Merge pull request #100 from Breeding-Insight/svg_add

polyRAD Bug Fix

R/DosageCall_functions.R

@@ -28,7 +28,36 @@ polyRAD_dosage_call <- function(vcf, ploidy, model, p1 = NULL, p2 = NULL, backcr
   # Having some issues formatting the output when multiallelic SNPs is input, so excluding for now
   temp_vcf <- vcfR::read.vcfR(vcf_path, verbose = FALSE)
   temp_vcf <- temp_vcf[is.biallelic(temp_vcf),]
-
+
+  # Function to randomly assign non-matching bases for polyRAD
+  assign_random_bases <- function(vcf) {
+    # Get the number of rows in the VCF
+    num_rows <- nrow(vcf@fix)
+
+    # Generate random bases for REF and ALT
+    bases <- c("A", "C", "G", "T")
+    ref_bases <- sample(bases, num_rows, replace = TRUE)
+    alt_bases <- character(num_rows) # Initialize an empty character vector
+
+    # Ensure REF and ALT are different for each row
+    for (i in 1:num_rows) {
+      alt_bases[i] <- sample(bases[bases != ref_bases[i]], 1)
+    }
+
+    # Assign the new bases to the vcf object
+    vcf@fix[, "REF"] <- ref_bases
+    vcf@fix[, "ALT"] <- alt_bases
+
+    return(vcf)
+  }
+
+  #Editing REF and ALT fields randomly temporarily if blank or AB
+  ref_base <- temp_vcf@fix[1, "REF"]
+  alt_base <- temp_vcf@fix[1, "ALT"]
+  if (is.na(ref_base) || is.na(alt_base) || alt_base == "B") {
+  temp_vcf <- assign_random_bases(temp_vcf)
+  }
+
   # Adding filtered VCF as a temp object
   temp_vcf_path <- tempfile(fileext = ".vcf.gz")
   vcfR::write.vcf(temp_vcf, file = temp_vcf_path)