Fixed IO deadlock when running SNAP as a read frontend.

Depends on https://github.com/bigdatagenomics/adam/pull/282. A few modifications to fix issues in the SNAP input stage:

* Fixed ordering issue that was causing input/output threads to lock up.
* Cleaned up logging.
* Moved the conversion from SAM/BAM to ADAM into the alignment stage to address some serialization issues due to BAMRecord fields that aren't properly serialized by SAMRecordWritable.