Addresses part of issue #18, Allele class refactoring.

[vruano]

More concretely it refactor the Allele class:

• Is now an interface.
• Added several methods to access properties from several allele types like breakends and whole contig insertions.
• Disentangles the current mixture of "display" bytes vs base bytes in the bases array... now only base are stored like that if it applies.
• Adds a "hidden" hierarchy of implementations for different allele subtypes.
• Improves reusing instances for common variants (single base and common symbolic alleles)
• Mark as deprecated several method that seem unnecessary.
• Disable the possibility of changing an allele bases and adds an API (BaseSequence interface) to access these efficiently wihtout the need of cloning a byte[] array each time.
• Makes impossible to create alleles that have invalid base (IUPAC codes that are not allowed by the VCF spec).
• Fixes (and also deprecates) some not well-though Allele method that only make sense for some subtypes of alleles.
• Breakend API, access to contig, position type of breakend and base.

Description

Please explain the changes you made here. Explain the motivation for making this change. What existing problem does the pull request solve?

Checklist

• [x] Code compiles correctly
• [ ] New tests covering changes and new functionality
• [ ] All tests passing
• [x] Extended the README / documentation, if necessary
• [x] Is not backward compatible (breaks binary or source compatibility)

[vruano]

Allele.java diffs rather messy perhaps reviewers should consider to assess it on the changed version of the file and go back to the github diff just report what they don't like.

[vruano]

Current test pass but need to add new ones, please review in the meantime.

[vruano]

I'm adding test code and fixing issues in the code as I come across them, you can start reviewing the first commit only for stability.