From 56d1678137ed34626064dc811314083174fc1360 Mon Sep 17 00:00:00 2001
From: noriakis <nori@hgc.jp>
Date: Fri, 21 Jun 2024 14:13:26 +0900
Subject: [PATCH] combineSeqs

---
 R/combineSeqs.R    | 14 ++++++++------
 man/combineSeqs.Rd |  4 ++--
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/R/combineSeqs.R b/R/combineSeqs.R
index fc2e885..4b35600 100644
--- a/R/combineSeqs.R
+++ b/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
   
diff --git a/man/combineSeqs.Rd b/man/combineSeqs.Rd
index 8d2ae37..3f285c0 100644
--- a/man/combineSeqs.Rd
+++ b/man/combineSeqs.Rd
@@ -9,7 +9,7 @@ combineSeqs(
   species,
   argList = list(),
   output_seq = FALSE,
-  minor_align = FALSE
+  align = FALSE
 )
 }
 \arguments{
@@ -21,7 +21,7 @@ combineSeqs(
 
 \item{output_seq}{output just the sequence}
 
-\item{minor_align}{minor allele alignment}
+\item{align}{major and minor allele alignment}
 }
 \value{
 new stana object