Updated the VCF parser to provide the user more control of the handling of complex loci. As before, the user can specify whether to keep indels and complex polymorphisms when they are the only polymorphism at the locus (because this doesn't involve haplotyping), but now the user can specify whether to skip complex polymorphisms (and build haplotypes with other sites at the RAD contig) or to remove all contigs that have a complex polymorphism.
Updated the VCF parser to provide the user more control of the handling of complex loci. As before, the user can specify whether to keep indels and complex polymorphisms when they are the only polymorphism at the locus (because this doesn't involve haplotyping), but now the user can specify whether to skip complex polymorphisms (and build haplotypes with other sites at the RAD contig) or to remove all contigs that have a complex polymorphism.