Adding RichADAMRecord.referenceLengthFromCigar

The new referenceLengthFromCigar method (and its associated ADAMRecord method, 'referenceLength')
is an implementation of a method which counts the length of an aligned read against the reference
sequence. This is useful because rec.start + rec.referenceLength is a logical "end" coordinate
to be used for testing overlap of an ADAMRecord against a reference range.
Merge pull request #263 from genomebridge/tdanford/referenceLengthFromCigar

Added AdamContext.referenceLengthFromCigar
.gitignore should _not_ ignore .vcf files
ADAMFlatGenotype is a smaller, flat, simpler version of a genotype schema.

Also:
1. Added support for missing genotypes in the VCFLineConverter for ADAMFlatGenotype.
2. Added a ReferenceMapping for the ADAMFlatGenotype
3. the flat genotype converter uses multiple writers for smaller output files.
Changed the argument 'bamFile' to 'vcfFile' in Vcf2FlatGenotype
Added comments to Vcf2FlatGenotype

Also, removed some extraneous imports.