Recombination prediction .gff output uses `SEQUENCE` as ref name.

[dfornika]

In the recombination_predictions.gff output file, the 'sequence-region' is named SEQUENCE.

##gff-version 3
##sequence-region SEQUENCE 1 5218953
SEQUENCE        GUBBINS CDS     1335886 1344279 0.000   .       0       node="internal_6->sample";neg_log_likelihood="200532.141081";taxa="sample";snp_count="199";
SEQUENCE        GUBBINS CDS     4764937 4767611 0.000   .       0       node="internal_6->sample";neg_log_likelihood="200219.990608";taxa="sample";snp_count="114";
SEQUENCE        GUBBINS CDS     4429790 4432177 0.000   .       0       node="internal_6->sample";neg_log_likelihood="200031.139330";taxa="sample";snp_count="122";
SEQUENCE        GUBBINS CDS     4432382 4433456 0.000   .       0       node="internal_6->sample";neg_log_likelihood="199827.790619";taxa="sample";snp_count="111";
SEQUENCE        GUBBINS CDS     1333664 1335005 0.000   .       0       node="internal_6->sample";neg_log_likelihood="199641.977650";taxa="sample";snp_count="122";
SEQUENCE        GUBBINS CDS     2966589 2967656 0.000   .       0       node="internal_6->sample";neg_log_likelihood="199432.658591";taxa="sample";snp_count="106";

This prevents us from loading these files into IGV and other tools that need to match the features to a specific reference.

We should rename to use the original reference ID (or get gubbins to output it that way directly if possible).