diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index e727f04a1..60a8298a4 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -162,7 +162,7 @@ public class VariantEvalWalker extends RodWalker { protected double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 50; @Argument(shortName="outputVCF", fullName="InterestingSitesVCF", doc="If provided, interesting sites emitted to this vcf and the INFO field annotated as to why they are interesting", required=false) - protected String outputVCF = null; + protected VCFWriter writer = null; @Argument(shortName="gcLog", fullName="GenotypeCocordanceLog", doc="If provided, sites with genotype concordance problems (e.g., FP and FNs) will be emitted ot this file", required=false) protected PrintStream gcLog = null; @@ -291,7 +291,6 @@ public class VariantEvalWalker extends RodWalker { private Set> evaluationClasses = null; /** output writer for interesting sites */ - private VCFWriter writer = null; private boolean wroteHeader = false; // -------------------------------------------------------------------------------------------------------------- @@ -348,9 +347,6 @@ public class VariantEvalWalker extends RodWalker { contexts = initializeEvaluationContexts(evalNames, compNames, selectExps); determineContextNamePartSizes(); - if ( outputVCF != null ) - writer = new StandardVCFWriter(new File(outputVCF)); - if ( rsIDFile != null ) { if ( maxRsIDBuild == Integer.MAX_VALUE ) throw new IllegalArgumentException("rsIDFile " + rsIDFile + " was given but associated max RSID build parameter wasn't available"); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 0e7acc5b0..eb39cd234 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -114,7 +114,7 @@ public class @Test public void testVEWriteVCF() { - String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30 -E MendelianViolationEvaluator"; + String extraArgs = "-L 1:1-10,000,000 -NO_HEADER -family NA19238+NA19239=NA19240 -MVQ 30 -E MendelianViolationEvaluator"; for (String tests : testsEnumerations) { WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s", 2,