bug fix: now contigs not present in the sequence dictionary are registered properly and do not cause the script to break
bug fix: now contigs not present in the sequence dictionary are registered properly and do not cause the script to break

git-svn-id: 4561c0a8f080806b19201efb9525134c00b76d40@3623 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