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more fixes for tests broken by indexing-on-the-fly; I think this should do it. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4486 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-10-13 01:54:32 +00:00
parent ed39af53cd
commit 272ac2ae4a
2 changed files with 2 additions and 6 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -162,7 +162,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
protected double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 50; 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) @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) @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; protected PrintStream gcLog = null;
@ -291,7 +291,6 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
private Set<Class<? extends VariantEvaluator>> evaluationClasses = null; private Set<Class<? extends VariantEvaluator>> evaluationClasses = null;
/** output writer for interesting sites */ /** output writer for interesting sites */
private VCFWriter writer = null;
private boolean wroteHeader = false; private boolean wroteHeader = false;
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
@ -348,9 +347,6 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
contexts = initializeEvaluationContexts(evalNames, compNames, selectExps); contexts = initializeEvaluationContexts(evalNames, compNames, selectExps);
determineContextNamePartSizes(); determineContextNamePartSizes();
if ( outputVCF != null )
writer = new StandardVCFWriter(new File(outputVCF));
if ( rsIDFile != null ) { if ( rsIDFile != null ) {
if ( maxRsIDBuild == Integer.MAX_VALUE ) if ( maxRsIDBuild == Integer.MAX_VALUE )
throw new IllegalArgumentException("rsIDFile " + rsIDFile + " was given but associated max RSID build parameter wasn't available"); throw new IllegalArgumentException("rsIDFile " + rsIDFile + " was given but associated max RSID build parameter wasn't available");

2
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -114,7 +114,7 @@ public class
@Test @Test
public void testVEWriteVCF() { 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) { for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s", WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s",
2, 2,