Question on Bimbam for Haploid organism

[Thurston Herricks]

Hello,

I am trying to run Bimbam on blood stage Plasmodium falciparum SNP data.  My issue is coding the genotype files as P. falciparum is a haploid organism.   I also have multiple genetic alleles at given location.  

How can I code the genotype file correctly?  Or if I just encode all SNPs as AA, GG how can I adjust the -A and -D flags to 1 and 0?  

For multiple genetic alleles is it possible to list multiple snps at the same location and utilize the genotype distribution file to list the probability of the reference allele and the appropriate reference allele where the probability of both alleles is zero if that individual does posses a different mutant allele?

Thanks for your time in reading.  If this is a very difficult question to reply to could you please point me in a direction that I could find the answer?  

again thanks for your time,

Thurston Herricks