Adding support for sequence dictionary extraction and handling.

(1) Adding referenceLength and referenceUrl to the ADAMRecord schema.

ADAMRecord now contains a (flattened) version of the sequence dictionary element
corresponding to each read.

An entire sequence dictionary will be able to be read out of the records associated
with a single BAM or SAM file.

(2) Added SequenceDictionary class

Aggregates a consistent set of SequenceRecord objects into a single dictionary.

SequenceRecords are derived from the reference{Id, Name, Length, Url} fields of the
ADAMRecord.

Most of the work here goes in to providing methods for combining and mapping between
sequence dictionaries, which will be used for cross-BAM or cross-ADAM comparisons.

(3) Extended Bam2Adam to create a SequenceDictionary .dict parquet file

When bam2adam is run on a BAM, we extract the sequence dictionary from the BAM's header
and insert its values into each ADAMRecord.

Also updated the adamBamLoad method in ADAMContext to do something similar, even without
the explicit parquet file.

(4) Adding the ListDict command.

ListDict reads a SequenceDictionary out of a set of ADAMRecords and prints out all the
component SequenceRecord objects contained in it.

(5) Adding the CompareAdam command

CompareAdam is a command that takes two ADAM files as arguments.

It assumes that the same read names are present in *both* input ADAM files --
for example, if the two files were produced by different alignment tools run
on the same set of reads.

It calculates the number of reads that are unique to each ADAM file, as well as
the number of shared reads which have the same alignment position across the two
BAMS.

This position is computed irrespective of the ordering of the Sequences in the
sequence dictionaries of the two ADAM files, and therefore is a useful end-to-end
test of the SequenceDictionary code, as well as being the basis for more useful
pairwise comparisons of ADAM files in the future.

(6) Extending AdamContext with methods to automate the loading of SequenceDictionary
objects out of any conformant Avro schema.
wip first version of ADAMCall
wip tweaking the ADAMCall definition.
Modifying .gitignore, adding test VCF file.
wip revised ADAMCall definition
Updated ADAMCall.genotypeQuality to be a double rather than an int.
Added VCFReader, turns VCF file into a Traversable[ADAMCall].
Added support for an extensible SequenceDictionary usage in VCFReader from a VCF file.