code format change

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

@@ -648,10 +648,11 @@ protected HaplotypeCallerGenotypingEngine getLocalGenotypingEngine(Locatable reg
     /**
      * Given a pileup, returns an ActivityProfileState containing the probability (0.0 to 1.0) that it's an "active" site.
      *
+     * <p>
      * Note that the current implementation will always return either 1.0 or 0.0, as it relies on the smoothing in
      * {@link org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile} to create the full distribution
      * of probabilities. This is consistent with GATK 3.
-     *
+     *</p>
      * @param context reads pileup to examine
      * @param ref reference base overlapping the pileup locus
      * @param features features overlapping the pileup locus
@@ -743,7 +744,7 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
 
         final List<VariantContext> VCpriors = new ArrayList<>();
         if (hcArgs.standardArgs.genotypeArgs.supportVariants != null) {
-            features.getValues(hcArgs.standardArgs.genotypeArgs.supportVariants).stream().forEach(VCpriors::add);
+            VCpriors.addAll(features.getValues(hcArgs.standardArgs.genotypeArgs.supportVariants));
         }
 
         if ( hcArgs.sampleNameToUse != null ) {
@@ -784,7 +785,7 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
         if (assemblyDebugOutStream != null) {
             try {
                 assemblyDebugOutStream.write("\nThere were " + untrimmedAssemblyResult.getHaplotypeList().size() + " haplotypes found. Here they are:\n");
-                for (final String haplotype : untrimmedAssemblyResult.getHaplotypeList().stream().map(Haplotype::toString).sorted().collect(Collectors.toList())) {
+                for (final String haplotype : untrimmedAssemblyResult.getHaplotypeList().stream().map(Haplotype::toString).sorted().toList()) {
                     assemblyDebugOutStream.write(haplotype);
                     assemblyDebugOutStream.append('\n');
                 }
@@ -1110,7 +1111,7 @@ public void shutdown() {
         if (pdhmmLikelihoodCalculationEngine != null) pdhmmLikelihoodCalculationEngine.close();
         aligner.close();
         haplotypeBAMWriter.ifPresent(HaplotypeBAMWriter::close);
-        assembledEventMapVcfOutputWriter.ifPresent(writer -> {assembledEventMapVariants.get().forEach(event -> writer.add(event)); writer.close();});
+        assembledEventMapVcfOutputWriter.ifPresent(writer -> {assembledEventMapVariants.get().forEach(writer::add); writer.close();});
         if ( referenceReader != null) {
             try {
                 referenceReader.close();

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java

@@ -53,12 +53,12 @@ public class RampedHaplotypeCallerEngine extends HaplotypeCallerEngine {
     // haplotype caller phases, as consumers
     final private List<Consumer<CallRegionContext>>   phases =
             Arrays.asList(
-                    p -> prepare(p),
-                    p -> assemble(p),
-                    p -> computeReadLikelihoods(p),
-                    p -> uncollapse(p),
-                    p -> filter(p),
-                    p -> genotype(p)
+                    this::prepare,
+                    this::assemble,
+                    this::computeReadLikelihoods,
+                    this::uncollapse,
+                    this::filter,
+                    this::genotype
             );
 
     public RampedHaplotypeCallerEngine(final HaplotypeCallerArgumentCollection hcArgs, AssemblyRegionArgumentCollection assemblyRegionArgs, boolean createBamOutIndex,
@@ -91,8 +91,6 @@ public void buildRamps() {
 
                 // create ramp
                 switch ( rpArgs.offRampType ) {
-                    case NONE:
-                        break;
                     case PRE_FILTER_OFF:
                         preFilterOffRamp = new PreFilterOffRamp(rpArgs.offRampFile);
                         break;
@@ -111,8 +109,6 @@ public void buildRamps() {
 
                 // create ramp
                 switch ( rpArgs.onRampType ) {
-                    case NONE:
-                        break;
                     case POST_FILTER_ON:
                         if ( rpArgs.offRampType == RampedHaplotypeCallerArgumentCollection.OffRampTypeEnum.PRE_FILTER_OFF ) {
                             throw new IllegalArgumentException("an on ramp, if present, must be before the off ramp");
@@ -145,7 +141,7 @@ private void tearRamps() {
             throw new RuntimeException(e);
         }
     }
-    private class CallRegionContext {
+    private static class CallRegionContext {
 
         // params
         final AssemblyRegion region;
@@ -232,7 +228,7 @@ private void prepare(final CallRegionContext context) {
 
         context.VCpriors = new ArrayList<>();
         if (hcArgs.standardArgs.genotypeArgs.supportVariants != null) {
-            context.features.getValues(hcArgs.standardArgs.genotypeArgs.supportVariants).stream().forEach(context.VCpriors::add);
+            context.VCpriors.addAll(context.features.getValues(hcArgs.standardArgs.genotypeArgs.supportVariants));
         }
 
         if (hcArgs.sampleNameToUse != null) {
@@ -324,7 +320,8 @@ private void assemble(final CallRegionContext context) {
 
             // run the local assembler, getting back a collection of information on how we should proceed
             RampUtils.logReads(rpArgs.rampsDebugReads, "BEFORE untrimmedAssemblyResult reads", context.region.getReads());
-            List<VariantContext> forcedPileupAlleles = Collections.emptyList(); // TODO: we currently do not support pileup alleles in RampedHaplotypeCaller, this should be added
+            // TODO: we currently do not support pileup alleles in RampedHaplotypeCaller, this should be added ...
+            // List<VariantContext> forcedPileupAlleles = Collections.emptyList();
             final AssemblyResultSet untrimmedAssemblyResult = AssemblyBasedCallerUtils.assembleReads(context.region, hcArgs, readsHeader, samplesList, logger, referenceReader, assemblyEngine, aligner,
                     !hcArgs.doNotCorrectOverlappingBaseQualities, postFilterOnRamp != null);
             RampUtils.logReads(rpArgs.rampsDebugReads, "AFTER untrimmedAssemblyResult reads", context.region.getReads());
@@ -342,7 +339,7 @@ private void assemble(final CallRegionContext context) {
 
             if (assemblyDebugOutStream != null) {
                 assemblyDebugOutStream.write("\nThere were " + untrimmedAssemblyResult.getHaplotypeList().size() + " haplotypes found. Here they are:");
-                for (final String haplotype : untrimmedAssemblyResult.getHaplotypeList().stream().map(Haplotype::toString).sorted().collect(Collectors.toList())) {
+                for (final String haplotype : untrimmedAssemblyResult.getHaplotypeList().stream().map(Haplotype::toString).sorted().toList()) {
                     assemblyDebugOutStream.write(haplotype);
                 }
             }

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java

@@ -612,7 +612,7 @@ public static double logLikelihoodRatio(final int refCount, final List<Byte> alt
      * @param altQuals      Phred-scaled qualities of alt-supporting reads
      * @param repeatFactor  Number of times each alt qual is duplicated
      * @param afPrior       Beta prior on alt allele fraction
-     * @return
+     * @return double
      */
     public static double logLikelihoodRatio(final int nRef, final List<Byte> altQuals, final int repeatFactor, final Optional<BetaDistributionShape> afPrior) {
         final int nAlt = repeatFactor * altQuals.size();
@@ -700,7 +700,7 @@ private static class PileupQualBuffer {
         private static double MULTIPLE_SUBSTITUTION_BASE_QUAL_CORRECTION;
 
         // indices 0-3 are A,C,G,T; 4 is other substitution (just in case it's some exotic protocol); 5 is indel
-        private List<ByteArrayList> buffers = IntStream.range(0,6).mapToObj(n -> new ByteArrayList()).collect(Collectors.toList());
+        private final List<ByteArrayList> buffers = IntStream.range(0,6).mapToObj(n -> new ByteArrayList()).toList();
 
         public PileupQualBuffer(final double multipleSubstitutionQualCorrection) {
             MULTIPLE_SUBSTITUTION_BASE_QUAL_CORRECTION = multipleSubstitutionQualCorrection;