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Add M2 to the HC annotations check

This commit is contained in:
Geraldine Van der Auwera 2016-05-27 13:48:27 -04:00
parent 5b80c92cb7
commit efbbbb1bd9
1 changed files with 3 additions and 2 deletions
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5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java
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@ -66,6 +66,7 @@ import org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller;
import org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import java.util.ArrayList; import java.util.ArrayList;
@ -75,7 +76,7 @@ import java.util.Set;
public class AnnotationUtils { public class AnnotationUtils {
public static final String ANNOTATION_HC_WARN_MSG = " annotation will not be calculated, must be called from HaplotypeCaller"; public static final String ANNOTATION_HC_WARN_MSG = " annotation will not be calculated, must be called from HaplotypeCaller or MuTect2";
public static final int WARNINGS_LOGGED_SIZE = 3; public static final int WARNINGS_LOGGED_SIZE = 3;
/** /**
@ -154,7 +155,7 @@ public class AnnotationUtils {
throw new ReviewedGATKException("Warnings logged array must have at least " + WARNINGS_LOGGED_SIZE + " elements, but has " + warningsLogged.length); throw new ReviewedGATKException("Warnings logged array must have at least " + WARNINGS_LOGGED_SIZE + " elements, but has " + warningsLogged.length);
} }
if ( !(walker instanceof HaplotypeCaller) ) { if ( !(walker instanceof HaplotypeCaller) && !(walker instanceof MuTect2)) {
if ( !warningsLogged[0] ) { if ( !warningsLogged[0] ) {
logger.warn(annotation + ANNOTATION_HC_WARN_MSG + ", not " + walker.getClass().getSimpleName()); logger.warn(annotation + ANNOTATION_HC_WARN_MSG + ", not " + walker.getClass().getSimpleName());
warningsLogged[0] = true; warningsLogged[0] = true;