From cfa18f67434ae589a9667d29ceba6ba15a24cf0f Mon Sep 17 00:00:00 2001 From: depristo Date: Fri, 4 Jun 2010 23:56:34 +0000 Subject: [PATCH] Fixing missed update with new Allele in it git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3490 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/BeagleOutputToVCFWalker.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java index cc4161aee..680f0b4e4 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java @@ -150,8 +150,8 @@ public class BeagleOutputToVCFWalker extends RodWalker { } bglRecord.GenotypeProbabilities = genotypeProbabilities; - bglRecord.AlleleA = new Allele(alleleA); - bglRecord.AlleleB = new Allele(alleleB); + bglRecord.AlleleA = Allele.create(alleleA); + bglRecord.AlleleB = Allele.create(alleleB); beagleSampleRecords.put(markerKey,bglRecord); } @@ -195,7 +195,7 @@ public class BeagleOutputToVCFWalker extends RodWalker { j = 2; for (String sample : samples) { - pair = new HaplotypePair(new Allele(phasedLine[j]), new Allele(phasedLine[j+1])); + pair = new HaplotypePair(Allele.create(phasedLine[j]), Allele.create(phasedLine[j+1])); j = j+2; haplotypePairs.put(sample,pair); } @@ -404,7 +404,7 @@ public class BeagleOutputToVCFWalker extends RodWalker { Boolean isRefA = (refByte == rA); - Allele refAllele = new Allele(r, isRefA ); + Allele refAllele = Allele.create(r, isRefA ); alleles.add(refAllele); r = hp.AlleleB.getBases(); @@ -412,7 +412,7 @@ public class BeagleOutputToVCFWalker extends RodWalker { //System.out.println((char)r[0]); Boolean isRefB = (refByte == rB); - Allele altAllele = new Allele(r,isRefB); + Allele altAllele = Allele.create(r,isRefB); alleles.add(altAllele);