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If no comp rod is specified, specify the dummy name none so that we still get counts. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5211 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-02-07 19:24:52 +00:00
parent 1fbfd4082e
commit ecbc38aff0
2 changed files with 40 additions and 1 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -139,6 +139,11 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
throw new UserException("No evaluation tracks were specified. Please bind one or more callsets to evaluate using the -B argument with a trackname that starts with the word 'eval'.");
}
// Add a dummy comp track if none exists
if (compNames.size() == 0) {
compNames.add("none");
}
// Set up set of known names
knownNames.addAll(Arrays.asList(KNOWN_NAMES));
@ -245,6 +250,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
* @param result an integer that doesn't get used for anything
*/
public void onTraversalDone(Integer result) {
logger.info("Finalizing variant report");
for ( StateKey stateKey : evaluationContexts.keySet() ) {
NewEvaluationContext nec = evaluationContexts.get(stateKey);

34
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -310,6 +310,38 @@ public class VariantEvalIntegrationTest extends WalkerTest {
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
}
@Test
public void testFundamentalsCountVariantsNoCompRod() {
// nProcessedLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | awk '{ print length($4) }' | ~kiran/bin/SimpleStats = 38
// nCalledLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -c PASS = 9
// nRefLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($5 == ".") print $0 }' | wc -l = 4
// nVariantLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($5 != ".") print $0 }' | wc -l = 5
// variantRate = nVariantLoci / nProcessedLoci = 0.131578947
// nSNPs = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($5 != "." && length($4) == 1 && length($5) == 1) print $0 }' | wc -l = 3
// nInsertions = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($5 != "." && length($5) > 1) print $0 }' | wc -l = 1
// nDeletions = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($5 != "." && length($4) > 1) print $0 }' | wc -l = 1
// nNoCalls = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "[[:punct:]]/[[:punct:]]") print $0 }' | wc -l = 4
// nHets = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "0/1" || $i ~ "1/0") print $0 }' | wc -l = 8
// nHomRef = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "0/0") print $0 }' | wc -l = 10
// nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5
WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder(
"-T VariantEval",
"-R " + b37KGReference,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("2a6215c86918a2f5c6748dd74057e79e")
);
executeTest("testFundamentalsCountVariantsNoCompRod", spec);
}
@Test
public void testSelect1() {
String extraArgs = "-L 1:1-10,000,000";
@ -402,7 +434,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testTranches() {
String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -tf " + testDir + "tranches.6.txt";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("68044a69f03ba4cc11d2061cc96e9eb5"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("b018ca01b374def71fcd1bf164326485"));
executeTestParallel("testTranches",spec);
//executeTest("testTranches",spec);
}