diff --git a/src/main/java/org/broadinstitute/hellbender/tools/dragstr/CalibrateDragstrModel.java b/src/main/java/org/broadinstitute/hellbender/tools/dragstr/CalibrateDragstrModel.java index d3e68a39218..24bb5df696f 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/dragstr/CalibrateDragstrModel.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/dragstr/CalibrateDragstrModel.java @@ -1,9 +1,32 @@ package org.broadinstitute.hellbender.tools.dragstr; -import htsjdk.samtools.*; -import htsjdk.samtools.cram.ref.ReferenceSource; -import htsjdk.samtools.util.IntervalTree; -import it.unimi.dsi.fastutil.ints.*; +import java.io.IOException; +import java.io.PrintWriter; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.Collections; +import java.util.Comparator; +import java.util.EnumSet; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Optional; +import java.util.Set; +import java.util.Spliterator; +import java.util.Vector; +import java.util.concurrent.atomic.AtomicLong; +import java.util.function.BiConsumer; +import java.util.function.BinaryOperator; +import java.util.function.Consumer; +import java.util.function.Function; +import java.util.function.Supplier; +import java.util.stream.Collector; +import java.util.stream.Collectors; +import java.util.stream.IntStream; +import java.util.stream.Stream; +import java.util.stream.StreamSupport; + import org.apache.commons.io.output.NullOutputStream; import org.broadinstitute.barclay.argparser.Argument; import org.broadinstitute.barclay.argparser.ArgumentCollection; @@ -11,12 +34,20 @@ import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup; -import org.broadinstitute.hellbender.engine.*; +import org.broadinstitute.hellbender.engine.GATKPath; +import org.broadinstitute.hellbender.engine.GATKTool; +import org.broadinstitute.hellbender.engine.ReadsDataSource; +import org.broadinstitute.hellbender.engine.ReadsPathDataSource; import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller; import org.broadinstitute.hellbender.transformers.DRAGENMappingQualityReadTransformer; import org.broadinstitute.hellbender.transformers.ReadTransformer; -import org.broadinstitute.hellbender.utils.*; +import org.broadinstitute.hellbender.utils.BinaryTableReader; +import org.broadinstitute.hellbender.utils.IntervalMergingRule; +import org.broadinstitute.hellbender.utils.IntervalUtils; +import org.broadinstitute.hellbender.utils.SequenceDictionaryUtils; +import org.broadinstitute.hellbender.utils.SimpleInterval; +import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.collections.AutoCloseableCollection; import org.broadinstitute.hellbender.utils.dragstr.DragstrParamUtils; import org.broadinstitute.hellbender.utils.dragstr.DragstrParams; @@ -24,14 +55,21 @@ import org.broadinstitute.hellbender.utils.gcs.BucketUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates; -import scala.Tuple4; -import java.io.IOException; -import java.io.PrintWriter; -import java.util.*; -import java.util.concurrent.atomic.AtomicLong; -import java.util.function.*; -import java.util.stream.*; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMFlag; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SamReaderFactory; +import htsjdk.samtools.util.IntervalTree; +import it.unimi.dsi.fastutil.ints.Int2ObjectMap; +import it.unimi.dsi.fastutil.ints.Int2ObjectMaps; +import it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap; +import it.unimi.dsi.fastutil.ints.IntArrayList; +import it.unimi.dsi.fastutil.ints.IntList; +import scala.Tuple4; /** * Estimates the parameters for the DRAGstr model for an input sample. @@ -500,7 +538,7 @@ private StratifiedDragstrLocusCases collectCaseStatsParallel(final List shards = shardIntervals(intervals, shardSize); - final List readSources = new ArrayList<>(threads); + final Collection readSources = new Vector<>(threads); final ThreadLocal threadReadSource = ThreadLocal.withInitial( () -> { final ReadsPathDataSource result = new ReadsPathDataSource(readArguments.getReadPaths(), factory); @@ -1033,4 +1071,4 @@ public String toString() { return "(" + period + ',' + repeatLength + ')'; } } -} \ No newline at end of file +}