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Log annotation warning once if using multithreads

This commit is contained in:
Ron Levine 2017-01-06 17:00:29 -05:00
parent c5df90b598
commit 44c0609418
8 changed files with 66 additions and 49 deletions
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8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java
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@ -105,13 +105,15 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) { final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
// Can only call from UnifiedGenotyper // Can only call from UnifiedGenotyper
if ( !(walker instanceof UnifiedGenotyper) ) { if ( !(walker instanceof UnifiedGenotyper) ) {
if ( !walkerIdentityCheckWarningLogged ) { synchronized (this) {
if ( walker != null ) if (!walkerIdentityCheckWarningLogged) {
logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper, not " + walker.getClass().getName()); if (walker != null)
logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper, not " + walker.getClass().getSimpleName());
else else
logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper"); logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper");
walkerIdentityCheckWarningLogged = true; walkerIdentityCheckWarningLogged = true;
} }
}
return null; return null;
} }

12
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java
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@ -109,13 +109,15 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements RodRequiri
// Can only be called from VariantAnnotator // Can only be called from VariantAnnotator
if ( !(walker instanceof VariantAnnotator) ) { if ( !(walker instanceof VariantAnnotator) ) {
if ( !walkerIdentityCheckWarningLogged ) { synchronized (this) {
if ( walker != null ) if (!walkerIdentityCheckWarningLogged) {
logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getName()); if (walker != null)
logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getSimpleName());
else else
logger.warn("Annotation will not be calculated, must be called from VariantAnnotator"); logger.warn("Annotation will not be calculated, must be called from VariantAnnotator");
walkerIdentityCheckWarningLogged = true; walkerIdentityCheckWarningLogged = true;
} }
}
return null; return null;
} }
@ -123,10 +125,12 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements RodRequiri
// Must have a pedigree file // Must have a pedigree file
trios = ((Walker) walker).getSampleDB().getTrios(); trios = ((Walker) walker).getSampleDB().getTrios();
if ( trios.isEmpty() ) { if ( trios.isEmpty() ) {
if ( !pedigreeCheckWarningLogged ) { synchronized (this) {
if (!pedigreeCheckWarningLogged) {
logger.warn("Annotation will not be calculated, mendelian violation annotation must provide a valid PED file (-ped) from the command line."); logger.warn("Annotation will not be calculated, mendelian violation annotation must provide a valid PED file (-ped) from the command line.");
pedigreeCheckWarningLogged = true; pedigreeCheckWarningLogged = true;
} }
}
return null; return null;
} }
mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP ); mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP );

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java
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@ -112,13 +112,15 @@ public class PossibleDeNovo extends InfoFieldAnnotation implements RodRequiringA
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) { final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if ( !(walker instanceof VariantAnnotator ) ) { if ( !(walker instanceof VariantAnnotator ) ) {
if ( !walkerIdentityCheckWarningLogged ) { synchronized (this) {
if ( walker != null ) if (!walkerIdentityCheckWarningLogged) {
logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getName()); if (walker != null)
logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getSimpleName());
else else
logger.warn("Annotation will not be calculated, must be called from VariantAnnotator"); logger.warn("Annotation will not be calculated, must be called from VariantAnnotator");
walkerIdentityCheckWarningLogged = true; walkerIdentityCheckWarningLogged = true;
} }
}
return null; return null;
} }

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java
View File

@ -95,13 +95,15 @@ public class SpanningDeletions extends InfoFieldAnnotation implements StandardUG
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) { final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
// Can only call from UnifiedGenotyper // Can only call from UnifiedGenotyper
if ( !(walker instanceof UnifiedGenotyper) ) { if ( !(walker instanceof UnifiedGenotyper) ) {
if ( !walkerIdentityCheckWarningLogged ) { synchronized (this) {
if ( walker != null ) if (!walkerIdentityCheckWarningLogged) {
logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper, not " + walker.getClass().getName()); if (walker != null)
logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper, not " + walker.getClass().getSimpleName());
else else
logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper"); logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper");
walkerIdentityCheckWarningLogged = true; walkerIdentityCheckWarningLogged = true;
} }
}
return null; return null;
} }

1
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java
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@ -79,7 +79,6 @@ import java.util.*;
*/ */
public class TandemRepeatAnnotator extends InfoFieldAnnotation implements StandardUGAnnotation, ActiveRegionBasedAnnotation { public class TandemRepeatAnnotator extends InfoFieldAnnotation implements StandardUGAnnotation, ActiveRegionBasedAnnotation {
private final static Logger logger = Logger.getLogger(TandemRepeatAnnotator.class); private final static Logger logger = Logger.getLogger(TandemRepeatAnnotator.class);
private boolean walkerIdentityCheckWarningLogged = false;
@Override @Override
public Map<String, Object> annotate(final RefMetaDataTracker tracker, public Map<String, Object> annotate(final RefMetaDataTracker tracker,

12
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java
View File

@ -101,13 +101,15 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
// Can only be called from VariantAnnotator // Can only be called from VariantAnnotator
if ( !(walker instanceof VariantAnnotator) ) { if ( !(walker instanceof VariantAnnotator) ) {
if ( !walkerIdentityCheckWarningLogged ) { synchronized (this) {
if ( walker != null ) if (!walkerIdentityCheckWarningLogged) {
logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getName()); if (walker != null)
logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getSimpleName());
else else
logger.warn("Annotation will not be calculated, must be called from VariantAnnotator"); logger.warn("Annotation will not be calculated, must be called from VariantAnnotator");
walkerIdentityCheckWarningLogged = true; walkerIdentityCheckWarningLogged = true;
} }
}
return null; return null;
} }
@ -115,10 +117,12 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
if ( trios == null ) { if ( trios == null ) {
trios = ((VariantAnnotator) walker).getSampleDB().getChildrenWithParents(); trios = ((VariantAnnotator) walker).getSampleDB().getChildrenWithParents();
if (trios == null || trios.isEmpty()) { if (trios == null || trios.isEmpty()) {
if ( !pedigreeCheckWarningLogged ) { synchronized (this) {
if (!pedigreeCheckWarningLogged) {
logger.warn("Transmission disequilibrium test annotation requires a valid ped file be passed in."); logger.warn("Transmission disequilibrium test annotation requires a valid ped file be passed in.");
pedigreeCheckWarningLogged = true; pedigreeCheckWarningLogged = true;
} }
}
return null; return null;
} }
} }

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySample.java
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@ -115,13 +115,15 @@ public class BaseQualitySumPerAlleleBySample extends GenotypeAnnotation implemen
// Can only call from MuTect2 // Can only call from MuTect2
if ( !(walker instanceof MuTect2) ) { if ( !(walker instanceof MuTect2) ) {
if ( !walkerIdentityCheckWarningLogged ) { synchronized (this) {
if ( walker != null ) if (!walkerIdentityCheckWarningLogged) {
logger.warn("Annotation will not be calculated, can only be called from MuTect2, not " + walker.getClass().getName()); if (walker != null)
logger.warn("Annotation will not be calculated, can only be called from MuTect2, not " + walker.getClass().getSimpleName());
else else
logger.warn("Annotation will not be calculated, can only be called from MuTect2"); logger.warn("Annotation will not be calculated, can only be called from MuTect2");
walkerIdentityCheckWarningLogged = true; walkerIdentityCheckWarningLogged = true;
} }
}
return; return;
} }

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/OxoGReadCounts.java
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@ -121,13 +121,15 @@ public class OxoGReadCounts extends GenotypeAnnotation {
// Can only call from MuTect2 // Can only call from MuTect2
if ( !(walker instanceof MuTect2) ) { if ( !(walker instanceof MuTect2) ) {
if ( !walkerIdentityCheckWarningLogged ) { synchronized (this) {
if ( walker != null ) if (!walkerIdentityCheckWarningLogged) {
logger.warn("Annotation will not be calculated, can only be called from MuTect2, not " + walker.getClass().getName()); if (walker != null)
logger.warn("Annotation will not be calculated, can only be called from MuTect2, not " + walker.getClass().getSimpleName());
else else
logger.warn("Annotation will not be calculated, can only be called from MuTect2"); logger.warn("Annotation will not be calculated, can only be called from MuTect2");
walkerIdentityCheckWarningLogged = true; walkerIdentityCheckWarningLogged = true;
} }
}
return; return;
} }