Swapped mito mode in Mutect to use the mode argument utils, providing…

… better override behavior and documentation (#8986)
broadinstitute · Sep 24, 2024 · e1b5f95 · e1b5f95
1 parent 6036d67
commit e1b5f95
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Showing 2 changed files with 30 additions and 27 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
@@ -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;
@@ -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();
 
@@ -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);
     }
 
     /**
@@ -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
      */
@@ -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);
     }
 
     /**
@@ -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);
     }
 
 

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2.java
@@ -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.*;
@@ -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));
@@ -322,6 +313,12 @@ public void closeTool() {
      */
     @Override
     protected String[] customCommandLineValidation() {
+        if (MTAC.mitochondria) {
+            ModeArgumentUtils.setArgValues(
+                    getCommandLineParser(),
+                    MTAC.getMitochondriaModeNameValuePairs(),
+                    M2ArgumentCollection.MITOCHONDRIA_MODE_LONG_NAME);
+        }
         if (MTAC.flowMode != M2ArgumentCollection.FlowMode.NONE) {
             ModeArgumentUtils.setArgValues(
                     getCommandLineParser(),