After artificially creating events in a FASTA file, how do I keep track of the old coordinates?
I've written a handful of programs from scratch to simulate mutations and variations in real or simulated sequences.

The trick has always been to sort the variants by genomic coordinate, apply the variant with the largest coordinate first, then apply the variant with the second largest coordinate, all the way down to the variant with the smallest coordinate.

Indels and other variants that affect sequence structure only affect subsequent coordinates. So going in reverse order ensures variants at the beginning of the sequence don't throw off variants at the end of the sequence.