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evolvedmicrobe / beast-mcmc

Automatically exported from code.google.com/p/beast-mcmc
GNU Lesser General Public License v2.1
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Complex charsets in nexus files don't parse #722

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
begin mrbayes;
    set autoclose=yes nowarn=yes;
    charset mG1_2 = 1-303\3 2-303\3;
    charset mG3 = 3-303\3;
 end;

Now, with BEAUti v1.8.0, this code block is not accepted, it generates a 
warning that '...charset was not parsed...' I proceeded without the code block, 
and specified the codon partitioning in BEAUti on the chance that the new 
version had dealt with the bug making BEAGLE incompatible with codon position 
partioning; no luck.

Original issue reported on code.google.com by ramb...@gmail.com on 7 Jan 2014 at 8:06

GoogleCodeExporter commented 9 years ago 
It will work if the first two codon position definitions have a comma:

    charset mG1_2 = 1-303\3, 2-303\3;

Delimiting with spaces is difficult because there can be spaces within the 
definitions. I will work on a solution.

Original comment by ramb...@gmail.com on 5 Aug 2014 at 8:39

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 5 Aug 2014 at 8:57