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master: 81%

Ran 11 Mar 2015 10:47PM UTC

Files 216

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Committed 11 Mar 2015 10:33PM UTC coverage: 74.595% (+0.003%) from 74.592%

Job # TERM=dumb

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push

travis-pro

Committed by

droazen

Commit Message

IntervalWalker, VariantWalker enhancements, and GenomeLoc -> SimpleInterval migration in the engine

-Created a new class of tool, IntervalWalker, that processes a single interval at a time,
 with the ability to query optional overlapping sources of reads, reference data, and/or
 features/variants. Current implementation is simple/naive with no special caching;
 performance issues will be addressed once we port this traversal type to dataflow.

-Added the ability for VariantWalkers to access contextual reads/reference/feature data.

-To enable the above changes, migrated the engine to use SimpleIntervals rather
 than GenomeLocs. This allows for the creation of intervals in traversals where there
 is not necessarily a sequence dictionary available.

-Since there isn't yet an htsjdk release that contains SimpleInterval, temporarily
 checked a copy of it into our repo, which we can remove the next time we
 rev htsjdk.

Resolves #109

Run Details

10368 of 13899 relevant lines covered (74.6%)

0.75 hits per line

broadinstitute / hellbender / 624 / 1
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