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Bug fix: don't assume users won't use arbitrary rods on the commandline 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5040 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-21 04:59:28 +00:00
parent b6497c404f
commit c3dbbe7f91
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -149,7 +149,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
private String getReferenceOrderedData( RefMetaDataTracker tracker ) { private String getReferenceOrderedData( RefMetaDataTracker tracker ) {
ArrayList<String> rodStrings = new ArrayList<String>(); ArrayList<String> rodStrings = new ArrayList<String>();
for ( GATKFeature datum : tracker.getAllRods() ) { for ( GATKFeature datum : tracker.getAllRods() ) {
if ( datum != null && ! (datum.getUnderlyingObject() instanceof DbSNPFeature)) { if ( datum != null && datum.getUnderlyingObject() instanceof ReferenceOrderedDatum ) {
rodStrings.add(((ReferenceOrderedDatum)datum.getUnderlyingObject()).toSimpleString()); // TODO: Aaron: this line still survives, try to remove it rodStrings.add(((ReferenceOrderedDatum)datum.getUnderlyingObject()).toSimpleString()); // TODO: Aaron: this line still survives, try to remove it
} }
} }