[TEST] Adding cli tests for detect_breakends. #19
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| 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); |
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without these lined the cli tests won't work.
| // EXPECT_EQ(result.err, "Conversion was a success. Congrats!\n"); | ||
| // } | ||
| // | ||
| // there is no file output option for "detect_breakends" |
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An output option would be nice, I will add an issue for that.
| EXPECT_EQ(result.err, expected_err); | ||
| } | ||
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| // There is no verbose mode for "detect_breakends". |
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If we want a verbose option, needs a discussion. I will add an issue.
|
The problem why this doesn't work is, because you didn't say that the test for the --------------------------- test/cli/CMakeLists.txt ---------------------------
index 9665c48..61e3237 100644
@@ -2,8 +2,9 @@ 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)fixes this... |
simonsasse
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If this change fixes the build problems, I'll apply it toe the other PR: #22 |
| { | ||
| cli_test_result result = execute_app("detect_breakends", | ||
| data("converted_bam_shorted.sam"), | ||
| "detect_breakends_out_short_10.fasta"); |
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Is this an output file? If yes then its content should also be checked.
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Oh, yes you're right.
I just see that there is an output in the std::out and one in a .fasta file.
Could you rename it into:
| "detect_breakends_out_short_10.fasta"); | |
| "detect_breakends_insertion_file_out.fasta"); |
But I think with our small example the file is empty. I will try to figure out a better example, that we can check the content aswell.
Perhaps you are now testing whether the file is empty so that the content check is already there and we just have to adjust it later.
| { | ||
| cli_test_result result = execute_app("detect_breakends", | ||
| data("converted_bam_shorted.sam"), | ||
| "detect_breakends_out_short_10.fasta"); |
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Oh, yes you're right.
I just see that there is an output in the std::out and one in a .fasta file.
Could you rename it into:
| "detect_breakends_out_short_10.fasta"); | |
| "detect_breakends_insertion_file_out.fasta"); |
But I think with our small example the file is empty. I will try to figure out a better example, that we can check the content aswell.
Perhaps you are now testing whether the file is empty so that the content check is already there and we just have to adjust it later.
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I am not sure about the
TEST_F(cli_test, with_arguments).It failed when I had just the result.out and then I added the result.err
I don't know why this is necessary. I think it should not produce any errors here right ?