Simplifications: removed command-line arguments to control SNP cluster filter parameters.  Infer the number of contigs to scatter indel cleaning from the contig list (which we should get rid of too).  Changed the PY argument to just Y for specifying the path to the YAML file.  Cleaned up command-line argument documentation.  See http://iwww.broadinstitute.org/gsa/wiki/index.php/Queue-based_pipeline for a list of remaining issues.
Simplifications: removed command-line arguments to control SNP cluster filter parameters.  Infer the number of contigs to scatter indel cleaning from the contig list (which we should get rid of too).  Changed the PY argument to just Y for specifying the path to the YAML file.  Cleaned up command-line argument documentation.  See http://iwww.broadinstitute.org/gsa/wiki/index.php/Queue-based_pipeline for a list of remaining issues.

git-svn-id: 4561c0a8f080806b19201efb9525134c00b76d40@4356 348d0f76-0448-11de-a6fe-93d51630548a

iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable