From 12492df719a8daf40df9735ab384846a5f5f4e63 Mon Sep 17 00:00:00 2001
From: Qiong Yang <qyang@scc-wi1.scc.bu.edu>
Date: Sat, 23 Nov 2024 20:53:56 -0500
Subject: [PATCH] replace refDosage() by imputedDosage() to read DS from format

---
 .Rbuildignore | 2 ++
 R/admixMap.R  | 4 +++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 4862ac6..4ff7437 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,5 @@
 ^renv$
 ^renv\.lock$
 ^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/R/admixMap.R b/R/admixMap.R
index 65ccf16..7c46ccd 100644
--- a/R/admixMap.R
+++ b/R/admixMap.R
@@ -81,7 +81,9 @@ admixMap <- function(admixDataList,
             if (is(admixDataList[[1]], "GenotypeIterator")) {
                 local[,,i] <- getGenotypeSelection(admixDataList[[i]], scan=sample.index, order="selection", transpose=TRUE, use.names=FALSE, drop=FALSE)
             } else {
-                local[,,i] <- refDosage(admixDataList[[i]], use.names=FALSE)[sample.index,,drop=FALSE]
+               # local[,,i] <- refDosage(admixDataList[[i]], use.names=FALSE)[sample.index,,drop=FALSE]
+               local[,,i] <- imputedDosage(admixDataList[[i]], use.names=FALSE)[sample.index,,drop=FALSE]
+              
             }
         }
         if (any(is.na(local))) warning("missing values in local ancestry will produce NA output for this block")