diff --git a/R/importReads.R b/R/importReads.R
index 7761213..7cfbbc8 100644
--- a/R/importReads.R
+++ b/R/importReads.R
@@ -93,14 +93,16 @@ readBamFileAsGRanges <- function(file, bamindex=file, chromosomes=NULL, pairedEn
 
             ## filter XA tag
             if (filtAlt) {
-                data.first <- is.na(mcols(data.first)$XA)
-                data.last <- is.na(mcols(data.last)$XA)
-            }
+                data.first.xa <- is.na(mcols(data.first)$XA)
+                data.last.xa <- is.na(mcols(data.last)$XA)
                 
-            mask <- data.first & data.last
+                mask <- data.first.xa & data.last.xa
 
-            data.first <- data.first[mask]
-            data.last <- data.last[mask]
+                data.first <- data.first[mask]
+                data.last <- data.last[mask]
+            }
+                
+            
 
             ## Filter by mapping quality and duplicate reads
             if (!is.null(min.mapq)) {