From ce954bf8019bd0ab3c043c71398379ca6150e941 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Mon, 11 Sep 2023 13:14:23 +0200
Subject: [PATCH] Adjusted unit tests for #25

---
 tests/testthat/test-greedyMix.R | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/tests/testthat/test-greedyMix.R b/tests/testthat/test-greedyMix.R
index 7a47ec3..ebef7e2 100644
--- a/tests/testthat/test-greedyMix.R
+++ b/tests/testthat/test-greedyMix.R
@@ -33,24 +33,25 @@ test_that("handleData works as expected", {
 
 context("Processing files through greedyMix")
 
-df_fasta <- greedyMix(
+raw_fasta <- importFile(
   data   = file.path(path_inst, "FASTA_clustering_haploid.fasta"),
   format = "FASTA"
 )
-df_vcf <- greedyMix(
+raw_vcf <- importFile(
   data    = file.path(path_inst, "vcf_example.vcf"),
   format  = "VCF",
   verbose = FALSE
 )
-df_bam <- greedyMix(
+df_bam <- importFile(
   data    = file.path(path_inst, "bam_example.bam"),
   format  = "BAM",
 )
+
 test_that("Files are imported correctly", {
-  expect_equal(dim(df_fasta), c(5, 99))
-  expect_equal(dim(df_vcf), c(variants = 2, fix_cols = 8, gt_cols = 3))
+  expect_equal(dim(raw_fasta), c(5, 99))
+  expect_equal(dim(raw_vcf), c(variants = 2, fix_cols = 8, gt_cols = 3))
   expect_error(
-    greedyMix(
+    importFile(
       data    = paste(path_inst, "sam_example.sam", sep = "/"),
       format  = "SAM",
     )
@@ -58,6 +59,15 @@ test_that("Files are imported correctly", {
   expect_equal(length(df_bam[[1]]), 13)
 })
 
+df_fasta <- greedyMix(
+  data   = file.path(path_inst, "FASTA_clustering_haploid.fasta"),
+  format = "FASTA"
+)
+test_that("greedyMix() works", {
+  expect_error(greedyMix(file.path(path_inst, "vcf_example.vcf")))
+  expect_error(greedyMix(file.path(path_inst, "bam_example.bam")))
+})
+
 context("Linkage")
 
 test_that("Linkages are properly calculated", {