diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java index 8672460e7..7fe6a39e5 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java @@ -50,4 +50,12 @@ public class KGenomesSNPROD extends TabularROD implements SNPCallFromGenotypes { public int nHomVarGenotypes() { return -1; } public List getGenotypes() { return null; } public int length() { return 1; } + + public String toString() { + StringBuffer sb = new StringBuffer(); + sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t"); + sb.append(getRefSnpFWD() + "\t" + getGenotype().get(0) + "\t"); + sb.append(getMAF() + "\t0\t0\t0\t" + getVariationConfidence()); + return sb.toString(); + } } \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java index 05bacfab6..3e71e0457 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java @@ -39,4 +39,11 @@ public class SangerSNPROD extends TabularROD implements SNPCallFromGenotypes { public int nHetGenotypes() { return -1; } public int nHomVarGenotypes() { return -1; } public List getGenotypes() { return null; } + + public String toString() { + StringBuffer sb = new StringBuffer(); + sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t"); + sb.append(getRefBasesFWD() + "\t" + getAltBasesFWD()); + return sb.toString(); + } } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java index 4260cd063..e657f97b2 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java @@ -79,12 +79,7 @@ public class VennCallSetsWalker extends RefWalker { static void printVariant(PrintWriter writer, AllelicVariant variant) { if ( variant != null ) - writer.println(variant.getLocation().getContig() + "\t" - + variant.getLocation().getStart() + "\t" - + variant.getRefSnpFWD() + "\t" - + variant.getGenotype().get(0) + "\t" - + variant.getMAF() + "\t0\t0\t0\t" - + variant.getVariationConfidence()); + writer.println(variant.toString()); } /**