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-erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2600 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-01-15 21:07:49 +00:00
parent a12933a26d
commit c8c5c176cd
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
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@ -59,7 +59,7 @@ public class TraverseLoci extends TraversalEngine {
//ReferenceOrderedView referenceOrderedDataView = new ReferenceOrderedView( dataProvider ); //ReferenceOrderedView referenceOrderedDataView = new ReferenceOrderedView( dataProvider );
ReferenceOrderedView referenceOrderedDataView = null; ReferenceOrderedView referenceOrderedDataView = null;
if ( ! GenomeAnalysisEngine.instance.getArguments().enableRodWalkers || WalkerManager.getWalkerDataSource(walker) != DataSource.REFERENCE_ORDERED_DATA ) if ( /* ! GenomeAnalysisEngine.instance.getArguments().enableRodWalkers || */ WalkerManager.getWalkerDataSource(walker) != DataSource.REFERENCE_ORDERED_DATA )
referenceOrderedDataView = new ManagingReferenceOrderedView( dataProvider ); referenceOrderedDataView = new ManagingReferenceOrderedView( dataProvider );
else else
referenceOrderedDataView = (RodLocusView)locusView; referenceOrderedDataView = (RodLocusView)locusView;
@ -110,7 +110,7 @@ public class TraverseLoci extends TraversalEngine {
// We have a final map call to execute here to clean up the skipped based from the // We have a final map call to execute here to clean up the skipped based from the
// last position in the ROD to that in the interval // last position in the ROD to that in the interval
if ( GenomeAnalysisEngine.instance.getArguments().enableRodWalkers && WalkerManager.getWalkerDataSource(walker) == DataSource.REFERENCE_ORDERED_DATA ) { if ( /* GenomeAnalysisEngine.instance.getArguments().enableRodWalkers && */ WalkerManager.getWalkerDataSource(walker) == DataSource.REFERENCE_ORDERED_DATA ) {
RodLocusView rodLocusView = (RodLocusView)locusView; RodLocusView rodLocusView = (RodLocusView)locusView;
long nSkipped = rodLocusView.getLastSkippedBases(); long nSkipped = rodLocusView.getLastSkippedBases();
if ( nSkipped > 0 ) { if ( nSkipped > 0 ) {
@ -144,7 +144,7 @@ public class TraverseLoci extends TraversalEngine {
DataSource dataSource = WalkerManager.getWalkerDataSource(walker); DataSource dataSource = WalkerManager.getWalkerDataSource(walker);
if( dataSource == DataSource.READS ) if( dataSource == DataSource.READS )
return new CoveredLocusView(dataProvider); return new CoveredLocusView(dataProvider);
else if( dataSource == DataSource.REFERENCE || ! GenomeAnalysisEngine.instance.getArguments().enableRodWalkers ) else if( dataSource == DataSource.REFERENCE ) //|| ! GenomeAnalysisEngine.instance.getArguments().enableRodWalkers )
return new AllLocusView(dataProvider); return new AllLocusView(dataProvider);
else if( dataSource == DataSource.REFERENCE_ORDERED_DATA ) else if( dataSource == DataSource.REFERENCE_ORDERED_DATA )
return new RodLocusView(dataProvider); return new RodLocusView(dataProvider);