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guanchangge / mosaik-aligner

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Mismatches/IUPAC codes #131

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 

What is the expected output? What do you see instead?
With extremely small example I set -mm 0 (meaning no mismatches) 
When this happens I get no alignment to the reference genome even though I 
should with the IUPAC codes in the reference genome.  Is there a setting that 
would all 0 mismatches but correct alignment to IUPAC codes. 
Any help would be appreciated.

What version of the product are you using? On what operating system?
2.2.26

Original issue reported on code.google.com by leanne...@gmail.com on 14 Apr 2014 at 4:47