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CompOverlap no longer keeps track of the number of comp sites since it wasn't (and cannot) keeping track of them correctly.

This commit is contained in:
Eric Banks 2011-09-09 09:45:24 -04:00
parent 510d5e7730
commit 6ad8943ca0
2 changed files with 4 additions and 8 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
View File

@ -22,9 +22,6 @@ public class CompOverlap extends VariantEvaluator implements StandardEval {
@DataPoint(description = "number of eval SNP sites")
long nEvalVariants = 0;
@DataPoint(description = "number of comp SNP sites")
long nCompVariants = 0;
@DataPoint(description = "number of eval sites outside of comp sites")
long novelSites = 0;
@ -76,9 +73,8 @@ public class CompOverlap extends VariantEvaluator implements StandardEval {
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
boolean evalIsGood = eval != null && eval.isPolymorphic();
boolean compIsGood = comp != null && comp.isNotFiltered() && (eval == null || comp.getType() == eval.getType());
boolean compIsGood = comp != null && comp.isNotFiltered();
if (compIsGood) nCompVariants++; // count the number of comp events
if (evalIsGood) nEvalVariants++; // count the number of eval events
if (compIsGood && evalIsGood) {

6
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -291,7 +291,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompOverlap() {
String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals --comp:comphapmap " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf --eval " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("462d4784dd55294ef9d5118217b157a5"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("009ecc8376a20dce81ff5299ef6bfecb"));
executeTestParallel("testCompOverlap",spec);
}
@ -332,13 +332,13 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -noST -noEV -ST Novelty -EV CompOverlap" +
" -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("a3c2177849cb00fdff99574cff7f0e4f"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("0b81d97f843ec4a1a4222d1f9949bfca"));
executeTestParallel("testMultipleCompTracks",spec);
}
@Test
public void testPerSampleAndSubsettedSampleHaveSameResults() {
String md5 = "dab415cc76846e18fcf8c78f2b2ee033";
String md5 = "b0565ac61b2860248e4abd478a177b5e";
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(