Added OTU table output and grep parsing

A giant batch commit. Sorry!

  * OTU table output
    * results are still different from matlab
    * sample names still have suffix
    * otherwise should be ok
    * only return rows which sum up to greater than zero (ie non empty)
  * Use grep instead of BIOseq because it is a lot faster to count our
    sequences this way.
  * re-enable our pool process management
  * refactor and rename records to headers
  * refactor final_output to output

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