Fixed up the DuplicateMarkingBuffer and added a (broken) test

Since DuplicateMarkingBuffer is an inner class of MarkDuplicatesWithMateCigarIterator
will have to test it indirectly through there.
Removed the erroneously created DuplicateMarkingBufferTest
Further changes to MarkDuplicatesWithMateCigarIterator

not working at the moment
Added wrappedSamRecord to MarkDuplicatesWithMateCigarIterator

Keeping the coordinate-sorted index associated with a SAMRecord
appropriately synchronized was difficult and causing bugs. Therefore
wrapped it alongside record at time of retrieval in a lightweight
wrapper class. Also changed the DuplicateMarkingBuffer BufferBlocks
to use byte arrays to track duplicate status for all reads, not just
those on disk.

Currently passes all unit tests. Untested on actual data.