Chris,
please take a look at issue #40 --
http://code.google.com/p/pygr/issues/detail?id=40
github branch 'review_issue40' contains tests for
NLMSA.add_aligned_intervals, and a few bug fixes.
http://github.com/ctb/pygr/commit/793fd92d31226411af2331054acc8ade34dc4da7
cheers,
--titus
--
C. Titus Brown, c...@msu.edu
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