broadgsa/gatk-protected — pull request #10 by smowton (2014-10-07 16:21:15+00:00)
Title: Improved scatter contigs algorithm to be fairer when splitting many contigs into few parts.

For details see: http://gatkforums.broadinstitute.org/discussion/comment/16010

Note this also impacts passes that split by read, since this is currently deferred to split more conservatively by contig. Passes that accept splits at arbitrary loci are not affected.