Extended API for symbolic alleles

[d-cameron]

Extending the htsjdk to parse symbolic alt alleles and return meaningful Alleles based on the parsed result would be useful to structural variation users of the API. In particular the following features would be useful:

• separation of symbolic alleles into named structural variations, named contig insertions (both with sequence such as "A" and without ""), breakends and breakpoints
• methods to expose the parsed breakpoint contig, position, directions
• incorporation of all 31 SV headers into VCFStandardHeaderLines (or split out into VCFStructuralVariationHeaderLines)
• methods to return the base call portions of symbolic alleles (ie: extract the ACGT from ACGT[chr1:1[ )

One possible design is to subclass Allele:
abstract Allele
Allele <- BaseCallAllele
Allele <- SymbolicAllele
Allele <- NoCallAllele
Allele <- MissingAllele
SymbolicAllele <- StructuralVariationAllele (with enum, subclass hierarchy or getters for SV type and subtypes (subsubtypes?) such as and DUP:TANDEM)
SymbolicAllele <- BreakendAllele
SymbolicAllele <- BreakpointAllele
SymbolicAllele <- NamedContigAllele

The low-level design and implementation depends on resolution of ambiguities in the VCF specifications as the are multiple points in which the VCF specifications are under-defined and ambiguous. For example, it is unclear as to whether "AA", "", "AA" are valid alleles.