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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
This commit is contained in:
depristo 2010-06-04 23:56:34 +00:00
parent 3ea506fe52
commit cfa18f6743
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
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@ -150,8 +150,8 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
}
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<Integer, Integer> {
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<Integer, Integer> {
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<Integer, Integer> {
//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);