Closed zmertens closed 6 years ago
Consider this file, it should print out an RNA sequence correctly:
Output.Rna = 1 [Tree] Tree = "((Man:0.1,Monkey:0.1):0.2,Dawg:0.25);" [Subst] Model = "HKY" Params = 2.0, 1.0 Freqs = 0.3, 0.2, 0.2, 0.3 [Root] Length = 1000 [Sim] Reps = 10
However, if the RNA output specifier is moved to the bottom, it will not print out an RNA sequence.
[Tree] Tree = "((Man:0.1,Monkey:0.1):0.2,Dawg:0.25);" [Subst] Model = "HKY" Params = 2.0, 1.0 Freqs = 0.3, 0.2, 0.2, 0.3 [Root] Length = 1000 [Sim] Reps = 10 Output.Rna = 1
I think this might be something worth investigating and fixing? On a side note, and relevant to the RootSequence patch, should the user be able to specify an RNA sequence as the root sequence?
Works as expected.
I your second example, you have places Output.Rna in the [Sim] section so it gets read as Sim.Output.Rna
[Sim]
Sim.Output.Rna
Consider this file, it should print out an RNA sequence correctly:
However, if the RNA output specifier is moved to the bottom, it will not print out an RNA sequence.
I think this might be something worth investigating and fixing? On a side note, and relevant to the RootSequence patch, should the user be able to specify an RNA sequence as the root sequence?