sortmerna option for OTU picking added
added fuction build_database_sortmerna
finalized integration of sortmerna in pick_otus
created a failures file from sortmerna output and changed default sortmerna OTU path to QIIME result path
removed debug messages
sumaclust added as option to pick_otus
moved clusters and failures computation to app controller
Merge branch 'master' of https://github.com/biocore/qiime into add-sortmerna

merge changes from master to add-sortmerna branch
added new OTU identifier
updated inline comments
moved cluster list to app controller
moved sumaclust class to a lower location in file to avoid merge conflicts with sortmerna
--threads=NUM_THREADS option edited to accept only integer values, as multithreading for usearch, sortmerna and sumaclust creates one thread per core available (default 1)
re-ordered sortmerna_ref_cluster() args
Merge branch 'master' of https://github.com/biocore/qiime into add-sumaclust

pulling latest updates
Fix failing compare_trajectories.py tests

Since trajectory results are no longer subclasses of namedtuple in skbio, a few tests were failing that relied on sorting of tuples. The changes here should allow the tests to pass with previous versions of skbio as well as the latest release and dev versions.
Merge pull request #1602 from ElBrogrammer/compare-trajectories-fix-tests

Thanks @ElBrogrammer
pep8 compliant
pep8
code review suggestions taken into account