greedyMix() broken on GUI and FASTA datasets

[wleoncio]

Reporting both because the solution may be identical.

Code to reproduce

baps("ExampleData/spatial clustering of individuals/Example data in FASTA format for clustering of haploid individuals.txt", "FASTA", "greedyMix")

Error message

Unknown file type
Output argument "processed_data" (and possibly others) not assigned a value in the execution with "process_data" function.

Error in greedyMix (line 18)
  tietue = process_data(tietue, file_type, partitionCompare);

Error in baps (line 36)
      greedyMix(file, file_type, partitionCompare);

[wleoncio]

FASTA is not implemented for greedyMix() on the original code, but it is for spatial*Mixture(). Maybe drop support for it on the former (for now).

[wleoncio]

From Jukka:

yes it does [make sense to use FASTA files on greedyMix()]. Essentially the greedyMix model would only use variable positions (SNPs) in the fasta file and assumes all those SNPs are unlinked. So effectively it has the same effect as stripping all nonvariable columns from the input FASTA file and then proceeding with the remaining columns as if they were categorical variables as in the BAPS format.

Since the code for processing of these files is already in place (in other parts of the code), it looks worthwhile to repurpose the implementation and make sure BAPS and rBAPS outputs match.

[wleoncio]

Regarding the idea of formatting FASTA as BAPS for processing on greedyMix(), Jukka wrote:

BAPS format is the easiest one to convert to, inside [the BAPS software] fasta is simply ripped into something akin BAPS formatting.