Add JVM methods

[btmonier]

This PR adds the following:

Class and function additions

• Added JVM connections via rJava interface
• Added new class, HaplotypeGraph
  • Wrapper for PHGv2 API Java graph object
• Added new class, PHGLocalCon
  • Interface to local hVCF database and file connections
• Added new function initPHG()
  • Initializes JVM and adds PHGv2 Java JARs to classpath
• Added new function readHapIds()
  • Reads haplotype IDs as a character matrix from a connection object
• Added new function readHapIdMetaData()
  • Reads ALT header metadata for each haplotype ID from a connection object
• Added new function readHapIdPosMetaData()
  • Reads ALT header positional metadata for each haplotype ID from a
    connection object
• Added new function readSamples()
  • Reads sample IDs from a connection object
• Added new function readRefRanges()
  • Read reference range positional information as a GRanges object from a
    connection object

Infrastructure

• Added new script setupt.R for CI/CD testing:
  • Leverages the GitHub API to retrieve the latest PHGv2 release which removes the need to bundle Java JARs in the source code for testing
  • Globally initializes the JVM and adds relevant PHGv2 JARs to classpath for all downstream tests