[TEST] Adding cli tests for detect_breakends.

test/cli/CMakeLists.txt

@@ -3,5 +3,8 @@ cmake_minimum_required (VERSION 3.8)
 add_cli_test (fastq_to_fasta_options_test.cpp)
 target_use_datasources (fastq_to_fasta_options_test FILES in.fastq)
 
+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 +1,87 @@
+#include <seqan3/alphabet/nucleotide/dna5.hpp>
+#include <seqan3/io/sequence_file/input.hpp>
+
+#include "cli_test.hpp"
+
+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_out_short_10.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);
+}
+
+// There is no verbose mode for "detect_breakends".
+//
+// TEST_F(cli_test, with_argument_verbose)
+// {
+//     cli_test_result result = execute_app("detect_breakends",
+//                                          data("converted_bam_shorted.sam"),
+//                                          data("detect_breakends_out_short_10.fasta"),
+//                                          "-v");
+//     EXPECT_EQ(result.exit_code, 0);
+//     EXPECT_EQ(result.out, result);
+//     EXPECT_EQ(result.err, "Conversion was a success. Congrats!\n");
+// }
+//
+// there is no file output option for "detect_breakends"
+//
+// TEST_F(cli_test, with_out_file)
+// {
+//     cli_test_result result = execute_app("detect_breakends",
+//                                          data("converted_bam_shorted.sam"),
+//                                          data("detect_breakends_out_short_10.fasta"),
+//                                          );
+//     seqan3::sequence_file_input fin{"out.fasta", seqan3::fields<seqan3::field::seq, seqan3::field::id>{}};
+//
+//    // create records to compare
+//     using record_type = typename decltype(fin)::record_type;
+//     using seqan3::operator""_dna5;
+//     std::vector<record_type> records{};
+//     records.emplace_back("ACGTTTGATTCGCG"_dna5, std::string{"seq1"});
+//     records.emplace_back("TCGGGGGATTCGCG"_dna5, std::string{"seq2"});
+//
+//     EXPECT_RANGE_EQ(fin, records);
+//     EXPECT_EQ(result.exit_code, 0);
+//     EXPECT_EQ(result.out, std::string{});
+//     EXPECT_EQ(result.err, std::string{});
+// }
+//
+