Get rid of ancient, unused option to track unique reads in a LIBS

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

@@ -60,7 +60,7 @@ public ActivityProfileStateIterator(final MultiIntervalShard<GATKRead> readShard
 
         // We wrap our LocusIteratorByState inside an IntervalAlignmentContextIterator so that we get empty loci
         // for uncovered locations. This is critical for reproducing GATK 3.x behavior!
-        LocusIteratorByState libs = new LocusIteratorByState(readShard.iterator(), DownsamplingMethod.NONE, false, ReadUtils.getSamplesFromHeader(readHeader), readHeader, true);
+        LocusIteratorByState libs = new LocusIteratorByState(readShard.iterator(), DownsamplingMethod.NONE, ReadUtils.getSamplesFromHeader(readHeader), readHeader, true);
         final IntervalLocusIterator intervalLocusIterator = new IntervalLocusIterator(readShard.getIntervals().iterator());
         this.locusIterator = new IntervalAlignmentContextIterator(libs, intervalLocusIterator, readHeader.getSequenceDictionary());
     }

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

@@ -89,7 +89,7 @@ public AssemblyRegionIterator(final MultiIntervalShard<GATKRead> readShard,
 
         // We wrap our LocusIteratorByState inside an IntervalAlignmentContextIterator so that we get empty loci
         // for uncovered locations. This is critical for reproducing GATK 3.x behavior!
-        this.libs = new LocusIteratorByState(readCachingIterator, DownsamplingMethod.NONE, false, ReadUtils.getSamplesFromHeader(readHeader), readHeader, true);
+        this.libs = new LocusIteratorByState(readCachingIterator, DownsamplingMethod.NONE, ReadUtils.getSamplesFromHeader(readHeader), readHeader, true);
         final IntervalLocusIterator intervalLocusIterator = new IntervalLocusIterator(readShard.getIntervals().iterator());
         this.locusIterator = new IntervalAlignmentContextIterator(libs, intervalLocusIterator, readHeader.getSequenceDictionary());
 

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

@@ -8,7 +8,6 @@
 import org.broadinstitute.hellbender.engine.filters.ReadFilter;
 import org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary;
 import org.broadinstitute.hellbender.engine.filters.WellformedReadFilter;
-import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.locusiterator.AlignmentContextIteratorBuilder;
 import org.broadinstitute.hellbender.utils.locusiterator.LIBSDownsamplingInfo;
@@ -43,13 +42,6 @@ public abstract class LocusWalker extends WalkerBase {
     @Argument(fullName = MAX_DEPTH_PER_SAMPLE_NAME, shortName = MAX_DEPTH_PER_SAMPLE_NAME, doc = "Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.", optional = true)
     protected int maxDepthPerSample = defaultMaxDepthPerSample();
 
-    /**
-     * Should the LIBS keep unique reads? Tools that do should override to return {@code true}.
-     */
-    protected boolean keepUniqueReadListInLibs() {
-        return false;
-    }
-
     /**
      * LocusWalkers requires read sources
      */
@@ -185,7 +177,6 @@ final Iterator<AlignmentContext> getAlignmentContextIterator(final CountingReadF
         alignmentContextIteratorBuilder.setDownsamplingInfo(getDownsamplingInfo());
         alignmentContextIteratorBuilder.setEmitEmptyLoci(emitEmptyLoci());
         alignmentContextIteratorBuilder.setIncludeDeletions(includeDeletions());
-        alignmentContextIteratorBuilder.setKeepUniqueReadListInLibs(keepUniqueReadListInLibs());
         alignmentContextIteratorBuilder.setIncludeNs(includeNs());
 
         return alignmentContextIteratorBuilder.build(

src/main/java/org/broadinstitute/hellbender/engine/spark/LocusWalkerSpark.java

@@ -10,7 +10,6 @@
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineException;
 import org.broadinstitute.hellbender.engine.*;
-import org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource;
 import org.broadinstitute.hellbender.utils.IntervalUtils;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
@@ -19,7 +18,10 @@
 import org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 
-import java.util.*;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Spliterators;
 import java.util.stream.Collectors;
 import java.util.stream.StreamSupport;
 
@@ -116,7 +118,6 @@ private static FlatMapFunction<Shard<GATKRead>, LocusWalkerContext> getAlignment
             final AlignmentContextIteratorBuilder alignmentContextIteratorBuilder = new AlignmentContextIteratorBuilder();
             alignmentContextIteratorBuilder.setDownsamplingInfo(downsamplingInfo);
             alignmentContextIteratorBuilder.setEmitEmptyLoci(isEmitEmptyLoci);
-            alignmentContextIteratorBuilder.setKeepUniqueReadListInLibs(false);
             alignmentContextIteratorBuilder.setIncludeNs(false);
 
             final Iterator<AlignmentContext> alignmentContextIterator = alignmentContextIteratorBuilder.build(

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

@@ -454,8 +454,7 @@ public static List<ReadPileup> getPileupsOverReference(final SAMFileHeader reads
         final List<GATKRead> reads = new ArrayList<>(readLikelihoods.sampleEvidence(0));
         reads.sort(new ReadCoordinateComparator(readsHeader));  //because we updated the reads based on the local realignments we have to re-sort or the pileups will be... unpredictable
 
-        final LocusIteratorByState libs = new LocusIteratorByState(reads.iterator(), LocusIteratorByState.NO_DOWNSAMPLING,
-                false, samples.asSetOfSamples(), readsHeader, true);
+        final LocusIteratorByState libs = new LocusIteratorByState(reads.iterator(), LocusIteratorByState.NO_DOWNSAMPLING, samples.asSetOfSamples(), readsHeader, true);
 
         final int startPos = activeRegionSpan.getStart();
         final List<ReadPileup> pileups = new ArrayList<>(activeRegionSpan.getEnd() - startPos);

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

@@ -38,8 +38,7 @@ public PileupReadErrorCorrector(final double logOddsThreshold, final SAMFileHead
     public final List<GATKRead> correctReads(final Collection<GATKRead> originalReads) {
         final List<GATKRead> reads = originalReads.stream().map(GATKRead::deepCopy).collect(Collectors.toList());
 
-        final Iterator<AlignmentContext> locusIterator = new LocusIteratorByState(reads.iterator(), DownsamplingMethod.NONE,
-                false, ReadUtils.getSamplesFromHeader(header), header, false);
+        final Iterator<AlignmentContext> locusIterator = new LocusIteratorByState(reads.iterator(), DownsamplingMethod.NONE, ReadUtils.getSamplesFromHeader(header), header, false);
 
         final Map<GATKRead, List<Pair<Integer, Byte>>> potentialCorrections = reads.stream().collect(Collectors.toMap(read -> read, read -> new ArrayList<>()));
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/FilterAlignmentArtifacts.java

@@ -225,7 +225,7 @@ public void apply(List<VariantContext> variantContexts, ReferenceContext referen
             readLikelihoods.changeEvidence(readRealignments);
             writeBamOutput(assemblyResult, readLikelihoods, new HashSet<>(readLikelihoods.alleles()), regionForGenotyping.getSpan());
 
-            final LocusIteratorByState libs = new LocusIteratorByState(regionForGenotyping.getReads().iterator(), DownsamplingMethod.NONE, false, samplesList.asListOfSamples(), bamHeader, true);
+            final LocusIteratorByState libs = new LocusIteratorByState(regionForGenotyping.getReads().iterator(), DownsamplingMethod.NONE, samplesList.asListOfSamples(), bamHeader, true);
 
             final List<byte[]> unitigs = getUnitigs(libs);
 

src/main/java/org/broadinstitute/hellbender/utils/locusiterator/AlignmentContextIteratorBuilder.java

@@ -27,7 +27,6 @@ public class AlignmentContextIteratorBuilder {
     protected static final Logger logger = LogManager.getLogger(AlignmentContextIteratorBuilder.class);
 
     private boolean isEmitEmptyLoci;
-    private boolean isKeepUniqueReadListInLibs;
     private boolean isIncludeDeletions;
     private boolean isIncludeNs;
     private LIBSDownsamplingInfo downsamplingInfo;
@@ -36,10 +35,6 @@ public void setEmitEmptyLoci(boolean emitEmptyLoci) {
         isEmitEmptyLoci = emitEmptyLoci;
     }
 
-    public void setKeepUniqueReadListInLibs(boolean keepUniqueReadListInLibs) {
-        isKeepUniqueReadListInLibs = keepUniqueReadListInLibs;
-    }
-
     public void setIncludeDeletions(boolean includeDeletions) {
         isIncludeDeletions = includeDeletions;
     }
@@ -54,7 +49,6 @@ public void setDownsamplingInfo(LIBSDownsamplingInfo downsamplingInfo) {
 
     public AlignmentContextIteratorBuilder() {
         isEmitEmptyLoci = false;
-        isKeepUniqueReadListInLibs = false;
         isIncludeDeletions = true;
         isIncludeNs = false;
         downsamplingInfo = LocusIteratorByState.NO_DOWNSAMPLING;
@@ -75,7 +69,7 @@ public Iterator<AlignmentContext> build(final Iterator<GATKRead> readIterator, f
         Utils.nonNull(readIterator, "Read iterator cannot be null");
         final boolean isDefinitelyReference = (dictionary != null) && isReference ;
         return createAlignmentContextIterator(intervalsForTraversal, header, readIterator, dictionary, downsamplingInfo,
-                isDefinitelyReference, isEmitEmptyLoci, isKeepUniqueReadListInLibs, isIncludeDeletions, isIncludeNs);
+                isDefinitelyReference, isEmitEmptyLoci, isIncludeDeletions, isIncludeNs);
     }
 
     /**
@@ -90,8 +84,6 @@ public Iterator<AlignmentContext> build(final Iterator<GATKRead> readIterator, f
      * @param downsamplingInfo how to downsample (for {@link LocusIteratorByState})
      * @param isReference the dictionary specified above is a reference, {@code false} if no reference being used or it is not a reference.
      * @param emitEmptyLoci whether loci with no coverage should be emitted.  In this case, the AlignmentContext will be empty (not null).
-     * @param isKeepUniqueReadListInLibs if true, we will keep the unique reads from the samIterator and make them
-     *                                       available via the transferReadsFromAllPreviousPileups interface (this parameter is specific to {@link LocusIteratorByState})
      * @param isIncludeDeletions include reads with deletion on the loci in question
      * @param isIncludeNs include reads with N on the loci in question
      * @return iterator that produces AlignmentContexts ready for consumption (e.g. by a {@link org.broadinstitute.hellbender.engine.LocusWalker})
@@ -103,7 +95,6 @@ private static Iterator<AlignmentContext> createAlignmentContextIterator(final L
                                                                              final LIBSDownsamplingInfo downsamplingInfo,
                                                                              final boolean isReference,
                                                                              boolean emitEmptyLoci,
-                                                                             boolean isKeepUniqueReadListInLibs,
                                                                              boolean isIncludeDeletions,
                                                                              boolean isIncludeNs) {
 
@@ -113,7 +104,7 @@ private static Iterator<AlignmentContext> createAlignmentContextIterator(final L
                 .collect(Collectors.toSet());
 
         // get the LIBS
-        final LocusIteratorByState libs = new LocusIteratorByState(readIterator, downsamplingInfo, isKeepUniqueReadListInLibs, samples, header, isIncludeDeletions, isIncludeNs);
+        final LocusIteratorByState libs = new LocusIteratorByState(readIterator, downsamplingInfo, samples, header, isIncludeDeletions, isIncludeNs);
 
         List<SimpleInterval> finalIntervals = intervalsForTraversal;
         validateEmitEmptyLociParameters(emitEmptyLoci, dictionary, intervalsForTraversal, isReference);