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KSW2 Test suite

  1. Clone and modify cli.c from https://github.com/lh3/ksw2 so that you can call your own kernels, e.g., extd2. Compiling this code produces the executable ksw2-test.

  2. Generate a test suite using

python3 generate_test_suite.py

This script will generate random data with a fixed seed for different alignment lengths. Modify this script to build your own test suites. In the current test suite, the "giant" test crashes ksw2-test due to insufficient memory. To overcome this issue, specify the bandwidth -w argument.

  1. Once you have generated data, run:
./run_test_suite.sh

Simply running the command in bash will show usage instructions.For example,

KSW2ID=reference ./run_test_suite.sh test_suite -t extd2_sse

will run ksw2_test for all tests in test_suite using the kernel extd2_sse (this name depends on how cli.c is configured). Run it using your own kernel by passing the name of your kernel to run script, e.g.,

./run_test_suite.sh test_suite -t extd2

By omitting, KSW2ID, the script will automatically create a output directory for you.

  1. Given both reference runs and your own runs, compare the two via
./compare_test_suite.sh myrun reference

Code coverage

To produce a code coverage report for ksw2_test, first compile with coverage enabled:

make coverage=y

Run the executable one or more times

./ksw2_test ..

Each time executable runs, code coverage data will be collected. To compile this data into a html report, use:

make report

This report is written to the directory coverage.

Code coverage script

The script coverage.sh is designed to run ksw2_test multiple times to take all branches inside a kernel. This script can be used in conjunction with the run_test_suite script as follows:

 KSW2ID=extd2_cpp KSW2=./coverage.sh ./run_test_suite.sh test_suite -t extd2_cpp # test
 KSW2ID=extd2_sse KSW2=./coverage.sh ./run_test_suite.sh test_suite -t extd2_sse # reference

Set KSW2COV if the main executable is not ./ksw2-test. Use the comparison script as before,

./compare_test_suite.sh extd2_cpp extd2_sse

To design your own code coverage tests, put one or more calls to ksw2-test in a script. See coverage.sh for an example.