Catch incorrect individual names used in tskit functions

bodkan · Sep 28, 2022 · da7e0bb · da7e0bb
1 parent cee535c
commit da7e0bb
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diff --git a/R/tree-sequences.R b/R/tree-sequences.R
@@ -2018,6 +2018,8 @@ get_node_ids <- function(ts, x) {
   if (is.null(x)) {
     ids <- ts_nodes(ts) %>% .[.$sampled, ]$node_id
   } else if (is.character(x)) {
+    if (length(intersect(x, ts_samples(ts)$name)) != length(x))
+      stop("Not all individual names are among those recorded in the tree sequence", call. = FALSE)
     ids <- ts_nodes(ts) %>% dplyr::filter(name %in% x) %>% .$node_id
   } else if (is.numeric(x)) {
     ids <- as.integer(x)

diff --git a/tests/testthat/test-ts.R b/tests/testthat/test-ts.R
@@ -704,3 +704,9 @@ test_that("metadata is the same for SLiM and msprime conditional on a model", {
   expect_equal(sdata5$time, mdata5$time)
   expect_equal(sdata6$time, mdata6$time)
 })
+
+test_that("all names of individuals must be present in the tree sequence", {
+  ts <- ts_load(file = msprime_ts, model = model)
+  expect_error(ts_diversity(ts, c("p1_1", "p2_2")), "Not all individual names")
+  expect_s3_class(ts_diversity(ts, c("pop1_1", "pop2_2")), "data.frame")
+})