Fix exception handling and boundary value checks in query_start and query_end
Fix exception handling and boundary value checks in query_start and
query_end

--HG--
branch : dev-0.3

brendanofallon/pysam,bioinformed/pysam,kyleabeauchamp/pysam,nlhepler/pysam,kyleabeauchamp/pysam,bioinformed/pysam,kyleabeauchamp/pysam,kyleabeauchamp/pysam,brendanofallon/pysam,nlhepler/pysam,carolinux/pysam,pysam-developers/pysam,kyleabeauchamp/pysam,bioinformed/pysam,brendanofallon/pysam,dannon/pysam,TyberiusPrime/pysam,mattions/pysam,dannon/pysam,TyberiusPrime/pysam,mattions/pysam,brendanofallon/pysam,dannon/pysam,carolinux/pysam,bioinformed/pysam,pysam-developers/pysam,nlhepler/pysam,daler/pysam,daler/pysam,brendanofallon/pysam,mattions/pysam,daler/pysam,daler/pysam,TyberiusPrime/pysam,mattions/pysam,pysam-developers/pysam,dannon/pysam,pysam-developers/pysam,TyberiusPrime/pysam,nlhepler/pysam,nlhepler/pysam,bioinformed/pysam,mattions/pysam,dannon/pysam,carolinux/pysam,carolinux/pysam,TyberiusPrime/pysam,carolinux/pysam,daler/pysam