m5nr2annot: Adding problematic data to test case 0
m5nr2annot: Now handling multiple KEGG hierarchies
m5nr2annot: More verbose output in search for duplication bug
m5nr2annot: Even more verbose output (--veryverbose) in search for duplication bug
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m5nr2annot: Threaded parsing of db files
m5nr2annot: Fixing test case to account for threads
m5nr2annot: Making threads voluntary
m5nr2annot: Minor loggin things. --threads now works.
m5nr2annot: Fixed duplication problem (hopefully\!)
m5nr2annot: Deleted threads. Considered using the parallel gem for reading the blast files in parallel but that would require locking output files for writing.
organisms2lca: Adding species with comma to test cases
organisms2lca: Fixed problem with commas in organism names by requiring citation marks (double quotes) around organism names