Speed up distance calculation by skipping obviously distant cases

What's Changed

• Add contributing docs (CONTRIBUTING.md) and update the README.md by @matthuska in #7
• Feature/speedup submat batches by @denisbeslic tweaked by @matthuska in #9
• Create output cache dir if it doesn't exist. by @matthuska in #15
• Add more tests for filtering mutations, more specific var-type options, option for controlling number of parallel threads (--jobs) by @matthuska in #14
• Add nextclade DNA test data @denisbeslic

Full Changelog: v0.3.3...v0.4.0