From c8c5c176cd8e4fca1db3ecb5cfda7807a1fbf649 Mon Sep 17 00:00:00 2001 From: asivache Date: Fri, 15 Jan 2010 21:07:49 +0000 Subject: [PATCH] -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 --- .../broadinstitute/sting/gatk/traversals/TraverseLoci.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java index 07a84519e..ead8af735 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java @@ -59,7 +59,7 @@ public class TraverseLoci extends TraversalEngine { //ReferenceOrderedView referenceOrderedDataView = new ReferenceOrderedView( dataProvider ); 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 ); else 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 // 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; long nSkipped = rodLocusView.getLastSkippedBases(); if ( nSkipped > 0 ) { @@ -144,7 +144,7 @@ public class TraverseLoci extends TraversalEngine { DataSource dataSource = WalkerManager.getWalkerDataSource(walker); if( dataSource == DataSource.READS ) 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); else if( dataSource == DataSource.REFERENCE_ORDERED_DATA ) return new RodLocusView(dataProvider);