# A test sample from TPO
#gt <-'/hits_mctp/users/hopkinal/mioncoseq2/test/SI_12742_HL5KVBCXX_0-genotype.csv'
#this will have to be adapted for Bob's geno output

#load the genotyping csv and alignstats file from TPO
alignid <- gsub('-genotype.csv','',basename(gt))
gtds <- read.csv(gt)


#convert the hets to IUPAC i.e. A/C -> M
gt <- as.character(gtds$final_call)
gt <- gsub('/','',gt)
gt <- gsub('UNKNOWN','ACGT',gt)
dict = names(IUPAC_CODE_MAP)
names(dict) = IUPAC_CODE_MAP
gtt <- as.character(dict[gt])
gtt <- paste(gtt, collapse='')

gtt