loci-parsing refactor - Githubissues

ryan-williams commented 8 years ago

PR on top of #605:

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

coveralls commented 8 years ago

Coverage increased (+0.5%) to 79.573% when pulling f4895a2342f17e0ca108976237fa241e2f18f0a1 on ryan-williams:loci into e27ba66219fa007776e723186c2532d408c4630f on hammerlab:read-filters.

coveralls commented 8 years ago

Coverage increased (+0.5%) to 79.573% when pulling 88b5ebb7268b2f1d686b1d22743e25bd40edb71d on ryan-williams:loci into e27ba66219fa007776e723186c2532d408c4630f on hammerlab:read-filters.

hammerlab / guacamole

loci-parsing refactor #606