Enable masking of sites in alignments prior to tree building
Enable masking of sites in alignments prior to tree building

Uses the existing interface for defining excluded sites in a VCF-based analysis
to also enable masking of sites from a multiple sequence alignment prior to
building a tree. This includes an initial refactor of the logic to load excluded
sites from a text file, but this refactor is not yet complete.

Users expect to define excluded sites in one-based coordinates when not
providing a BED file, so this commit also enforces this expectation. Excluded
sites are converted to zero-based positions internally regardless of the input
format for consistency with other Python tools that expect zero-based indexing.

blab/nextstrain-augur,nextstrain/augur,nextstrain/augur,nextstrain/augur