starting the ability to check to see if contigs have beginning and end.
Merge branch 'refactoring'
Merge branch 'master' into check_for_ends

Conflicts:
	sTRAM.pl
Merge branch 'juliema'
Merge branch 'master' into check_for_ends
change 0-prepare_files to makelibrary in POD
Merge branch 'master' into check_for_ends
add debug flag
change $blast_file check
Fixes #22
Merge branch 'check_for_ends' into juliema

Conflicts:
	sTRAM.pl