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

Conflicts:
	sTRAM.pl
Merge branch 'master' into check_for_ends
Merge branch 'master' into check_for_ends
added flags for evalue and max_target_seqs
add debug flag
change $blast_file check
Fixes #22
Merge branch 'check_for_ends' into juliema

Conflicts:
	sTRAM.pl
Merge branch 'juliema'