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shane-c-lawson / breseq

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Multiple SNPs or changes to the same codon not annotated correctly #23

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
For example point mutations 47,315 and 47,317 in the "lambda_mixed_pop" test 
predict two separate single base pair changes and the associated amino acid 
changes in the same codon.

Simple solution is to look for nearby SNPs in the list of mutations and add 
them to the codon's changes. 

Also, there might be a SNP and another kind of mutation affecting the codon, in 
which case we should probably invalidate predicting an amino acid change and 
revert to a simple "243/987 nt" style annotation.

Original issue reported on code.google.com by jeffrey....@gmail.com on 14 Sep 2011 at 2:56

GoogleCodeExporter commented 8 years ago 
I am starting on this.

Original comment by aaronr...@gmail.com on 31 May 2012 at 9:29

GoogleCodeExporter commented 8 years ago 
Resolved?

Original comment by jeffrey....@gmail.com on 12 Jul 2012 at 3:43

GoogleCodeExporter commented 8 years ago 
2 SNPs to a single codon is correctly shown and annotated, but for more complex 
cases the annotation is still incorrect. I will change it to the "243/987 nt" 
style on 7/16.

Original comment by aaronr...@gmail.com on 13 Jul 2012 at 9:27

GoogleCodeExporter commented 8 years ago 
Believe this is fixed.

Original comment by jeffrey....@gmail.com on 9 Dec 2012 at 9:53