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NewEvaluationContext needs to be generated in the inner loop. Otherwise, multiple comp tracks end up getting routed to the same row of the output table. Added test to cover multiple comp tracks. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5181 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-02-03 07:04:53 +00:00
parent a9d0921529
commit 9ddc95c833
2 changed files with 27 additions and 12 deletions
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9
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -265,14 +265,13 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
Stack<VariantStratifier> newStratStack = new Stack<VariantStratifier>();
newStratStack.addAll(stratStack);
NewEvaluationContext nec = new NewEvaluationContext();
if (ec != null) {
nec.putAll(ec);
}
VariantStratifier vs = newStratStack.pop();
for ( String state : vs.getAllStates() ) {
NewEvaluationContext nec = new NewEvaluationContext();
if (ec != null) {
nec.putAll(ec);
}
nec.put(vs, state);
ecs.putAll(initializeEvaluationContexts(stratificationObjects, evaluationObjects, newStratStack, nec));

30
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -29,7 +29,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-L 1:1-10,000,000";
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
1, Arrays.asList("0087b2a096aa99135b065aa9a0fff34c"));
1, Arrays.asList("c803c90f587796146286217ab30930a3"));
executeTestParallel("testSelect1", spec);
//executeTest("testSelect1", spec);
}
@ -60,8 +60,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testVESimple() {
HashMap<String, String> expectations = new HashMap<String, String>();
expectations.put("-L 1:1-10,000,000", "e46e8e7457b338c4cfec62ee7aa51ffe");
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "a0554ca0baa097a1761da3f7e8487833");
expectations.put("-L 1:1-10,000,000", "47990cfb955720421c29991954af4450");
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "ce7bb86e6281b1aef1ad94f9ba7301a9");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
@ -84,10 +84,10 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
String matchingMD5 = "5050011ad00b859faf2be679830bec90";
String matchingMD5 = "6388fbad81b0f281298812496fd3ed6c";
expectations.put("", matchingMD5);
expectations.put(" -knownName comp_hapmap -knownName dbsnp", matchingMD5);
expectations.put(" -knownName comp_hapmap", "5050011ad00b859faf2be679830bec90");
expectations.put(" -knownName comp_hapmap", "6388fbad81b0f281298812496fd3ed6c");
for (String tests : testsEnumerations) {
for (Map.Entry<String, String> entry : expectations.entrySet()) {
String extraArgs2 = entry.getKey();
@ -176,8 +176,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testMultipleEvalTracksWithoutGenotypes() {
String dbsnp = GATKDataLocation + "dbsnp_129_b37.rod";
String extraArgs = "-T VariantEval -R " +
b37KGReference +
String extraArgs = "-T VariantEval -R " + b37KGReference +
" -L 20" +
" -D " + dbsnp +
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
@ -187,6 +186,23 @@ public class VariantEvalIntegrationTest extends WalkerTest {
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}
@Test
public void testMultipleCompTracks() {
String dbsnp = GATKDataLocation + "dbsnp_132_b37.vcf";
String extraArgs = "-T VariantEval" +
" -R " + b37KGReference +
" -B:comp,VCF " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
" -B:eval,VCF " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
" -B:dbsnp,VCF " + dbsnp +
" -L 20:10000000-10100000" +
" -noST -noEV -ST Novelty -EV CompOverlap" +
" -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2d2c6e7850ec964624bb032d24834e2f"));
executeTestParallel("testMultipleCompTracks",spec);
}
// @Test
// public void testVEValidatePass() {