[pygr-notify] Issue 40 in pygr: add NLMSA convenience method for loading aligned intervals from any source

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Comment #8 on issue 40 by cjlee112: add NLMSA convenience method for  
loading aligned intervals from any source
http://code.google.com/p/pygr/issues/detail?id=40

Hi Titus,
I don't understand why you moved the "if srcDB is None..." default-setting  
code from
read_aligned_coords() to add_aligned_coords() in your branch  
review_issue40.  First
of all, srcDB/destDB are *never* used in add_aligned_coords() other than  
for passing
them into read_aligned_coords(), so I don't see how this can fix any  
problem.
Second, read_aligned_coords() needs to guarantee that srcDB / destDB are  
not None;
due to your change that is no longer guaranteed if it is called from  
anywhere other
than add_aligned_coords().

The test code that seemed possibly relevant to this (test_no_seqDict_args)  
appears
not to be used (it is not even part of a test case class).  What bug was  
this change
intended to fix?

-- Chris

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