Hi Picard community,
Some major changes to the Picard project will be happening this weekend 3 May -- 4 May. The motivations for these changes are the following:
- More clearly separate API code from programs to provide a compact usable API for next gen sequencing informatics in Java.
- Prepare for the merger of the sam-jdk and cram-jdk codebases.
- Switch from Subversion hosted on Sourceforge to Git hosted on GitHub, to facilitate collaborative software development.
The following changes will be made:
- Picard source will be moving from Sourceforge to GitHub. Picard binaries will continue to be published to Sourceforge.
- The package structure will change:
- There will be two library jars: htsjdk and picard, in contrast to the current organization where sam-jdk, tribble and vcf are in separate jars.
- There will be some movement of code from the current picard package into the htsjdk package.
Other things to be aware of:
- Eventually htsjdk will support other file formats, e.g. CRAM.
- The new source repositories may be unstable for the next 2 weeks or so.
- Legacy source code will still be available on Sourceforge for a while.
These changes should not affect users of the command-line tools, only users of the libraries and source code.
Please let us know if you have questions or concerns.