test(query): test tabix colnames - bismark, mergecg, colname warnings

inst/extdata/tabix_dataframe_bismark.test

@@ -0,0 +1,8 @@
+"chr","start","end","methylation.percentage","count.methylated","count.unmethylated"
+"chr1",1,1,100,1,0
+"chr1",3,3,100,1,0
+"chr1",5,5,0,0,2
+"chr1",7,7,0,0,1
+"chr1",9,9,50,1,1
+"chr1",11,11,100,2,0
+"chr1",13,13,100,3,0

tests/testthat/test-query.R

@@ -1,8 +1,11 @@
 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)
+biscuit_tabix_beds <- list.files(extdata, pattern = "[a|b|c|d].bed.gz$", full.names = T)
+bismark_tabix_beds <- list.files(extdata, pattern = "[a|b|c|d].cov.gz$", full.names = T)
 tabix_df_result <- list.files(extdata, pattern = "tabix_dataframe.test", full.names = T)
+tabix_df_result_bismark <- list.files(extdata, pattern = "tabix_dataframe_bismark.test", full.names = T)
+mergecg_bed <- list.files(extdata, pattern = "*_mergecg.bed.gz$", 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")
 
@@ -21,14 +24,18 @@ test_that("query_chroms", {
 
 test_that("tabix dataframe", {
   expect_equal(
-    tabix(tabix_beds[1], regions),
-    fread(tabix_df_result, colClasses = c("character", "integer", "integer", "numeric", "integer"))
+    tabix(biscuit_tabix_beds[1], regions),
+    fread(tabix_df_result, colClasses = c("character", "numeric", "numeric", "numeric", "numeric"))
+  )
+  expect_equal(
+    tabix(bismark_tabix_beds[1], regions, aligner = 'bismark'),
+    fread(tabix_df_result_bismark, colClasses = c("character", "numeric", "numeric", "numeric", "numeric", "numeric"))
   )
 })
 
 test_that("tabix raw list", {
   expect_equal(
-    tabix(tabix_beds[3], regions, raw = T),
+    tabix(biscuit_tabix_beds[3], regions, raw = T),
     tabix_raw_res
   )
 })
@@ -39,3 +46,47 @@ test_that("tabix dataframe", {
     "No records found"
   )
 })
+
+test_that("tabix > 1 file", {
+  expect_error(
+    tabix(chrom_beds, regions),
+    "Cannot tabix multiple files - only single-file queries are currently supported"
+  )
+})
+
+custom_cols <- paste0("c", 1:5)
+test_that("tabix custom colnames", {
+  expect_equal(
+    colnames(tabix(chrom_beds[1], regions, colnames = custom_cols)),
+    custom_cols
+  )
+})
+
+custom_cols <- paste0("c", 1:6)
+test_that("tabix custom colnames too many", {
+  expect_warning(
+    tabix(chrom_beds[1], regions, colnames = custom_cols),
+    "Fewer columns in data than provided colnames"
+  )
+})
+
+custom_cols <- paste0("c", 1:4)
+test_that("tabix custom colnames too few", {
+  expect_warning(
+    tabix(chrom_beds[1], regions, colnames = custom_cols),
+    paste("Did not use input 'colnames' - only", length(custom_cols), "names provided for 5 column data.table")
+  )
+})
+
+
+base_colnames <- c("chr", "start", "end")
+biscuit_colnames <- c("beta", "coverage")
+bismark_colnames <- c("methylation.percentage", "count.methylated", "count.unmethylated")
+test_that("tabix mergecg colnames", {
+  expect_equal(
+    colnames(tabix(mergecg_bed, regions, aligner = "biscuit")),
+    c(base_colnames, biscuit_colnames, "mergecg")
+  )
+})
+
+