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Tests

This document explains how to run HAlign-4 tests under the test/ directory.

HAlign-4 uses doctest for unit tests and CTest for registration.

1. Quick start (recommended)

Use the helper script:

cd test
./run_tests.sh -t Release -j 8

What it does:

  • configures the test build into build-test/ (or your chosen -B directory)
  • builds the test binaries
  • runs ctest (verbose by default)

2. Common workflows

2.1 Run a single CTest test by name

Example: run the align test only:

cd test
./run_tests.sh -t Release -- -- -R align

(Everything after -- is passed to ctest.)

2.2 Enable perf tests

Some tests are heavier and are guarded by an environment variable.

cd test
./run_tests.sh -t Release --perf

This sets:

  • HALIGN4_RUN_PERF=1

2.3 Build directory management

To build tests into a custom directory:

cd test
./run_tests.sh -B ../build-test-release -t Release -j 16

To clean rebuild:

cd test
./run_tests.sh --clean -t Release

3. Run CTest directly (advanced)

If you already have a configured build directory:

ctest --test-dir build-test -V

4. Using test/data as example inputs

The repository includes small datasets that are useful for smoke tests and documentation examples:

  • test/data/mt1x.fasta.gz (minimal dataset)
  • test/data/covid-ref.fasta.gz / test/data/covid-test.fasta.gz

For runnable CLI examples, see docs/usage.md.