[Seqan-dev] Fatal Error in Banded Chain Alignment Traceback

[Brett Bowman <bnbowman@gmail.com>]

I'm trying to build a tool with SeqAn to quickly align some PacBio data, using "bandedChainAlignment", but I'm consistently getting a crash during the trace-back step.  The generation of the Seeds (SuffixArray) and the finding of the base SeedChain works fine, but the final step of turning that into an alignment doesn't appear to work.  

Suggestions?

Error Log:

"""

bbowman@localhost:~/git/SRSLI$ ./src/C++/srsli test/data/query/ecoli_5p_sample.fastq test/data/reference/ecoliK12_5p_assembly.fasta 

Query 0

Finished finding seeds

Finishing chaining seeds

Starting alignment of sequences

/usr/include/seqan/seeds/banded_chain_alignment_traceback.h:195 Assertion failed : isGlued == true was: 0 != 1 (Fatal error while trying to connect trace backs: No glue point available!)

Aborted (core dumped)

"""

-Brett