SamReader.query() should handle when coordinates are given < 1 or > end of contig

[tfenne]

The underlying SAMFileReader throws exceptions back if you ask to query off the ends of contigs, rather than just gracefully capping the query at the ends of the contig. I think it would be nice to have SamReader min/max the query coordinates with 1/contig_length on the way through to prevent these kinds of exceptions.

This often comes up when running queries with position - flank to position + flank and forgetting to limit the positions.