Verify vsearch compatibility

[Jason Vander Heiden]

Need to verify that we can substitute usearch for vsearch. Currently, TestClusterSets.test_runUClust() does not appear to be returning the same clusters.

[Jason Vander Heiden]

vsearch appears to have a bug and will not properly cluster the unit test data, but it seems to otherwise be compatible. usearch appears to have the same bug with lowercase input.

Need to contact the others and figure out what's up.

[Jason Vander Heiden]

usearch treats all lowercase letters as masked. Masked bases are ignored for indexing, but included for calculating identity.

This can be worked around by specifying -qmask none, which also seems to fix vsearch's behavior.

[Jason Vander Heiden]

A bug in the uc format output by vsearch was fixed in vsearch 2.3.2. This version works for uclust (ClusterSets), but vsearch does not provide local alignment (usearch_local or ublast algorithms), therefore it will not work for AssemblePairs-reference. Likely we will have to add support for a different local alignment package.