Merge with ALT percentage from ngs_mapper.vcf

[averagehat]

We want to pull out the PAC (integer list of ALT percentages) from the INFO column as well as the ALT column (character list of the ALT bases). Also include the DP. This needs to be done for every nucleotide in the codon, which makes the output tricky.

Right now the output looks like:

ID	Codon	NTPos  	AA  AAPos	 RowType   
2055	RAC	 1927 	N/D  643	Non_Synonymous

Maybe add the following columns:

Nt1                Nt2             Nt3       Nt1DP     Nt2DP      Nt3DP
A=28,G=62,T=10    A=90,C=5,G=5    C=99,A=1     990        100        360

NtXDP could be placed into the NtX columns instead of having the extra columns for DP.

Thoughts?

[InaMBerry]

So I do not think we need it for the whole codon, we just need the nucleotide percentages for the called mixed position. In this case only Nt1 and its DP.

[mmelendrez]

@averagehat Let me know when this is implemented and I'll get started on the runs requested by Ina and our collaborators. Or if it's going to be a bit, let me know and I'll start with the original MAAPs and will visit this when you are finished. thanks!

[averagehat]

@mmelendrez this is ready, I posted the module usage in gitter.
For github, the change can be seen in the vcfmerge branch

[mmelendrez]

great thanks!