Added test for intersection utility,

Also protect against differences in the number of rows between the
test and reference datasets when no intersection is performed.

R/trainSingleR.R

@@ -338,6 +338,7 @@ trainSingleR <- function(
     }
 
     if (is.null(test.genes)) {
+        stopifnot(nrow(test) == nrow(ref))
         test.genes <- ref.genes <- seq_len(nrow(ref))
     } else {
         intersection <- .create_intersection(test.genes, rownames(ref))

tests/testthat/test-utils.R

@@ -0,0 +1,15 @@
+# library(testthat); library(SingleR); source("test-utils.R")
+
+test_that("intersection works as expected for edge cases", {
+    out <- SingleR:::.create_intersection(c("A", "B", "C", "a"), LETTERS)
+    expect_identical(out$test, 1:3)
+    expect_identical(out$reference, 1:3)
+
+    out <- SingleR:::.create_intersection(c("a", "Z", "b", "G", "c", "B", "d"), LETTERS)
+    expect_identical(out$test, c(2L, 4L, 6L))
+    expect_identical(out$reference, c(26L, 7L, 2L))
+
+    out <- SingleR:::.create_intersection(c("y", "y", "x", "z", NA, "z", "x"), letters)
+    expect_identical(out$test, c(1L, 3L, 4L))
+    expect_identical(out$reference, c(25L, 24L, 26L))
+})