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Cleanup: Don't require likelihood ROD in Beagle parameters when generating output VCF. Likelihoods file is only an input to Beagle but the Walker that generates a VCF doesn't need it, so it's silly to ask for it and it's error-prone. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3579 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-06-17 17:45:48 +00:00
parent c1595a383a
commit b694ca9633
1 changed files with 0 additions and 15 deletions
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15
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
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@ -55,7 +55,6 @@ import static java.lang.Math.log10;
* Takes files produced by Beagle imputation engine and creates a vcf with modified annotations. * Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
*/ */
@Requires(value={},referenceMetaData=@RMD(name=BeagleOutputToVCFWalker.INPUT_ROD_NAME,type= VCFRecord.class)) @Requires(value={},referenceMetaData=@RMD(name=BeagleOutputToVCFWalker.INPUT_ROD_NAME,type= VCFRecord.class))
//@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="r2",type= ReferenceOrderedDatum.class), @RMD(name="beagleR2",type= BeagleR2ROD.class)})
public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> { public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
@ -67,13 +66,6 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
public static final String INPUT_ROD_NAME = "inputvcf"; public static final String INPUT_ROD_NAME = "inputvcf";
/*
protected static BeagleFileReader gprobsReader = null;
protected static BeagleFileReader phasedReader = null;
protected static BeagleFileReader likeReader = null;
protected static BeagleFileReader r2Reader = null;
*/
protected static String line = null; protected static String line = null;
// protected HashMap<String,BeagleSampleRecord> beagleSampleRecords; // protected HashMap<String,BeagleSampleRecord> beagleSampleRecords;
@ -125,13 +117,6 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
return 0; return 0;
List<Object> likerods = tracker.getReferenceMetaData("beagleLike");
// ignore places where we don't have a variant
if ( likerods.size() == 0 )
return 0;
BeagleFeature beagleLikeFeature = (BeagleFeature)likerods.get(0);
List<Object> r2rods = tracker.getReferenceMetaData("beagleR2"); List<Object> r2rods = tracker.getReferenceMetaData("beagleR2");
// ignore places where we don't have a variant // ignore places where we don't have a variant