Improved conversion from FASTA to BAPS (#24)

R/convert_FASTA_to_BAPS.R

@@ -11,5 +11,6 @@ convert_FASTA_to_BAPS <- function(file) {
   data <- load_fasta(file) # Processing data
   data <- cbind(data, seq_len(nrow(data))) # Add IDs of individuals (sequential)
   data[data == 0] <- -9 # Because zeros (missing) in BAPS are coded as -9
+  colnames(data) <- paste("V", seq_len(ncol(data)), sep = "")
   return(data)
 }

R/handleData.R

@@ -56,11 +56,15 @@ handleData <- function(raw_data, format = "Genepop") {
   }
 
   # This is where data gets converted to {1, 2, 3, 4} for {A, C, G, T}
+  codes <- unique(as.vector(data[, -ncol(data)]))
+  skip_conversion <- base::min(codes) == -9 && base::max(codes) == 4
+  if (!skip_conversion) {
     for (loc in seq_len(nloci)) {
       for (all in seq_len(noalle[loc])) {
         data[matlab2r::find(data[, loc] == alleleCodes[all, loc]), loc] <- all
       }
     }
+  }
 
   nind <- as.integer(base::max(data[, ncol(data)]))
   nrows <- size(data, 1)