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shane-c-lawson / breseq

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Reference sequences containing ambiguous (N) bases #22

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
1) Add a test case where a mutation causes a change in an ambiguous codon.

This should report '?' for the amino acid (and not crash).

2) Check how reads are aligned to stretches with many N bases by SSAHA2

Good behavior would be that these do not count for or against the alignment 
score.

Original issue reported on code.google.com by jeffrey....@gmail.com on 14 Sep 2011 at 2:23

GoogleCodeExporter commented 8 years ago 
There is a now a test case for this.

Original comment by jeffrey....@gmail.com on 4 Oct 2011 at 2:19