Add colapse_paralogs to merging function

[pamelacamejom]

Hi Gerry, I wonder if you could incorporate the "colapse_paralogs" step to the merging function. After merging, I find many issues when having paralogs in one of the merged pangenomes. It looks like this stops merging some clusters, even when they are the same gene with the same neighbours.

[gtonkinhill]

Hi, I will look into adding this in the future. In the mean time I would suggest using the --merge_paralogs option.

[revinici]

I'm trying to decrease the runtime of panaroo by processing my input genomes in batches and then merging. However, I've noticed that specifying the --merge_paralogs flag causes the merge step to take much longer than when not specifying the flag. What does the --merge_paralogs flags do exactly and how does it compare to the colapse_paralogs step? I'm trying to determine if I can get away with not using the flag.