Move `index` to last argument and document it in docstring
Move `index` to last argument and document it in docstring

pysam-developers/pysam,pysam-developers/pysam,kyleabeauchamp/pysam,kyleabeauchamp/pysam,pysam-developers/pysam,kyleabeauchamp/pysam,kyleabeauchamp/pysam,kyleabeauchamp/pysam,pysam-developers/pysam