Upgrade htsjdk to v3.0.1 and picard to 2.27.5 (#8025)

This upgrades htsjdk h was attempted in #7867 and then reverted in #7960
in order to unblock the jukebox merge.

* upgrade htsjdk 2.24.1 -> 3.0.1
* upgrade picard 2.27.1 -> 2.27.5

Co-authored-by: David Roazen <droazen@broadinstitute.org>

build.gradle

@@ -60,8 +60,8 @@ repositories {
     mavenLocal()
 }
 
-final htsjdkVersion = System.getProperty('htsjdk.version','2.24.1')
-final picardVersion = System.getProperty('picard.version','2.27.1')
+final htsjdkVersion = System.getProperty('htsjdk.version','3.0.1')
+final picardVersion = System.getProperty('picard.version','2.27.5')
 final barclayVersion = System.getProperty('barclay.version','4.0.2')
 final sparkVersion = System.getProperty('spark.version', '2.4.5')
 final scalaVersion = System.getProperty('scala.version', '2.11')

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

@@ -9,6 +9,7 @@
 import de.javakaffee.kryoserializers.guava.ImmutableMapSerializer;
 import htsjdk.samtools.*;
 import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.SimpleAllele;
 import htsjdk.variant.vcf.VCFHeaderLineType;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
 import org.apache.spark.serializer.KryoRegistrator;
@@ -65,13 +66,13 @@ public VCFInfoHeaderLine newInstance() {
                 return new VCFInfoHeaderLine("TMP", 2, VCFHeaderLineType.String, "");
             }
         });
-        registration = kryo.register(Allele.class);
+        registration = kryo.register(SimpleAllele.class);
         registration.setInstantiator(new ObjectInstantiator<Allele>() {
             public Allele newInstance() {
                 return Allele.create("TCGA");
             }
         });
-    }
+   }
 
     @Override
     public void registerClasses(Kryo kryo) {

src/main/java/org/broadinstitute/hellbender/tools/funcotator/StrandCorrectedAllele.java

@@ -1,12 +1,13 @@
 package org.broadinstitute.hellbender.tools.funcotator;
 
 import htsjdk.tribble.annotation.Strand;
+import htsjdk.variant.variantcontext.SimpleAllele;
 
 /**
  * Class to represent a strand-corrected {@link htsjdk.variant.variantcontext.Allele}.
  * Created by jonn on 10/24/18.
  */
-public class StrandCorrectedAllele extends htsjdk.variant.variantcontext.Allele {
+public class StrandCorrectedAllele extends SimpleAllele {
     public static final long serialVersionUID = 1L;
 
     /**

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

@@ -1,19 +1,21 @@
 package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
 import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.SimpleAllele;
 
 /**
  * This class is similar to {@link org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LocationAndAlleles} but
  * allows keeping only an allele/ref pair rather than a list of alleles. The comparison is done on allele by allele basis and
  * not in the way it is done on LocationAndAlleles
  */
 
-public class AlleleAndContext extends Allele {
+public class AlleleAndContext extends SimpleAllele {
     final static public long serialVersionUID = 1L;
     private final int loc;
     private final String contig;
     private final Allele refAllele;
+
     public AlleleAndContext(final String contig, final int loc, final Allele allele, final Allele refAllele) {
-        super(allele, false);
+        super(allele.getBases(), allele.isReference());
         this.loc = loc;
         this.contig = contig;
         this.refAllele = refAllele;
@@ -42,7 +44,7 @@ public boolean equals(final Object o) {
 
     @Override
     public int hashCode() {
-        return 31 * loc + (this != null ? super.hashCode() : 0);
+        return 31 * loc + super.hashCode();
     }
 
     public String toString() {return String.format("(%d) %s/%s", loc, getBaseString(), getRefAllele().getBaseString());}

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

@@ -415,11 +415,11 @@ public static AssemblyResultSet assembleReads(final AssemblyRegion region,
      * Handle pileup detected alternate alleles.
      */
     @VisibleForTesting
+    @SuppressWarnings("deprecation")
     static void processPileupAlleles(final AssemblyRegion region, final List<VariantContext> givenAlleles, final int maxMnpDistance,
                                      final int snpAdjacentToIndelLimit, final SmithWatermanAligner aligner, final Haplotype refHaplotype,
                                      final AssemblyResultSet assemblyResultSet, final int numHaplotypesPerIteration, final int hapFilteringKmerSize,
                                      final SWParameters haplotypeToReferenceSWParameters) {
-        final int assemblyRegionStart = region.getPaddedSpan().getStart();
         final int activeRegionStart = refHaplotype.getAlignmentStartHapwrtRef();
         final Map<Integer, VariantContext> assembledVariants = assemblyResultSet.getVariationEvents(maxMnpDistance).stream()
                 .collect(Collectors.groupingBy(VariantContext::getStart, Collectors.collectingAndThen(Collectors.toList(), AssemblyBasedCallerUtils::makeMergedVariantContext)));
@@ -496,10 +496,10 @@ public static void addGivenAlleles(final List<VariantContext> givenAlleles, fina
             final Allele longerRef = (assembledVC == null || givenVCRefLength > assembledVC.getReference().length()) ? givenVC.getReference() : assembledVC.getReference();
             final List<Allele> unassembledGivenAlleles = getAllelesNotPresentInAssembly(givenVC, assembledVC, givenVCRefLength, longerRef);
 
-            final List<Allele> unassembledNonSymbolicAlleles = unassembledGivenAlleles.stream().filter(a -> {
-                final byte[] bases = a.getBases();
-                return !(Allele.wouldBeNoCallAllele(bases) || Allele.wouldBeNullAllele(bases) || Allele.wouldBeStarAllele(bases) || Allele.wouldBeSymbolicAllele(bases));
-            }).collect(Collectors.toList());
+            final List<Allele> unassembledNonSymbolicAlleles = unassembledGivenAlleles.stream()
+                    //TODO, update the null allele check when htsjdk adds a NULL_ALLELE constant to Allele
+                    .filter(a -> !(a.equals(Allele.NO_CALL) || a.getDisplayString().equals(String.valueOf(VCFConstants.NULL_ALLELE)) || a.equals(Allele.SPAN_DEL) || a.isSymbolic()))
+                    .collect(Collectors.toList());
 
             // choose the highest-scoring haplotypes along with the reference for building force-calling haplotypes
             final List<Haplotype> baseHaplotypes = unassembledNonSymbolicAlleles.isEmpty() ? Collections.emptyList() : assembledHaplotypes.stream()

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/InverseAllele.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs;
 
 import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.SimpleAllele;
 
 /**
  * Utility class for defining a "not" allele concept that is used to score haplotypes that are not supporting the allele.
@@ -10,15 +11,14 @@
  * @author Ilya Soifer <ilya.soifer@ultimagen.com
  */
 
-public class InverseAllele extends Allele {
+public class InverseAllele extends SimpleAllele {
     final static public long serialVersionUID = 1L;
 
     private final Allele internalAllele;
-    private final boolean referenceStatus;
+
     private InverseAllele(final Allele allele, boolean isReference) {
-        super(allele, false);
+        super(allele.getBases(), isReference);
         this.internalAllele = allele;
-        referenceStatus = isReference;
     }
 
     // InverseAllele of inverseAllele. By definition it is the allele. In Allele filtering code we normally genotype
@@ -35,10 +35,6 @@ public static Allele of(final Allele allele, boolean refFlag){
     public byte [] getBases(){
         return getDisplayString().getBytes();
     }
-    @Override
-    public boolean isReference() {
-        return referenceStatus;
-    }
 
     @Override
     public boolean isSymbolic() {

src/main/java/org/broadinstitute/hellbender/utils/haplotype/FlowBasedHaplotype.java

@@ -3,6 +3,7 @@
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.util.Locatable;
 import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.SimpleAllele;
 import org.apache.commons.lang3.ArrayUtils;
 import org.broadinstitute.hellbender.utils.read.FlowBasedKeyCodec;
 import org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils;
@@ -11,7 +12,7 @@
  * Haplotype that also keeps information on the flow space @see FlowBasedRead
  * Haplotype can't be extended, so this extends Allele
  */
-public class FlowBasedHaplotype  extends Allele {
+public class FlowBasedHaplotype  extends SimpleAllele {
     private static final long serialVersionUID = 42L;
     private int [] key;
     private int [] rKey;

src/main/java/org/broadinstitute/hellbender/utils/haplotype/Haplotype.java

@@ -5,6 +5,7 @@
 import htsjdk.samtools.CigarOperator;
 import htsjdk.samtools.util.Locatable;
 import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.SimpleAllele;
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
@@ -17,7 +18,7 @@
 import java.util.Arrays;
 import java.util.Comparator;
 
-public final class Haplotype extends Allele {
+public final class Haplotype extends SimpleAllele {
     private static final long serialVersionUID = 1L;
 
     /**

src/testUtils/java/org/broadinstitute/hellbender/testutils/testers/SamFileTester.java

@@ -95,7 +95,7 @@ public File getOutputDir() {
     }
 
     private void setOutputDir() {
-        this.outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".", ".tmp");
+        this.outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".tmp").toFile();
         if (deleteOnExit) {
             outputDir.deleteOnExit();
         }