[Samtools-announce] Impending move of Picard to GitHub, and Picard restructuring

[Alec W. <al...@br...>]

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: 
htsjdk package will contain SAM, BAM, Tribble and VCF code.  Repository: https://github.com/samtools/htsjdk
picard package will contain command-line tools. Repository: https://github.com/broadinstitute/picard
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.

Thanks, Alec