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The picard repository on github contains all picard public tools. Libraries live under the htsjdk, which includes the samtools-jdk, tribble, and variant packages (which includes VariantContext and associated classes as well as the VCF/BCF codecs).
If you just need to check out the sources and don't need to make any commits into the picard repository, the command is:
Then within the picard directory, clone the htsjdk.
cd picard git clone https://github.com/samtools/htsjdk.git
Then you can attach the
picard/htsjdk/src/java directories in IntelliJ as a source directory (File -> Project Structure -> Libraries -> Click the plus sign -> "Attach Files or Directories" in the latest IntelliJ).
To build picard and the htsjdk all at once, type
ant from within the picard directory. To run tests, type
If you do need to make commits into the picard repository, first you'll need to create a github account, fork picard or htsjdk, make your changes, and then issue a pull request. For more info on pull requests, see: https://help.github.com/articles/using-pull-requests