Better support for comparison to truth.  Now emits FP rates for each covariate if a truth file is provided.  Also now writes out a detailed recal.log file that can be parsed directly into R
Better support for comparison to truth.  Now emits FP rates for each covariate if a truth file is provided.  Also now writes out a detailed recal.log file that can be parsed directly into R

git-svn-id: 4561c0a8f080806b19201efb9525134c00b76d40@2179 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