Removed create_chromosome_index() function, and references to it, as this isn't required and actually made things more complicated. There is no need to create my own dictionary of chromosome names since Pysam creates one anyway for free based on the SQ info in the SAM/BAM header. Thus I now use the read.tid as the chromosome_index, as required by WithinFragmentComethylationNTuple class. This removes the previous limitation of a hard-coded sequence dictionary. This fixes #6.
Removed create_chromosome_index() function, and references to it, as this isn't required and actually made things more complicated. There is no need to create my own dictionary of chromosome names since Pysam creates one anyway for free based on the SQ info in the SAM/BAM header. Thus I now use the read.tid as the chromosome_index, as required by WithinFragmentComethylationNTuple class. This removes the previous limitation of a hard-coded sequence dictionary. This fixes #6.

PeteHaitch/methtuple,PeteHaitch/methtuple,PeteHaitch/methtuple