ReferenceBroadcast improvements

hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

Apache License 2.0

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ReferenceBroadcast improvements #602

Closed ryan-williams closed 8 years ago

ryan-williams commented 8 years ago

use Locus type-alias in ContigSequence
- callers pass loci, usage of Ints to index into Arrays under the hood is hidden
- coming soon: sub-contig ContigSequences, defined by each partition's loci, that expose the same API as the current full-contig-byte-array ContigSequence impl.
be more explicit in tests / MapBackedReferenceSequence about what reference bases are being accessed; don't default missing bases to N.

coveralls commented 8 years ago

Coverage increased (+0.3%) to 78.982% when pulling 95db8841f887e3d4b1504ffa4d57af4bcad1e767 on ryan-williams:ns into be6074747e1ae2f628d1d53be18e5eb091b611dd on hammerlab:master.