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CONTRIBUTING.md

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Contributing

Contributions to strobealign are very welcome!

  • To report a bug, open an issue.
  • To suggest a small change, just submit a pull request.
  • To suggest a larger change, it may be a good idea to first open an issue or to send an e-mail so we can discuss it.

Instead of one large PR, consider submitting multiple small, logically self-contained PRs if it makes sense. This facilitates review and allows for a more focused discussion.

Debugging

When compiling strobealign, you can add -DCMAKE_BUILD_TYPE=RelWithDebInfo to the cmake options to get debug symbols.

If needed, run make with VERBOSE=1 to get more logging output at build time.

To get more logging output when running strobealign, add the -v option to the command line.

Add --details to get more detailed SAM output with some strobealign-specific tags added to each alignment record. (See below.)

To get even more verbose output, add -DTRACE=ON to your CMake options and re-compile strobealign. This outputs a list of the found NAMs for each read.

Testing

After CMake has been run, you can use this one-liner to compile strobealign and run the tests:

make -s -j -C build && tests/run.sh

Whenever you make changes that could potentially affect mapping results, you can run a more elaborate test that compares strobealign against a “baseline” (know good) commit. Just run this script:

tests/compare-baseline.sh

The first time, it will download a D. melanogaster genome and some reads from the Sequence Read Archive (SRA). Since the dataset is truncated to the first 100'000 reads, mapping it should take less than 30 seconds.

The baseline commit is configured in tests/baseline-commit.txt. The script builds strobealign from that commit and runs it against the downloaded test data, then builds strobealign as it is in your working copy and compares the two produced BAM files. The baseline BAM is cached and re-used as long as the baseline commit does not change.

Making a release

  • Update changelog (adjust section header)
  • Bump version in CMakeLists.txt
  • Bump version in setup.py
  • Commit
  • Push and wait for CI to pass
  • Do git tag ... and git push --tags
  • Make a release via the GitHub releases page
  • Wait for the Bioconda bot to pick up the new release and then approve its version bump PR

Style guide

Existing code in strobealign is currently not necessarily consistent with this style guide, but new code should follow it.

  • Use the clang-format code formatter with the -style=file option.
  • Use Python-like naming of functions, methods, variables, etc. That is, it should be ClassName, variable_name, method_name, CONSTANT.
  • The header guard of a file named xyz.hpp should be named STROBEALIGN_XYZ_HPP.

Detailed SAM output (--details)

When --details is provided, the following additional SAM tags are output for mapped reads.

na: Number of NAMs (seeds) found nr: Whether NAM rescue was needed (1 if yes, 0 if not) mr: Number of times mate rescue was attempted (local alignment of a mate to the expected region given its mate) al: Number of times an attempt was made to extend a seed (by gapped or ungapped alignment) ga: Number of times an attempt was made to extend a seed by gapped alignment X0: Number of equally scored best alignments (greater than 1 for multimappers). For paired-end reads, the tag is output for both reads, but the value is identical and is the number of equally scored best alignment pairs.