improvements / bugfix in capped-regions partitioner

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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improvements / bugfix in capped-regions partitioner #587

Closed ryan-williams closed 8 years ago

ryan-williams commented 8 years ago

surface alternate coverage-computation strategy, "exploding" reads into per-base, depth-1 tuples, controllable by a flag
- opens a part of the performance-space where memory-use is not proportional to maximum depth of reads, partly inspired by discussions on #572
fix a bug with how read-starts are tallied given loci strings that start and stop in the interior of contigs
rename the loci-partitioners

coveralls commented 8 years ago

Coverage increased (+0.08%) to 78.911% when pulling a8973a9d40ac34d44347c6473307935ad197ae49 on ryan-williams:cci into 5fff3ea1bfbe877870a87d68d49b5b09c0a8a7ef on hammerlab:master.

coveralls commented 8 years ago

Coverage increased (+0.08%) to 78.911% when pulling b133a5f08478e4e8abf67144bf874e4150bf3c1f on ryan-williams:cci into 5fff3ea1bfbe877870a87d68d49b5b09c0a8a7ef on hammerlab:master.