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Same as v0.3.0, except this has the correct version in the code, so `--version` does the right thing
* add option to not use maxmatch option with nucmer, for big genomes * expose minimap2 and nucmer threads options * improved handling of indels, in particular fixes a bug where FP indels could be called as TP, and also now uses current latest mummer version 4.0.0rc1 for better variant calls for recall. * small bug fixes: handle whitespace in fasta header lines, non-ACGT characters, and lowercase characters
Backwards incompatible output compared to v0.1.0. Changes: * added `--filter_pass` option to up front filter records in input VCF * only reports one set of precision and recall, not filtered and unfiltered * algorithm change to fix problem with clustered SNPs and indels. Was incorrectly calling TPs as FPs in cases where indels caused ref/probe alleles to not be aligned in the right place. Solved by applying all filtered variants to the probe flanks.