Updating htsjdk, disq, and Picard.

* Updating htsjdk 2.18.2 -> 2.19.0
* Updating disq 0.2.0 -> 0.3.0

* Disabling test that was relying on broken behavior that was fixed in htsjdk
* Removing code that has migrated to htsjdk

build.gradle

@@ -58,12 +58,12 @@ repositories {
 }
 
 final requiredJavaVersion = "8"
-final htsjdkVersion = System.getProperty('htsjdk.version','2.18.2')
-final picardVersion = System.getProperty('picard.version','2.18.25')
+final htsjdkVersion = System.getProperty('htsjdk.version','2.19.0')
+final picardVersion = System.getProperty('picard.version','2.19.0')
 final barclayVersion = System.getProperty('barclay.version','2.1.0')
 final sparkVersion = System.getProperty('spark.version', '2.2.0')
 final hadoopVersion = System.getProperty('hadoop.version', '2.8.2')
-final disqVersion = System.getProperty('disq.version','0.2.0')
+final disqVersion = System.getProperty('disq.version','0.3.0')
 final genomicsdbVersion = System.getProperty('genomicsdb.version','1.0.0-rc2')
 final testNGVersion = '6.11'
 // Using the shaded version to avoid conflicts between its protobuf dependency

src/main/java/org/broadinstitute/hellbender/tools/spark/CreateHadoopBamSplittingIndex.java

@@ -125,7 +125,7 @@ private static void createBaiAndSplittingIndex(final File inputBam, final File i
                 assertBamIsCoordinateSorted(header);
                 final SBIIndexWriter indexer = new SBIIndexWriter(out, granularity);
 
-                final BAMIndexer bamIndexer = new BAMIndexer(IOUtils.replaceExtension(index, BAMIndex.BAMIndexSuffix), header);
+                final BAMIndexer bamIndexer = new BAMIndexer(IOUtils.replaceExtension(index, BAMIndex.BAI_INDEX_SUFFIX), header);
                 BAMFileSpan lastFilePointer = null;
                 for(final SAMRecord read : reader){
                     BAMFileSpan filePointer = (BAMFileSpan) read.getFileSource().getFilePointer();
@@ -149,7 +149,7 @@ private static void createBaiAndSplittingIndex(final File inputBam, final File i
 
     private static void assertBamIsCoordinateSorted(final SAMFileHeader header) {
         if( header.getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
-            throw new UserException.BadInput("Cannot create a " + BAMIndex.BAMIndexSuffix + " index for a file " +
+            throw new UserException.BadInput("Cannot create a " + BAMIndex.BAI_INDEX_SUFFIX + " index for a file " +
                     "that isn't coordinate sorted.");
         }
     }

src/main/java/org/broadinstitute/hellbender/tools/spark/sv/utils/SingleSequenceReferenceAligner.java

@@ -1,23 +1,18 @@
 package org.broadinstitute.hellbender.tools.spark.sv.utils;
 
 import htsjdk.samtools.SAMFlag;
+import htsjdk.samtools.reference.FastaReferenceWriter;
 import org.broadinstitute.hellbender.exceptions.GATKException;
 import org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig;
 import org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.bwa.BwaMemAligner;
 import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
 import org.broadinstitute.hellbender.utils.bwa.BwaMemIndex;
-import org.broadinstitute.hellbender.utils.reference.FastaReferenceWriter;
 
 import java.io.File;
 import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 import java.util.function.BiFunction;
 import java.util.function.Function;
 import java.util.function.Predicate;

src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaReferenceMaker.java

@@ -1,6 +1,8 @@
 package org.broadinstitute.hellbender.tools.walkers.fasta;
 
 import com.google.common.primitives.Bytes;
+import htsjdk.samtools.reference.FastaReferenceWriter;
+import htsjdk.samtools.reference.FastaReferenceWriterBuilder;
 import it.unimi.dsi.fastutil.bytes.ByteArrayList;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
@@ -13,7 +15,6 @@
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
-import org.broadinstitute.hellbender.utils.reference.FastaReferenceWriter;
 import picard.cmdline.programgroups.ReferenceProgramGroup;
 
 import java.io.IOException;
@@ -82,7 +83,10 @@ public class FastaReferenceMaker extends ReferenceWalker {
     public void onTraversalStart() {
         final Path path = IOUtils.getPath(output);
         try {
-            writer = new FastaReferenceWriter(path, basesPerLine, true, true);
+            writer = new FastaReferenceWriterBuilder()
+                    .setFastaFile(path)
+                    .setBasesPerLine(basesPerLine)
+                    .build();
         } catch (IOException e) {
             throw new UserException.CouldNotCreateOutputFile("Couldn't create " + output + ", encountered exception: " + e.getMessage(), e);
         }

src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java

@@ -384,8 +384,7 @@ private OutputAlleleSubset calculateOutputAlleleSubset(final AFCalculationResult
             } else {
                 // we want to keep the NON_REF symbolic allele but only in the absence of a non-symbolic allele, e.g.
                 // if we combined a ref / NON_REF gVCF with a ref / alt gVCF
-                final boolean isNonRefWhichIsLoneAltAllele = alternativeAlleleCount == 1 && allele.equals(
-                        Allele.NON_REF_ALLELE);
+                final boolean isNonRefWhichIsLoneAltAllele = alternativeAlleleCount == 1 && allele.equals(Allele.NON_REF_ALLELE);
                 final boolean isPlausible = afCalculationResult.isPolymorphicPhredScaledQual(allele, configuration.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING);
 
                 siteIsMonomorphic &= !isPlausible;

src/main/java/org/broadinstitute/hellbender/utils/io/DeleteRecursivelyOnExitPathHook.java

@@ -54,7 +54,7 @@ static void runHooks() {
         for (Path path : toBeDeleted) {
             try {
                 IOUtils.deleteRecursively(path);
-            } catch (IOException | SecurityException e) {
+            } catch (SecurityException e) {
                 // do nothing if cannot be deleted, because it is a shutdown hook
             }
         }

src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java

@@ -5,6 +5,7 @@
 import htsjdk.samtools.BamFileIoUtils;
 import htsjdk.samtools.cram.build.CramIO;
 import htsjdk.samtools.util.BlockCompressedInputStream;
+import htsjdk.samtools.util.IOUtil;
 import htsjdk.tribble.Tribble;
 import htsjdk.tribble.util.TabixUtils;
 import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
@@ -702,7 +703,7 @@ public static Path createTempPath(String name, String extension) {
             final String filename = path.getFileName().toString();
             IOUtils.deleteOnExit(path.resolveSibling(filename + Tribble.STANDARD_INDEX_EXTENSION));
             IOUtils.deleteOnExit(path.resolveSibling(filename + TabixUtils.STANDARD_INDEX_EXTENSION));
-            IOUtils.deleteOnExit(path.resolveSibling(filename + BAMIndex.BAMIndexSuffix));
+            IOUtils.deleteOnExit(path.resolveSibling(filename + BAMIndex.BAI_INDEX_SUFFIX));
             IOUtils.deleteOnExit(path.resolveSibling(filename.replaceAll(extension + "$", ".bai")));
             IOUtils.deleteOnExit(path.resolveSibling(filename + ".md5"));
 
@@ -1021,14 +1022,8 @@ public static void deleteOnExit(final Path fileToDelete){
      * Delete rootPath recursively
      * @param rootPath is the file/directory to be deleted
      */
-    public static void deleteRecursively(final Path rootPath) throws IOException {
-        final List<Path> pathsToDelete = Files.walk(rootPath)
-                        .sorted(Comparator.reverseOrder())
-                        .collect(Collectors.toList());
-
-        for (Path path : pathsToDelete) {
-            Files.deleteIfExists(path);
-        }
+    public static void deleteRecursively(final Path rootPath) {
+        IOUtil.recursiveDelete(rootPath);
     }
 
     /**