Fixup imports and class references that are a consequence of htsjdk's `SamReaderFactory` refactor.
Merge pull request #4 from broadinstitute/mm_import_fixup

Fixup imports and class references that are a consequence of htsjdk's `SamReaderFactory` refactor.
Pass #2 on improving the performance of IlluminaBasecallsToSam. Spawn RAM based threads for bcl reading when possible.
Use a standard fixed thread pool. Since we are writing with another thread pool and the tile queue is already ordered we don't need a priority queue.