matToFastaStitcher in chromosome order

[coopergrace]

Hello,

Is there a way to specify the conversion from MAF to fasta be in chromosome order please, e.g. via the sequence used as reference? Or is this something that needs to be specified at the MAF construction stage?

Having had a few goes at MAF > fasta, the chromosome order changes each time. Considering the output fasta is one massive sequence, determining chromosome boundaries is impossible.

Cheers

Cooper