rGFA support (experimental) #1186
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This adds the
--rgfaoption tocactus-pangenome. It will get yougraph.rgfa.gz: Like the usual GFA file, but no paths -- only rGFA tags. These tags will cover off-reference sequence as determined by greedy cover. By default, only intervals >= 50bp are included. (graph.gfa.gzchanged to no longer have rank-0 tags)graph.rgfa.gbz: This is the usual GBZ, but with the full rGFA cover added as reference path fragments (that have special sample name_rGFA)graph.rgfa.vcf.gz: This VCF contains nested calls inside insertions by means of the rGFA cover. It does not go throughvcfbublike usual.It'd be nice to not have different GBZ/VCF outputs, but keeping them separate will make it easier to benchmark. There's also still some work needed regarding VCF tags...