diff --git a/.gitignore b/.gitignore
index f06ac644..5a7c2dee 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 src/*.o
+src/*.gcda
 src/*.so
 src/*.dylib
 src/Makevars
diff --git a/R/QtlDataset.R b/R/QtlDataset.R
index 684f6724..c0620680 100644
--- a/R/QtlDataset.R
+++ b/R/QtlDataset.R
@@ -343,7 +343,9 @@ setMethod("getScaleResiduals", "QtlDataset", function(x) x@scaleResiduals)
     si <- x@genotypes@snpInfo
     snpMask <- nchar(as.character(si$A1[snpIdx])) == 1L &
                nchar(as.character(si$A2[snpIdx])) == 1L
-    snpIdx <- snpIdx[snpMask]
+    # which() (not snpMask directly) so any NA in the mask drops that variant
+    # rather than injecting an NA index that would corrupt the extracted block.
+    snpIdx <- snpIdx[which(snpMask)]
     if (length(snpIdx) == 0L) {
       return(list(
         geno       = matrix(numeric(0), nrow = 0L, ncol = 0L,
diff --git a/R/genotypeIo.R b/R/genotypeIo.R
index a9cd187a..68c6d975 100644
--- a/R/genotypeIo.R
+++ b/R/genotypeIo.R
@@ -116,8 +116,12 @@ setMethod("readGenotypes",
       stop("Plink file not found: ", f)
   }
 
+  # colClasses = "character" so type.convert() never coerces a column: a bim
+  # whose allele column is uniformly "T"/"F" (e.g. all-A/T SNPs) would otherwise
+  # be read as logical TRUE/FALSE, silently corrupting A1/A2 (BP is cast to
+  # integer explicitly below).
   bim <- read.table(bimFile, header = FALSE,
-                            stringsAsFactors = FALSE,
+                            colClasses = "character",
                             col.names = c("CHR", "SNP", "CM", "BP", "A1", "A2"))
   fam <- read.table(famFile, header = FALSE, stringsAsFactors = FALSE)
   sampleIds <- as.character(fam[, 2])  # IID column