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Old 11-08-2012, 09:11 AM   #1
Ashreid
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Location: Germany

Join Date: Jun 2012
Posts: 1
Default Contributions to the source

Is there a list of new features requested or bugs that need to be fixed. How would developers contribute if the were just getting involved on some volenteer part time basis?
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Old 11-20-2012, 06:53 PM   #2
leecbaker
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Hello Ashreid,

We would love to have more people contributing to the codebase.

Getting started, I would first make sure you can:
  • Clone the source from github and build openge (See the developer docs for compilation instructions)
  • Run the tests (make test)
  • Branch the source so you have something to develop against

We don't have a public list of features and bugs to work on, but here are a couple of things off the top of my head:
  • Add additional testing. Most of the built in tests simply execute openge with valid inputs, but don't check the output of tests. More robust testing would be useful to us. Check out run.sh from this test that I just checked in for an example: here

    I have been meaning to verify that we have full test coverage for both SAM and BAM inputs, being passed in as a filename, as well as piped into OpenGE. A good test (or set of tests) would verify that we can run:
    Code:
    cat asdf.bam | ./openge count
    just as well as
    Code:
    ./openge asdf.bam
    or
    Code:
    ./openge count < asdf.bam.
    Complete test coverage of all input types would be helpful; IO code is where we find the most bugs currently.
  • The CMake build system supports building packages for linux platforms (see here). It would be great if we could build .deb and .rpm packages with a command that included the appropriate binary and referenced necessary dependencies.
  • Additional features. If you're interested on working on additional features, we will need to coordinate with David (adaptivegenome). He's the guy in charge of deciding what goes into openge.

If you have patches to contribute, please branch the openge source on github and submit a pull request with your modifications and we'll have a look.

-Lee
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