test(query): add tests for tabix

inst/extdata/tabix_dataframe.test

@@ -0,0 +1,8 @@
+"chr","start","end","beta","coverage"
+"chr1",1,2,1.000,1
+"chr1",3,4,1.000,1
+"chr1",5,6,0.000,2
+"chr1",7,8,0.000,1
+"chr1",9,10,0.500,2
+"chr1",11,12,1.000,2
+"chr1",13,14,1.000,3

tests/testthat/test-query.R

@@ -1,11 +1,41 @@
-extdata <- system.file("extdata/test_chroms", package = "iscream")
-bedfiles <- list.files(extdata, pattern = "*.bed.gz$", full.names = T)
+library(data.table)
+extdata <- system.file("extdata", package = "iscream")
+chrom_beds <- list.files(paste0(extdata, "/test_chroms"), pattern = "*.bed.gz$", full.names = T)
+tabix_beds <- list.files(extdata, pattern = "*.bed.gz$", full.names = T)
+tabix_df_result <- list.files(extdata, pattern = "tabix_dataframe.test", full.names = T)
 chrs <- sort(paste0("chr", c(seq(1:22), "M", "X", "Y")))
+regions <- c(A = "chr1:1-6", B = "chr1:7-10", C = "chr1:11-14")
+
+tabix_raw_res <- list(
+    `chr1:1-6` =  c("chr1\t3\t4\t1.000\t2"),
+    `chr1:7-10` = c("chr1\t7\t8\t0.000\t2", "chr1\t9\t10\t1.000\t1"),
+    `chr1:11-14` = character(0)
+)
 
 test_that("query_chroms", {
   expect_equal(
     chrs,
-    query_chroms(bedfiles)
+    query_chroms(chrom_beds)
+  )
+})
+
+test_that("tabix dataframe", {
+  expect_equal(
+    tabix(tabix_beds[1], regions),
+    fread(tabix_df_result, colClasses = c("character", "integer", "integer", "numeric", "integer"))
   )
 })
 
+test_that("tabix raw list", {
+  expect_equal(
+    tabix(tabix_beds[3], regions, raw = T),
+    tabix_raw_res
+  )
+})
+
+test_that("tabix dataframe", {
+  expect_warning(
+    tabix(chrom_beds[2], regions),
+    "No records found"
+  )
+})