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SeqAn

  • Q: I'd like to participate. How do I begin?

    • 0

      You can start by reading the tutorial, especially the Getting Started section. This will describe how to download the source code using Subversion and compile it with a C++ compiler.

      http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial
      http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/GettingStarted

      The next thing to do is probably to subscribe to our mailing list.

      https://lists.fu-berlin.de/listinfo/seqan-dev

      Then, have a look at the currently open tickets or our current nightly documentation and look for problems there.

      http://trac.mi.fu-berlin.de/seqan/report/3
      http://www.seqan.de/dddoc/html_devel/

      You can also write an email to the mailing list to introduce yourself and ask for mentoring on problems.

      Fixing bugs/tickets involves three points: (1) Send an email to the mailing list, tell us that you want to help out and ask for any directions you might need. (2) We will point you in the right direction and/or give you any help you might need. (3) You fix the problem with any mentoring you need and submit a patch through the bug tracker.

      Fixing documentation problems can involve two things (most often, it's (a), though): (a) Go into the source and fix the documentation entries in the source code comments. (b) The documentation build system (written in Python) is broken and needs fixing.


         — Manuel Holtgrewe (Manuel) · 6 years ago
    • [X]

      • Tip:

        Talk about diverse kinds of contributions. Include URLs if relevant (we'll automatically linkify them).

      • Examples:

        Here's how to download and patch our codes…

        Read about our death-defying mailing list and momentous IRC channel at http://lobstermag.net.

  • Q: Other than writing code, how can I contribute?

  • Q: What's a good bug for a newcomer to tackle?

    • 0
      Complain About Bugs/Missing Documentation

      Use our library and tell us where it is lacking in documentation and bugs.


         — Manuel Holtgrewe (Manuel) · 6 years ago
    • 0
      Write Examples/Demos

      Lots of code does not have examples in their documentation. Have a look at how to include examples in the documentation. You can see how to include examples by grepping for ".example.code" to find places where examples were included.

      Then, pick functions where there are not yet any examples and add some. You might want to ask on the mailing list for us to point out areas with weaker examples.

      Also, we could use more demos of the library's functionality. Look into the demos folders to see other examples and ask on the mailing list for things that could need a demo.


         — Manuel Holtgrewe (Manuel) · 6 years ago
    • 0
      Write Tests

      We could use more tests!

      Ask on the mailing list for pointers on the areas that could use tests and which kind of tests are appropriate.


         — Manuel Holtgrewe (Manuel) · 6 years ago
    • 0
      Missing File Parsers

      Is there a bioinformatics format that you need that is not yet available in SeqAn? Tell us about it and maybe ask for directions on how to implement it yourself!


         — Manuel Holtgrewe (Manuel) · 6 years ago
    • [X]

      • Tip:

        Many projects have good small tasks that can teach newcomers how the project works. Now's your chance to share one of them!

        Include URLs if relevant (we'll automatically linkify them).

      • Example:

        Someone could improve the photo upload dialog box so that it lets you resize the photo before sending it to the web.

  • Q: What is a bug or issue with SeqAn that you've been putting off, neglecting, or just plain avoiding?

    • 0
      Refactor Documentation System

      The current documentation system (dddoc) works okay but could need a lot of maintainance. Also, it should probably be refactored/rewritten to ease maintenance.


         — Manuel Holtgrewe (Manuel) · 6 years ago
    • 0
      Banded Chain Alignment

      The banded chain alignment algorithm in the new seeds2 module is not working correctly.

      Fixing it requires to understand the algorithm and all corner cases, fixing it and testing it comprehensively.


         — Manuel Holtgrewe (Manuel) · 6 years ago
    • [X]

      • Examples:

        I don't know how to get started with internationalizing my app.

        Bug 392 about printing was filed five years ago, and I don't even know if printing still works.

        I want help from a C coder writing a Maildir patch for Alpine.

      • Note:

        If this issue was formally filed on the web, be sure to include the URL.

What else do you want to talk about?

About SeqAn

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SeqAn is the C++ template library for biological sequence analysis. It features algorithms and data structures to build efficient bioinformatics tools.

from the profile of Manuel Holtgrewe (Manuel)

The code is mostly written in C++.

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There are 157 people who can mentor in C++, SeqAn's primary language.

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