Add some test data, simple test case, atlas script #2
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I added some simulated test data using the arabidopsis mitochondrial genome, with some mutations added with mutate.sh. I also added a version of the script for Atlas that can handle gz files correctly.
TODO: script should account for how much the the two genomes are actually aligned, and use this as the denominator rather than the genome size. This should get closer to the 1.234% percent heterozygosity that I simulated.
@emilydelorean there should be some way to get this out of nucmer?