test(query_all): add tests for query_all output

tests/testthat/test-query_all.R

@@ -0,0 +1,110 @@
+library(data.table)
+library(Matrix)
+extdata <- system.file("extdata", package = "iscream")
+biscuit_bedfiles <- list.files(extdata, pattern = "[a|b|c|d].bed.gz$", full.names = T)
+bismark_bedfiles <- list.files(extdata, pattern = "[a|b|c|d].cov.gz$", full.names = T)
+regions <- c(A = "chr1:1-6", B = "chr1:7-10", C = "chr1:11-14")
+
+M <- matrix(c(1, 0, 0, 1,
+              1, 0, 2, 2,
+              0, 2, 0, 0,
+              0, 1, 0, 0,
+              1, 0, 1, 1,
+              2, 0, 0, 0,
+              3, 1, 0, 1),
+            nrow = 7,
+            byrow = TRUE)
+Cov <- matrix(c(1, 2, 0, 1,
+                 1, 0, 2, 2,
+                 2, 2, 0, 0,
+                 1, 1, 2, 1,
+                 2, 0, 1, 2,
+                 2, 2, 0, 0,
+                 3, 1, 0, 1),
+               nrow = 7,
+               byrow = TRUE)
+M_sp <- Matrix(M, sparse = T)
+Cov_sp <- Matrix(Cov, sparse = T)
+row_names <- c("chr1:2", "chr1:4", "chr1:6", "chr1:8", "chr1:10", "chr1:12", "chr1:14")
+col_names <- c("a", "b", "c", "d")
+rownames(M) <- row_names
+colnames(M) <- col_names
+rownames(Cov) <- row_names
+colnames(Cov) <- col_names
+rownames(M_sp) <- row_names
+colnames(M_sp) <- col_names
+rownames(Cov_sp) <- row_names
+colnames(Cov_sp) <- col_names
+
+exp_pos <- seq(1, 13, by = 2)
+exp_seq <- rep("chr1", 7)
+
+set_threads(1)
+biscuit_test <- query_all(biscuit_bedfiles, regions, prealloc = 2)
+bismark_test <- query_all(bismark_bedfiles, regions, aligner = "bismark")
+biscuit_sparse_test <- query_all(biscuit_bedfiles, regions, sparse = T)
+bismark_sparse_test <- query_all(bismark_bedfiles, regions, sparse = T, aligner = "bismark")
+results <- list(biscuit_test, bismark_test, biscuit_sparse_test, bismark_sparse_test)
+
+dense_class <- "matrix"
+sparse_class <- "dgCMatrix"
+
+test_types <- function(result_obj, sparse) {
+
+  if (sparse) {
+    cl <- sparse_class
+  } else {
+    cl <- dense_class
+  }
+
+  expect_equal(class(result_obj), "list")
+  expect_equal(class(result_obj$M)[1], cl)
+  expect_equal(class(result_obj$Cov)[1], cl)
+
+}
+
+test_that("matrix metadata", {
+  test_types(biscuit_test, sparse = F)
+  test_types(bismark_test, sparse = F)
+  test_types(biscuit_sparse_test, sparse = T)
+  test_types(bismark_sparse_test, sparse = T)
+})
+
+test_content <- function(result_obj, sparse) {
+
+  if (sparse) {
+    exp_m <- M_sp
+    exp_c <- Cov_sp
+  } else {
+    exp_m <- M
+    exp_c <- Cov
+  }
+
+  expect_equal(result_obj$M, exp_m)
+  expect_equal(result_obj$Cov, exp_c)
+
+}
+test_that("matrix content", {
+  lapply(results[1:2], test_content, FALSE)
+  lapply(results[3:4], test_content, TRUE)
+})
+
+exp_dims <- c(7, length(biscuit_bedfiles))
+test_dims <- function(result_obj, exp_dims) {
+  expect_equal(dim(result_obj$M), exp_dims)
+  expect_equal(dim(result_obj$Cov), exp_dims)
+}
+
+test_rownames <- function(result_obj) {
+  expect_equal(rownames(result_obj$M), row_names)
+  expect_equal(rownames(result_obj$Cov), row_names)
+  expect_equal(colnames(result_obj$M), col_names)
+  expect_equal(colnames(result_obj$Cov), col_names)
+  expect_equal(result_obj$sampleNames, col_names)
+  expect_equal(result_obj$sampleNames, col_names)
+}
+
+test_that("matrix row,colnames,sampleNames", {
+  lapply(results, test_dims, exp_dims)
+  lapply(results, test_rownames)
+})