hammerlab / guacamole / 2525

80%

master: 78%

Pull #606

travis-ci

loci-parsing refactor

- LociParser → ParsedLoci, removed state+mutation pattern, leaving an
  object that just wraps loci, after we've parsed strings, but before
  we have contig-lengths / a LociSet
  - uses ParsedLociRange and ParsedLociRanges classes, which
    encapsulate "all loci" special-casing.
  - parseLoci method is moved in there, since it's basically a
    constructor for a ParsedLoci.
- removed all non-test calls of unsafe ParsedLoci.result and
  LociSet(String), that assume no contig-lengths are needed because
  provided ranges will be closed.
- changed some callers to reflect that the ReadSets() call now
  integrates building loci and filters in addition to loading
  read-sets.
- move a couple of InputFilters ctors that were only used in tests to
  TestInputFilters

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