove redundant blasting on sequences originating from gbk files
Actual push
Need to mod the genbank retrieval to circumvent redundant blasting
changes:
Replaced sections dependent on string parsing with lists
No longer blasting glimmer verified sequences from gbk files
	will improve RNA identification
Changed equivalence check in glimmerComparison to probability over exact match

todo:
Sort final annotations
Move equivalence check to it's own file
create annotation comparison with readable output