combineSeqs

R/combineSeqs.R

@@ -7,15 +7,17 @@
 #' @param species species ID
 #' @param argList args to passed to consensusSeq
 #' @param output_seq output just the sequence
-#' @param minor_align minor allele alignment
+#' @param align major and minor allele alignment
 #' @export
 #' @return new stana object
 combineSeqs <- function(stana_list, species, argList=list(), output_seq=FALSE,
-    minor_align=FALSE) {
+    align=FALSE) {
   if (!is.list(stana_list)) {stop("Please provide list of stana object")}
   each_ID <- lapply(stana_list, function(x) {
-    if (minor_align) {
-        ids <- paste0(row.names(x@snpsInfo[[species]]), ":minor", x@snpsInfo[[species]]$minor_allele)
+    if (align) {
+        ids <- paste0(row.names(x@snpsInfo[[species]]),
+          ":major", x@snpsInfo[[species]]$major_allele,
+          ":minor", x@snpsInfo[[species]]$minor_allele)
     } else {
         ids <- x@snpsInfo[[species]] |> row.names()    
     }
@@ -26,8 +28,8 @@ combineSeqs <- function(stana_list, species, argList=list(), output_seq=FALSE,
 
   qqcat("Common SNVs: @{length(intersected)}\n")
   argList[["return_mat"]] <- TRUE
-  if (minor_align) {
-      intersected <- strsplit(intersected, ":minor") %>% lapply("[", 1) %>% unlist()
+  if (align) {
+      intersected <- strsplit(intersected, ":major") %>% lapply("[", 1) %>% unlist()
   }
   argList[["site_list"]] <- intersected