[TEST] Adding cli tests for detect_breakends.

test/cli/CMakeLists.txt

@@ -7,5 +7,9 @@ add_cli_test(find_deletions_cli_test.cpp)
 add_dependencies (find_deletions_cli_test "find_deletions")
 target_use_datasources (find_deletions_cli_test FILES detect_breakends_shorted.vcf)
 
+add_cli_test(detect_breakends_cli_test.cpp)
+add_dependencies (detect_breakends_cli_test "detect_breakends")
+target_use_datasources (detect_breakends_cli_test FILES converted_bam_shorted.sam)
+
 # add_cli_test (iGenVar_options_test.cpp)
 # target_use_datasources (iGenVar_options_test FILES in.fastq)

test/cli/detect_breakends_cli_test.cpp

@@ -0,0 +1,70 @@
+#include <seqan3/alphabet/nucleotide/dna5.hpp>
+#include <seqan3/io/sequence_file/input.hpp>
+
+#include "cli_test.hpp"
+#include <fstream>
+#include <sstream>
+TEST_F(cli_test, no_options)
+{
+    cli_test_result result = execute_app("detect_breakends");
+    std::string expected
+    {
+            "detectJunctions - Detect junctions in a read alignment file\n"
+            "===========================================================\n"
+            "    Try -h or --help for more information.\n"
+    };
+    EXPECT_EQ(result.exit_code, 0);
+    EXPECT_EQ(result.out, expected);
+    EXPECT_EQ(result.err, std::string{});
+}
+
+TEST_F(cli_test, fail_no_argument)
+{
+    cli_test_result result = execute_app("detect_breakends", "-v");
+    std::string expected
+    {
+        "[Error] Unknown option -v. In case this is meant to be a non-option/argument/parameter, please specify "
+        "the start of non-options with '--'. See -h/--help for program information.\n"
+    };
+    EXPECT_NE(result.exit_code, 0);
+    EXPECT_EQ(result.out, std::string{});
+    EXPECT_EQ(result.err, expected);
+}
+
+
+TEST_F(cli_test, with_arguments)
+{
+    cli_test_result result = execute_app("detect_breakends",
+                                         data("converted_bam_shorted.sam"),
+                                         "detect_breakends_insertion_file_out.fasta");
+    std::string expected
+    {
+        "Reference\tchr9\t70103073\tForward\tReference\tchr9\t70103147\tForward\tm13802/6999/CCS\n"
+    };
+    std::string expected_err
+    {
+        "DEL: Reference\tchr9\t70103073\tForward\tReference\tchr9\t70103147\tForward\tm13802/6999/CCS\nDone. Found 1 junctions.\n"
+    };
+    EXPECT_EQ(result.exit_code, 0);
+    EXPECT_EQ(result.out, expected);
+    EXPECT_EQ(result.err, expected_err);
+}
+
+TEST_F(cli_test, test_outfile)
+{
+    cli_test_result result = execute_app("detect_breakends",
+                                         data("converted_bam_shorted.sam"),
+                                         "detect_breakends_insertion_file_out.fasta");
+    std::ifstream f;
+    f.open("detect_breakends_insertion_file_out.fasta");
+    std::stringstream buffer;
+    buffer << f.rdbuf();
+    //expected string currently empty:
+    std::string expected
+    {
+	    ""
+    };
+    //this does not specifically check if file exists, rather if its readable.
+    EXPECT_TRUE(f.is_open());
+    EXPECT_EQ(buffer.str(), expected);
+}