Using Utils.stream and Utils.validate

Author: davidbenjamin

src/main/java/org/broadinstitute/hellbender/engine/AbstractConcordanceWalker.java

@@ -3,14 +3,11 @@
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.util.Locatable;
 import htsjdk.samtools.util.PeekableIterator;
-import htsjdk.samtools.util.SequenceUtil;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextComparator;
 import htsjdk.variant.vcf.VCFHeader;
 import org.apache.commons.collections4.Predicate;
 import org.apache.commons.collections4.iterators.FilterIterator;
-import org.apache.commons.lang3.tuple.ImmutablePair;
-import org.apache.commons.lang3.tuple.Pair;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.hellbender.exceptions.GATKException;
 import org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState;
@@ -23,7 +20,6 @@
 import java.util.Optional;
 import java.util.Spliterator;
 import java.util.Spliterators;
-import java.util.stream.StreamSupport;
 
 /**
  * Base class for concordance walkers, which process one variant at a time from one or more sources of variants,
@@ -88,10 +84,10 @@ protected Predicate<VariantContext> makeVariantFilter() {
         return vc -> !vc.isFiltered();
     }
 
-    private Spliterator<TruthVersusEval> getSpliteratorForDrivingVariants() {
+    private Iterator<TruthVersusEval> getIteratorForDrivingVariants() {
         final Iterator<VariantContext> truthIterator = new FilterIterator<>(truthVariants.iterator(), makeVariantFilter());
         final Iterator<VariantContext> evalIterator = new FilterIterator<>(evalVariants.iterator(), makeVariantFilter());
-        return new ConcordanceIterator(truthIterator, evalIterator).spliterator();
+        return new ConcordanceIterator(truthIterator, evalIterator);
     }
 
     // ********** The basic traversal structure of GATKTool
@@ -118,7 +114,7 @@ protected final void onStartup() {
     @Override
     public final void traverse() {
         // Process each variant in the input stream.
-        StreamSupport.stream(getSpliteratorForDrivingVariants(), false)
+        Utils.stream(getIteratorForDrivingVariants())
                 .forEach(truthVersusEval -> {
                     final SimpleInterval variantInterval = new SimpleInterval(truthVersusEval);
                     apply(truthVersusEval, new ReadsContext(reads, variantInterval), new ReferenceContext(reference, variantInterval));

src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java

@@ -45,7 +45,6 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
-import java.util.stream.StreamSupport;
 
 /**
  * Call germline SNPs and indels via local re-assembly of haplotypes
@@ -178,15 +177,10 @@ private static FlatMapFunction<Iterator<Tuple2<AssemblyRegion, SimpleInterval>>,
             //HaplotypeCallerEngine isn't serializable but is expensive to instantiate, so construct and reuse one for every partition
             final ReferenceMultiSourceAdapter referenceReader = new ReferenceMultiSourceAdapter(referenceBroadcast.getValue(), authHolder);
             final HaplotypeCallerEngine hcEngine = new HaplotypeCallerEngine(hcArgsBroadcast.value(), header, referenceReader);
-            return iteratorToStream(regionAndIntervals).flatMap(regionToVariants(hcEngine)).iterator();
+            return Utils.stream(regionAndIntervals).flatMap(regionToVariants(hcEngine)).iterator();
         };
     }
 
-    private static <T> Stream<T> iteratorToStream(Iterator<T> iterator) {
-        Iterable<T> regionsIterable = () -> iterator;
-        return StreamSupport.stream(regionsIterable.spliterator(), false);
-    }
-
     private static Function<Tuple2<AssemblyRegion, SimpleInterval>, Stream<? extends VariantContext>> regionToVariants(HaplotypeCallerEngine hcEngine) {
         return regionAndInterval -> {
             final List<VariantContext> variantContexts = hcEngine.callRegion(regionAndInterval._1(), new FeatureContext());
@@ -258,7 +252,7 @@ private static FlatMapFunction<Iterator<Shard<GATKRead>>, Tuple2<AssemblyRegion,
             final ReferenceMultiSourceAdapter referenceSource = new ReferenceMultiSourceAdapter(referenceMultiSource, authHolder);
             final HaplotypeCallerEngine hcEngine = new HaplotypeCallerEngine(hcArgsBroadcast.value(), header, referenceSource);
 
-            return iteratorToStream(shards).flatMap(shardToRegion(assemblyArgs, header, referenceSource, hcEngine)).iterator();
+            return Utils.stream(shards).flatMap(shardToRegion(assemblyArgs, header, referenceSource, hcEngine)).iterator();
         };
     }
 
@@ -279,8 +273,7 @@ private static Function<Shard<GATKRead>, Stream<? extends Tuple2<AssemblyRegion,
                     assemblyArgs.assemblyRegionPadding, assemblyArgs.activeProbThreshold,
                     assemblyArgs.maxProbPropagationDistance);
 
-            return StreamSupport.stream(assemblyRegions.spliterator(), false)
-                    .map(a -> new Tuple2<>(a, shard.getInterval()));
+            return Utils.stream(assemblyRegions).map(a -> new Tuple2<>(a, shard.getInterval()));
         };
     }
 

src/main/java/org/broadinstitute/hellbender/tools/exome/CombineReadCounts.java

@@ -9,6 +9,7 @@
 import org.broadinstitute.hellbender.exceptions.GATKException;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
+import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.tsv.DataLine;
 import org.broadinstitute.hellbender.utils.tsv.TableColumnCollection;
 import org.broadinstitute.hellbender.utils.tsv.TableReader;
@@ -504,9 +505,7 @@ private void composeCountColumnNamesAndSourceIndexMapping() {
             for (final TableReader<ReadCountRecord> reader : readers) {
                 unsortedCountColumnNames.addAll(readCountColumnNames(reader.columns()));
             }
-            if (unsortedCountColumnNames.isEmpty()) {
-                throw new IllegalStateException("there must be at least one count column");
-            }
+            Utils.validate(!unsortedCountColumnNames.isEmpty(), "there must be at least one count column");
             countColumnSourceIndexMap = IntStream.range(0, unsortedCountColumnNames.size()).boxed()
                     .sorted(Comparator.comparing(unsortedCountColumnNames::get))
                     .mapToInt(Integer::intValue).toArray();

src/main/java/org/broadinstitute/hellbender/tools/exome/ReadCountCollectionUtils.java

@@ -151,9 +151,7 @@ public static TableWriter<ReadCountRecord> writerWithIntervals(final Writer writ
             @Override
             protected void composeLine(final ReadCountRecord record, final DataLine dataLine) {
                 final SimpleInterval interval = record.getTarget().getInterval();
-                if (interval == null) {
-                    throw new IllegalStateException("invalid combination of targets with and without intervals defined");
-                }
+                Utils.validate(interval != null, "invalid combination of targets with and without intervals defined");
                 dataLine.append(interval.getContig())
                         .append(interval.getStart())
                         .append(interval.getEnd())

src/main/java/org/broadinstitute/hellbender/tools/exome/Target.java

@@ -98,25 +98,19 @@ public String getName() {
      // Three methods to implement Locatable
     @Override
     public String getContig() {
-        if (interval == null) {
-            throw new IllegalStateException("the target does not have an interval assigned");
-        }
+        Utils.validate(interval != null, "the target does not have an interval assigned");
         return interval.getContig();
     }
 
     @Override
     public int getStart() {
-        if (interval == null) {
-            throw new IllegalStateException("the target does not have an interval assigned");
-        }
+        Utils.validate(interval != null, "the target does not have an interval assigned");
         return interval.getStart();
     }
 
     @Override
     public int getEnd() {
-        if (interval == null) {
-            throw new IllegalStateException("the target does not have an interval assigned");
-        }
+        Utils.validate(interval != null, "the target does not have an interval assigned");
         return interval.getEnd();
     }
 

src/main/java/org/broadinstitute/hellbender/tools/exome/convertbed/ConvertBedToTargetFile.java

@@ -14,11 +14,11 @@
 import org.broadinstitute.hellbender.tools.exome.Target;
 import org.broadinstitute.hellbender.tools.exome.TargetWriter;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
+import org.broadinstitute.hellbender.utils.Utils;
 
 import java.io.File;
 import java.util.List;
 import java.util.stream.Collectors;
-import java.util.stream.StreamSupport;
 
 @CommandLineProgramProperties(
         summary = "Converts a target bed file to the target file format. Empty files will probably fail. Drops bed file columns other than the first four.",
@@ -55,7 +55,7 @@ protected Object doWork() {
         final Class<? extends Feature> featureType = codec.getFeatureType();
         if (BEDFeature.class.isAssignableFrom(featureType)) {
             final FeatureDataSource<? extends BEDFeature> source = new FeatureDataSource<>(inputBedFile);
-            final List<Target> targets = StreamSupport.stream(source.spliterator(), false).map(ConvertBedToTargetFile::createTargetFromBEDFeature)
+            final List<Target> targets = Utils.stream(source).map(ConvertBedToTargetFile::createTargetFromBEDFeature)
                     .collect(Collectors.toList());
             TargetWriter.writeTargetsToFile(outFile, targets);
         } else {

src/main/java/org/broadinstitute/hellbender/tools/exome/eval/EvaluateCopyNumberTriStateCalls.java

@@ -33,7 +33,6 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
-import java.util.stream.StreamSupport;
 
 /**
  * Tool to evaluate the output of {@link XHMMSegmentCaller}.
@@ -651,8 +650,7 @@ private CopyNumberTriStateAllele copyNumberToTrueAllele(final int cn) {
      * @return never {@code null}, potentially immutably
      */
     private List<VariantContext> variantQueryToList(final VCFFileReader reader, final Locatable interval) {
-        return StreamSupport.stream(Spliterators.spliteratorUnknownSize(reader.query(interval.getContig(),
-                interval.getStart(), interval.getEnd()), Spliterator.NONNULL),false)
+        return Utils.stream(reader.query(interval.getContig(), interval.getStart(), interval.getEnd()))
                 .sorted(IntervalUtils.LEXICOGRAPHICAL_ORDER_COMPARATOR)
                 .collect(Collectors.toList());
     }

src/main/java/org/broadinstitute/hellbender/tools/exome/eval/VariantEvaluationContext.java

@@ -69,9 +69,8 @@ private double[] getAlleleDoubleArrayFromAlternativeAlleleArrayAttribute(final S
         final double[] alternativeAllelesFrequencies = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(this, key,
                 () -> { return new double[alleles.size() - 1]; }, missingValue);
         final double[] result = new double[alleles.size()];
-        if (alternativeAllelesFrequencies.length != alleles.size() - 1) {
-            throw new IllegalStateException(String.format("We expect the %s Info annotation to contain an array of %d elements (alt. allele count)", key, alleles.size() - 1));
-        }
+        Utils.validate(alternativeAllelesFrequencies.length == alleles.size() - 1,
+                () -> String.format("We expect the %s Info annotation to contain an array of %d elements (alt. allele count)", key, alleles.size() - 1));
         System.arraycopy(alternativeAllelesFrequencies, 0, result, 1, alternativeAllelesFrequencies.length);
         final double nonRefSum = MathUtils.sum(result);
         Utils.validateArg(nonRefSum <= 1.0, () -> String.format("The sum of element on annotation %s cannot greater than 1.0: %g", key, nonRefSum));

src/main/java/org/broadinstitute/hellbender/tools/exome/eval/VariantEvaluationContextBuilder.java

@@ -81,9 +81,7 @@ public VariantEvaluationContextBuilder alleles(final String... alleleStrings) {
     @Override
     public List<Allele> getAlleles() {
         final List<Allele> result = super.getAlleles();
-        if (result == null) {
-            throw new IllegalStateException("you must set the alleles before calling getAlleles");
-        }
+        Utils.validate(result != null, "you must set the alleles before calling getAlleles");
         return result;
     }
 

src/main/java/org/broadinstitute/hellbender/tools/exome/sexgenotyper/SexGenotypeData.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.tools.exome.sexgenotyper;
 
 import org.broadinstitute.hellbender.exceptions.UserException;
+import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.param.ParamUtils;
 
 import javax.annotation.Nonnull;
@@ -60,11 +61,8 @@ public SexGenotypeData(@Nonnull final String sampleName,
      * @return set of genotype string identifiers
      */
     public Set<String> getSexGenotypesSet() {
-        if (logLikelihoodMap != null) {
-            return logLikelihoodMap.keySet();
-        } else {
-            throw new IllegalStateException("Genotyping inference data is not available");
-        }
+        Utils.validate(logLikelihoodMap != null, "Genotyping inference data is not available");
+        return logLikelihoodMap.keySet();
     }
 
     /**
@@ -73,11 +71,8 @@ public Set<String> getSexGenotypesSet() {
      * @return log likelihood
      */
     public double getLogLikelihoodPerGenotype(@Nonnull final String genotype) {
-        if (logLikelihoodMap != null) {
-            return logLikelihoodMap.get(genotype);
-        } else {
-            throw new IllegalStateException("Genotyping inference data is not available");
-        }
+        Utils.validate(logLikelihoodMap != null, "Genotyping inference data is not available");
+        return logLikelihoodMap.get(genotype);
     }
 
     /**