Add option to reorder reference and scaffolds iteratively

[JustinChu]

When comparing assembles that are both fragmented, some reference seqeunces are likely not well ordered, leading to the appearance of incongurent linkts. It may be possible to iteratively place the reference seqeunces relative to their best locations on the scaffolds.

Current behavior: Reference is ordered by input file order.

Workflow:

1. Order Scaffolds to reference (input: alignment position of scafftigs, order of reference chr; output: array of order of scaffolds)
2. Order Reference to scaffolds (input: alignment position of scafftigs, order of scaffolds; output: array of order of reference chr)
3. go back to 1

If done continously, will this eventually reach an equalibrium?