broadinstitute / hellbender / 160

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Port most existing hellbender tools to ReadWalker interface

-CompareSAMs not ported because ReadWalker traversal is not suited
 for it

-SplitNCigarReads not ported because of the way it uses the reference
 (could be ported to ReadWalker with some refactoring, however)

There were a few engine changes as well to accomodate the new ReadWalker tools:

-Method to allow walkers to access the SAM header from the reads data source

-No longer require an index for BAM/SAM files when no intervals are
 provided and no queries are performed.

-onTraversalDone() now allows tools to return a value, which is printed
 out by the engine

Resolves #113

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