Restore basic form of Genome::File::Vcf even though read/write ops move out.

(This class is still referenced in the build input table!)
separate CreateCrossSampleVcf into an indel and snv version
fix the use_ok to test the correct module
Changed VarScan default version to v2.3.6
Updated blessed builds for tabix indexing vcf changes
Merge branch 'master' into gb_master
Make test name more descriptive
New test data for indels

Hand curated the diffs due to switching to varscan 2.3.6 as the default.
Updated test data for create-cross-sample-vcf

Hand curated the diffs due to switching to varscan 2.3.6 as the default.
Updated test data for varscan consensus

Hand curated the diffs due to switching to varscan 2.3.6 as the default.
build view finds all software results for a build

Instead of using ->results we now use ->all_results which has the
advantage of finding results that use other results not just results
that the build was using
fully qualify name of find method
Rearranged directory structure for chimerascan

The old structure was messy and didn't clearly segregate chimerascan
from any of the other detectors.  We want to add additional chimerascan
related code here like the filtering that is always done after
chimerascan is run but in the old structure it wasn't clear where to put
it.
Deduplicate logic surrounding Chimerascan commands

The old vanilla Chimerascan and ChimerascanVrl differ but the commands
are essentially identical, so the command logic was pulled into a base
class.
Fix weird lib managment
Cleaned up command directory in rnaseq
Rearrange directory structure for Chimerascan Commands
Reimagined directory structure yet again
Pull decision logic out of RnaSeq Model

DetectFusions command now determines what commands to fire off to do
fusion detection based on the parameters it is passed.
Make Result directory structure echo Command structure