Inconsistent Number of Individuals on Output

[ahulsekemp]

Hi David,
Following the last fix, it appears that while it will now work without an error for those offending contig files the output for those files now generates an inconsistent output for number of samples. It would be ultimately beneficial if we can impose a fix to have consistent output according to the input regarding number of samples. I am working on a downstream fix but I think it would be great to incorporate upstream for greater user utility.
Best,
Amanda

[dauglyon]

is the solution you are looking for to leave empty lines for the contigs with no data like:

ID0    0,a,4,b,60,h,100
ID1    .                               <--- this?
ID2    0,a,4,b,60,h,100

[ahulsekemp]

Yes, in order to flow through to the next step to allow:

ID0,a,b,h
ID1,-,-,-
ID2,a,b,h

Outputs from all different chrs or contigs can then easily be joined together using paste etc to correlate data.