broadinstitute / hellbender / 482
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Feature support: stripped-down replacement for the old GATK ROD system

Replicates most of the functionality of the old ROD system in ~5% of the
code. The incomprehensible tangle of nested iterators, bindings, views, states,
tracks, trackers, builders etc., etc., is gone, replaced by about 4 core classes:
FeatureContext, FeatureDataSource, FeatureInput, and FeatureManager.

FeatureContext: This is tool-facing interface (replaces RefMetaDataTracker).
                Allows particular sources of Features to be queried.

FeatureDataSource: Handles the low-level details of querying a source of Features.
                   Uses a caching scheme optimized for the use case of queries over
                   intervals with gradually increasing start/stop positions.

FeatureInput: This is used to declare Feature arguments in tools (replaces RodBinding).
              The engine discovers all FeatureInput arguments declared in the tool's class
              hierarchy, and initializes data sources for each one that was specified
              on the command line.

FeatureManager: Manages the pool of data sources, as well as codec and file format
                discovery and type checking.

-ReadWalker interface has changed: apply() now takes a FeatureContext argument
 (will be null if there are no sources of Features).

-Included an example tool PrintReadsWithVariants to demonstrate use of the new
 ReadWalker interface.

-Since Feature files must be indexed in order to query them, I have provided a
 tool IndexFeatureFile that can index any Feature-containing file.

-Made required changes to the argument-parsing system. Feature argument discovery
 is as de-coupled as possible from the main arg parser.

-Made required changes to BQSR, and eliminated the temporary HACKRefMetaDataTracker.

-Comprehensive tests

10206 of 13680 relevant lines covered (74.61%)

0.75 hits per line

Jobs
ID Job ID Ran Files Coverage
1 482.1 (TERM=dumb) 0
74.61
 Travis Job 482.1
Source Files on build 482
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