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This PR adds cactus-mafviz, which takes as input a MAF file (ie from cactus-hal2maf) and makes a set of dot and synteny plots using taffy_alignment_plot.py. I wrote it to make a set of sample-to-reference synteny plots for every chromosome for every sample in a human pangenome graph, which was pretty helpful for debugging.

But it's not finished yet, before merging, at minimum it needs:

  • integration into cactus docker / installation (right now script path is hardcoded)
  • interface to pass through options from the cactus-mafviz cli into taffy_alignment_plot.py

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