Reader with any location sorting doesn't allow for passing of contigs

[Kyle Hernandez]

If I read BarcodeAndCoordinate sorted MAF that used the fai file for chromosome order, an exception will be thrown because there is no way to pass the fai file to the reader. I think that there are two things that should be done:

• All coordinate sortings should be able to place a , list of chromosomes in the header on the sort_order pragma if a fai file was passed, otherwise it will use the default python-style sorting
• Potentially, add the ability of reader to accept a fai file and/or pass assume_sorted=True to it