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Swapped mito mode in Mutect to use the mode argument utils #8986

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merged 2 commits into from
Sep 24, 2024
Merged

Swapped mito mode in Mutect to use the mode argument utils #8986

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370d5ea
Swapped MitochondriaMode in mutect to use the mode argument utils
jamesemery Sep 23, 2024
1eaeb7d
checked the OA looks like its being tested in the mito tests
jamesemery Sep 23, 2024
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38 changes: 22 additions & 16 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,13 @@
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.ArgumentCollection;
import org.broadinstitute.barclay.argparser.DeprecatedFeature;
import org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection;
import org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.engine.FeatureInput;
import org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection;
import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod;
import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentArgumentCollection;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.*;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;
Expand Down Expand Up @@ -95,18 +100,6 @@ protected ReadThreadingAssemblerArgumentCollection getReadThreadingAssemblerArgu
return new MutectReadThreadingAssemblerArgumentCollection();
}

@Override
public ReadThreadingAssembler createReadThreadingAssembler(){
if(mitochondria ) {
assemblerArgs.recoverAllDanglingBranches = true;
if (assemblerArgs.pruningLogOddsThreshold == ReadThreadingAssemblerArgumentCollection.DEFAULT_PRUNING_LOG_ODDS_THRESHOLD) {
assemblerArgs.pruningLogOddsThreshold = DEFAULT_MITO_PRUNING_LOG_ODDS_THRESHOLD;
}
}

return super.createReadThreadingAssembler();
}

@ArgumentCollection
public CollectF1R2CountsArgumentCollection f1r2Args = new CollectF1R2CountsArgumentCollection();

Expand Down Expand Up @@ -164,8 +157,7 @@ public ReadThreadingAssembler createReadThreadingAssembler(){

public double getDefaultAlleleFrequency() {
return afOfAllelesNotInGermlineResource >= 0 ? afOfAllelesNotInGermlineResource :
(mitochondria ? DEFAULT_AF_FOR_MITO_CALLING:
(normalSamples.isEmpty() ? DEFAULT_AF_FOR_TUMOR_ONLY_CALLING : DEFAULT_AF_FOR_TUMOR_NORMAL_CALLING));
(normalSamples.isEmpty() ? DEFAULT_AF_FOR_TUMOR_ONLY_CALLING : DEFAULT_AF_FOR_TUMOR_NORMAL_CALLING);
}

/**
Expand All @@ -176,6 +168,20 @@ public double getDefaultAlleleFrequency() {
@Argument(fullName = MITOCHONDRIA_MODE_LONG_NAME, optional = true, doc="Mitochondria mode sets emission and initial LODs to 0.")
public Boolean mitochondria = false;

/**
* List of arguments to be set when a user specifies mitochondria mode. Each argument will be displayed in the help message.
*/
public String[] getMitochondriaModeNameValuePairs() {
return new String[]{
DEFAULT_AF_LONG_NAME, String.valueOf(DEFAULT_AF_FOR_MITO_CALLING),
EMISSION_LOD_LONG_NAME, String.valueOf(DEFAULT_MITO_EMISSION_LOD),
INITIAL_TUMOR_LOG_10_ODDS_LONG_NAME, String.valueOf(DEFAULT_MITO_INITIAL_LOG_10_ODDS),
ReadThreadingAssemblerArgumentCollection.RECOVER_ALL_DANGLING_BRANCHES_LONG_NAME, "true",
ReadThreadingAssemblerArgumentCollection.PRUNING_LOD_THRESHOLD_LONG_NAME, String.valueOf(DEFAULT_MITO_PRUNING_LOG_ODDS_THRESHOLD),
StandardArgumentDefinitions.ANNOTATION_LONG_NAME, "OriginalAlignment"
};
}

/**
* If true, collect Mutect3 data for learning; otherwise collect data for generating calls with a pre-trained model
*/
Expand Down Expand Up @@ -250,7 +256,7 @@ public double getEmissionLogOdds() {
if (emitReferenceConfidence != ReferenceConfidenceMode.NONE) {
return MathUtils.log10ToLog(DEFAULT_GVCF_LOG_10_ODDS);
}
return MathUtils.log10ToLog(mitochondria && emissionLog10Odds == DEFAULT_EMISSION_LOG_10_ODDS ? DEFAULT_MITO_EMISSION_LOD : emissionLog10Odds);
return MathUtils.log10ToLog(emissionLog10Odds);
}

/**
Expand All @@ -263,7 +269,7 @@ public double getInitialLogOdds() {
if (emitReferenceConfidence != ReferenceConfidenceMode.NONE) {
return MathUtils.log10ToLog(DEFAULT_GVCF_LOG_10_ODDS);
}
return MathUtils.log10ToLog(mitochondria && initialLog10Odds == DEFAULT_INITIAL_LOG_10_ODDS ? DEFAULT_MITO_INITIAL_LOG_10_ODDS : initialLog10Odds);
return MathUtils.log10ToLog(initialLog10Odds);
}


Expand Down
20 changes: 9 additions & 11 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,11 @@
import org.broadinstitute.barclay.argparser.CommandLineException;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup;
import org.broadinstitute.hellbender.engine.*;
import org.broadinstitute.hellbender.engine.filters.MappingQualityReadFilter;
import org.broadinstitute.hellbender.engine.filters.ReadFilter;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.tools.walkers.annotator.*;
Expand Down Expand Up @@ -283,17 +285,6 @@ public void onTraversalStart() {
m2Engine.writeHeader(vcfWriter, getDefaultToolVCFHeaderLines());
}

@Override
public Collection<Annotation> makeVariantAnnotations(){
final Collection<Annotation> annotations = super.makeVariantAnnotations();

if (MTAC.mitochondria) {
annotations.add(new OriginalAlignment());
}

return annotations;
}

@Override
public Object onTraversalSuccess() {
m2Engine.writeExtraOutputs(new File(outputVCF + DEFAULT_STATS_EXTENSION));
Expand Down Expand Up @@ -322,6 +313,13 @@ public void closeTool() {
*/
@Override
protected String[] customCommandLineValidation() {
if (MTAC.mitochondria) {
//TODO check the OA argument, that might be the only thing that doesn't work
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ModeArgumentUtils.setArgValues(
getCommandLineParser(),
MTAC.getMitochondriaModeNameValuePairs(),
M2ArgumentCollection.MITOCHONDRIA_MODE_LONG_NAME);
}
if (MTAC.flowMode != M2ArgumentCollection.FlowMode.NONE) {
ModeArgumentUtils.setArgValues(
getCommandLineParser(),
Expand Down
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