broadinstitute / hellbender
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LAST BUILD ON BRANCH dr_feature_support
branch: dr_feature_support
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travis-pro

droazen 
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

Relevant lines Covered
13680 RELEVANT LINES 10206 COVERED LINES
0.75 HITS PER LINE
Source Files on dr_feature_support
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
482 dr_feature_support 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, buil... push droazen travis-pro pending completion  
480 dr_feature_support Address code review comments push droazen travis-pro pending completion  
478 dr_feature_support Address code review comments push droazen travis-pro pending completion  
460 dr_feature_support 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, buil... push droazen travis-pro pending completion  
458 dr_feature_support 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, buil... push droazen travis-pro pending completion  
456 dr_feature_support 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, buil... push droazen travis-pro pending completion  
454 dr_feature_support 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, buil... push droazen travis-pro pending completion  
453 dr_feature_support 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, buil... push droazen travis-pro pending completion  
452 dr_feature_support 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, buil... push droazen travis-pro pending completion  
451 dr_feature_support 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, buil... push droazen travis-pro pending completion  
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