Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

How to access the picard-public repository (containing sam-jdk, picard, tribble, and variant)

droazendroazen Posts: 48GSA Member mod
edited April 2013 in Developer Zone

The picard-public repository on sourceforge, in addition to housing the sam-jdk and picard-public, is now home to tribble and the org.broadinstitute.variant package (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:

svn checkout svn://svn.code.sf.net/p/picard/code/trunk picard-public

Then you can attach the picard-public/src/java directory 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, sam-jdk, tribble, and org.broadinstitute.variant all at once, type ant from within the picard-public directory. To run tests, type ant test

If you do need to make commits into the picard repository, first you'll need to create a sourceforge account, then contact the Picard team and request access for that account. Once you've been given access, you'll need to check out their repository using a command of this form:

svn checkout --username=YOUR_USERNAME svn+ssh://YOUR_USERNAME@svn.code.sf.net/p/picard/code/trunk picard-public
Post edited by Geraldine_VdAuwera on

Comments

  • tguchtguch BostonPosts: 3Member

    I was actually able to find the VCF files in this path GenomeAnalysisTK-2.6-5\GenomeAnalysisTK-2.6-5-gba531bd\GenomeAnalysisTK\org\broadinstitute\variant\vcf and I changed the path location in the code, but it still can't seem to find or recognize it. Do you happen to know why this is and how to fix it?

    Thanks!

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