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

… better override behavior and documentation (#8986)

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);
  }
 
 

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(),