vcf-supported version

SVTopo

• Adds support for sawfish VCF to improve variant identification accuracy with the new --supporting-reads and --vcf.
• Simplifies user interface by removing the following:
  • --quiet
  • --allow-unphased
  • --no-filter
• Changes the --prefix to the simpler option --json-out
• Adds the --exclude-regions argument as a required bed file for region exclusion.

SVTopoVz

• Changes --log-level to --verbose for consistency with svtopo.
• Alters the exclusion of simple variants to default by changing the --ignore-simple-dels and --ignore-simple-dups to --include-simple-dels and --include-simple-dups, respectively.