broadinstitute / hellbender / 670
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master: 81%

LAST BUILD BRANCH: dr_disentangle_spark_and_dataflow
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droazen 
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 most of the engine to use SimpleIntervals rather
 than GenomeLocs. This allows for the creation of Context objects in traversals where there
 is not necessarily a sequence dictionary available (eg., VariantWalker).

-Moved shared arguments/code from Walker classes up into GATKTool. Still some issues
 related to marking engine-wide arguments as optional/required on a per-traversal or
 per-tool basis, but tickets have been created for these.

-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.

TODOs:

-We currently still require a sequence dictionary to actually parse intervals in
 IntervalArgumentCollection. This is due entirely to our support of intervals without
 specific stop positions (eg., "chr1" and "chr1:1+") -- for these intervals we must
 look up the stop position in a sequence dictionary. This means that IntervalWalkers
 currently require at least one input that contains a sequence dictionary (although
 VariantWalkers do not). We should look into ways of relaxing this restriction.

Resolves #109

10427 of 13898 relevant lines covered (75.03%)

0.75 hits per line

Jobs
ID Job ID Ran Files Coverage
1 670.1 (TERM=dumb) 0
75.03
 Travis Job 670.1
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