[Biojava-l] SequenceMixin Error in BioJava3 Alignment

[Chris Friedline]

Hello,

Found another potential error case, this time in beta2 (fresh pull
from git last evening).  For more info, please see
http://pastie.org/1351388 for test case and stack trace.  The JUnit
test passes simply because the pair object is not null, but fails when
trying to extract any information from the pair itself (toString(),
getIdenticals(), etc). The substitution matrix file is from
ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
pairwise alignments, which do not all fail, but most do with this same
error.

Thanks,
Chris

--
PhD Candidate, Integrative Life Sciences
Virginia Commonwealth University
Richmond, VA