broadinstitute / hellbender / 213

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Allow reference window in ReferenceContext objects to be set dynamically by tools

Some tools need to dynamically resize the reference context window based upon other
input. This commit exposes a setWindow() method to allow tools to do this.

-To change the reference context size, tools should invoke setWindow() on the
 ReferenceContext provided by the engine before invoking getBases()/getBasesIterator().

-Hopefully eliminates the need for tools to create their own reference readers

-ReferenceContext still caches previous query results, but cache gets invalidated
 every time the window size changes.

Resolves #131

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