Merge of new VCF features

Command line script, modules and tests to write multiple Fluidigm/Sequenom CSV files into a single VCF file, and run a consistency check between samples using bcftools. A plex manifest, and JSON file listing chromosome lengths are required. Input files may be in iRODS or the local filesystem. In the former case, the manifest and chromosome files can be found using iRODS metadata.

VCF tests require the bcftools module version 0.2.0-rc9 to run: /software/gapi/Modules/apps/bcftools/0.2.0-rc9
"load bcftools" has been added to the Jenkins config for genotyping tests.