From 53612c023787fbaa3721a28b768ce925d952e905 Mon Sep 17 00:00:00 2001
From: Yang-Yang Feng <yanyang.f@gmail.com>
Date: Tue, 26 Mar 2019 14:04:46 -0500
Subject: [PATCH] add tests

---
 tests/integration-test/test_junctions_extract.py     | 12 ++++++++++++
 .../test_cis_splice_effects_identifier.cc            | 11 +++++++++++
 2 files changed, 23 insertions(+)

diff --git a/tests/integration-test/test_junctions_extract.py b/tests/integration-test/test_junctions_extract.py
index d01f3b9..645a082 100755
--- a/tests/integration-test/test_junctions_extract.py
+++ b/tests/integration-test/test_junctions_extract.py
@@ -90,6 +90,18 @@ def test_no_bam(self):
         rv, err = self.execute(params)
         self.assertEqual(rv, 1)
 
+    def test_missing_bam(self):
+        output_file = self.tempFile("extract.out")
+        params = ["junctions", "extract", "-s 0", "-o", output_file, "does_not_exist.bam"]
+        rv, err = self.execute(params)
+        self.assertEqual(rv, 1)
+
+    def test_no_strandness(self):
+        output_file = self.tempFile("extract.out")
+        params = ["junctions", "extract", "-o", output_file]
+        rv, err = self.execute(params)
+        self.assertEqual(rv, 1)
+
     def test_help(self):
         output_file = self.tempFile("extract.out")
         params = ["junctions", "extract", "-h"]
diff --git a/tests/lib/cis-splice-effects/test_cis_splice_effects_identifier.cc b/tests/lib/cis-splice-effects/test_cis_splice_effects_identifier.cc
index 49c4341..29a454c 100644
--- a/tests/lib/cis-splice-effects/test_cis_splice_effects_identifier.cc
+++ b/tests/lib/cis-splice-effects/test_cis_splice_effects_identifier.cc
@@ -62,6 +62,17 @@ TEST_F(CisSpliceEffectsIdentifierTest, ParseInput3) {
     EXPECT_THROW(csei1.parse_options(argc, argv), common::cmdline_help_exception);
 }
 
+//Check for missing files
+TEST_F(CisSpliceEffectsIdentifierTest, ParseInput5) {
+    int argc = 5;
+    char * argv[] = {"identify",
+                     "test_does_not_exist.vcf",
+                     "test.fa",
+                     "test.gtf",
+                     "test.bam"};
+    EXPECT_THROW(csei1.parse_options(argc, argv), std::runtime_error);
+}
+
 //Test if constructor works as expected.
 TEST_F(CisSpliceEffectsIdentifierTest, ConstructorTest) {
     EXPECT_EQ(csei1.vcf(), "NA");