also updating in wdls

Author: lbergelson

scripts/cnn_variant_wdl/cnn_variant_common_tasks.wdl

@@ -234,7 +234,7 @@ task SplitIntervals {
     }
 
     output {
-        Array[File] interval_files = glob("*.intervals")
+        Array[File] interval_files = glob("*.interval_list")
     }
 }
 

scripts/mutect2_wdl/mutect2.wdl

@@ -488,7 +488,7 @@ task SplitIntervals {
             -scatter ${scatter_count} \
             -O interval-files \
             ${split_intervals_extra_args}
-        cp interval-files/*.intervals .
+        cp interval-files/*.interval_list .
     }
 
     runtime {
@@ -502,7 +502,7 @@ task SplitIntervals {
     }
 
     output {
-        Array[File] interval_files = glob("*.intervals")
+        Array[File] interval_files = glob("*.interval_list")
     }
 }
 

scripts/mutect2_wdl/mutect2_nio.wdl

@@ -433,7 +433,7 @@ task SplitIntervals {
             -scatter ${scatter_count} \
             -O interval-files \
             ${split_intervals_extra_args}
-        cp interval-files/*.intervals .
+        cp interval-files/*.interval_list .
     }
 
     runtime {
@@ -447,7 +447,7 @@ task SplitIntervals {
     }
 
     output {
-        Array[File] interval_files = glob("*.intervals")
+        Array[File] interval_files = glob("*.interval_list")
     }
 }
 

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

@@ -235,7 +235,7 @@ private static GATKRead createQualityModifiedRead(final GATKRead read,
      * @param perSampleReadList a mapping from sample -> reads
      */
     private void initializePairHMM(final List<Haplotype> haplotypes, final Map<String, List<GATKRead>> perSampleReadList) {
-        final int readMaxLength = perSampleReadList.entrySet().stream().flatMap(e -> e.getValue().stream()).mapToInt(read -> read.getLength()).max().orElse(0);
+        final int readMaxLength = perSampleReadList.entrySet().stream().flatMap(e -> e.getValue().stream()).mapToInt(GATKRead::getLength).max().orElse(0);
         final int haplotypeMaxLength = haplotypes.stream().mapToInt(h -> h.getBases().length).max().orElse(0);
 
         // initialize arrays to hold the probabilities of being in the match, insertion and deletion cases

src/main/java/org/broadinstitute/hellbender/utils/nio/SeekableByteChannelPrefetcher.java

@@ -1,25 +1,21 @@
 package org.broadinstitute.hellbender.utils.nio;
 
 import com.google.common.base.Stopwatch;
-import java.util.concurrent.ThreadFactory;
 import org.broadinstitute.hellbender.exceptions.GATKException;
+import shaded.cloud_nio.com.google.common.util.concurrent.ThreadFactoryBuilder;
 
 import java.io.Closeable;
 import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.nio.channels.ClosedChannelException;
 import java.nio.channels.NonWritableChannelException;
+import java.nio.channels.ReadableByteChannel;
 import java.nio.channels.SeekableByteChannel;
+import java.nio.file.StandardOpenOption;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UnknownFormatConversionException;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.TimeUnit;
-import shaded.cloud_nio.com.google.common.util.concurrent.ThreadFactoryBuilder;
+import java.util.concurrent.*;
 
 /**
  * SeekableByteChannelPrefetcher wraps an existing SeekableByteChannel to add prefetching.