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print full genotype for alt allele 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1297 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-23 01:35:23 +00:00
parent 298cc24524
commit ee8ed534e0
2 changed files with 2 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java
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@ -52,7 +52,7 @@ public class rodFLT extends TabularROD implements SNPCallFromGenotypes {
return (value > 0.0 ? value : 1.0); return (value > 0.0 ? value : 1.0);
} }
public double getConsensusConfidence() { return -1; } public double getConsensusConfidence() { return -1; }
public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); } public List<String> getGenotype() throws IllegalStateException { return Arrays.asList(getAltBasesFWD()); }
public int getPloidy() throws IllegalStateException { return 2; } public int getPloidy() throws IllegalStateException { return 2; }
public boolean isBiallelic() { return true; } public boolean isBiallelic() { return true; }

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java
View File

@ -6,7 +6,6 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
@ -83,7 +82,7 @@ public class VennCallSetsWalker extends RefWalker<Integer, Integer> {
writer.println(variant.getLocation().getContig() + "\t" writer.println(variant.getLocation().getContig() + "\t"
+ variant.getLocation().getStart() + "\t" + variant.getLocation().getStart() + "\t"
+ variant.getRefSnpFWD() + "\t" + variant.getRefSnpFWD() + "\t"
+ variant.getAltSnpFWD() + "\t" + variant.getGenotype().get(0) + "\t"
+ variant.getMAF() + "\t0\t0\t0\t" + variant.getMAF() + "\t0\t0\t0\t"
+ variant.getVariationConfidence()); + variant.getVariationConfidence());
} }