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If present, VE's AlleleCount stratification uses the MLE AC by default (and otherwise drops down to use the greedy AC). Added integration test to cover it.

This commit is contained in:
Eric Banks 2012-06-18 13:36:14 -04:00
parent 82a2c40338
commit 4393adf9e7
2 changed files with 35 additions and 10 deletions
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13
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
View File

@ -1,10 +1,10 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -14,8 +14,9 @@ import java.util.*;
/**
* Stratifies the eval RODs by the allele count of the alternate allele
*
* Looks at the AC value in the INFO field, and uses that value if present. If absent,
* computes the AC from the genotypes themselves. For no AC can be computed, 0 is used.
* Looks first at the MLEAC value in the INFO field, and uses that value if present.
* If not present, it then looks for the AC value in the INFO field. If both are absent,
* it computes the AC from the genotypes themselves. If no AC can be computed, 0 is used.
*/
public class AlleleCount extends VariantStratifier {
@Override
@ -41,8 +42,10 @@ public class AlleleCount extends VariantStratifier {
if (eval != null) {
int AC = 0; // by default, the site is considered monomorphic
if ( eval.hasAttribute("AC") && eval.getAttribute("AC") instanceof Integer ) {
AC = eval.getAttributeAsInt("AC", 0);
if ( eval.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) && eval.isBiallelic() ) {
AC = eval.getAttributeAsInt(VCFConstants.MLE_ALLELE_COUNT_KEY, 0);
} else if ( eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) && eval.isBiallelic() ) {
AC = eval.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
} else if ( eval.isVariant() ) {
for (Allele allele : eval.getAlternateAlleles())
AC = Math.max(AC, eval.getCalledChrCount(allele));

32
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -32,11 +32,12 @@ import java.util.Arrays;
public class VariantEvalIntegrationTest extends WalkerTest {
private static String variantEvalTestDataRoot = validationDataLocation + "VariantEval/";
private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf";
private static String fundamentalTestSNPsSplit1of2VCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.split_1_of_2.vcf";
private static String fundamentalTestSNPsSplit2of2VCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.split_2_of_2.vcf";
private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.NA12045.vcf";
private static String fundamentalTestVCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.final.vcf";
private static String fundamentalTestSNPsWithMLEVCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.final.withMLE.vcf";
private static String fundamentalTestSNPsSplit1of2VCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.final.split_1_of_2.vcf";
private static String fundamentalTestSNPsSplit2of2VCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.final.split_2_of_2.vcf";
private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.final.NA12045.vcf";
private static String cmdRoot = "-T VariantEval" +
" -R " + b36KGReference;
@ -457,6 +458,27 @@ public class VariantEvalIntegrationTest extends WalkerTest {
executeTest("testAlleleCountStrat", spec);
}
@Test
public void testAlleleCountStratWithMLE() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"--dbsnp " + b37dbSNP132,
"--eval " + fundamentalTestSNPsWithMLEVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST AlleleCount",
"-L " + fundamentalTestSNPsWithMLEVCF,
"-o %s"
),
1,
Arrays.asList("cadd4e32ab82f7e43d0e510dfe5e6dda")
);
executeTest("testAlleleCountStratWithMLE", spec);
}
@Test
public void testMultipleEvalTracksAlleleCountWithMerge() {
WalkerTestSpec spec = new WalkerTestSpec(