Upate to htsjdk 4.0.2

Htsjdk added a new NamedFeature interface that is clashing with IGV's slightly different NamedFeature.
Renamed NamedFeature -> IGVNamedFeature
Slight change to IGVFeatureReader interface to make it return a CloseableIterator so that it can be handled with try-with-resources.

build.gradle

@@ -111,7 +111,7 @@ dependencies {
             [group: 'org.xerial.snappy', name: 'snappy-java', version: '1.1.7.3'],
             [group: 'org.apache.commons', name: 'commons-jexl', version: '2.1.1'],
             [group: 'org.apache.commons', name: 'commons-lang3', version: '3.9'],
-            [group: 'com.github.samtools', name: 'htsjdk', version: '3.0.5'],
+            [group: 'com.github.samtools', name: 'htsjdk', version: '4.0.2'],
             [group: 'org.swinglabs', name: 'swing-layout', version: '1.0.3'],
             [group: 'com.formdev', name: 'jide-oss', version: '3.7.12'],
             [group: 'com.google.guava', name: 'guava', version: '27.0.1-jre'],

src/main/java/org/broad/igv/feature/Cytoband.java

@@ -26,7 +26,7 @@
 package org.broad.igv.feature;
 
 
-public class Cytoband implements NamedFeature {
+public class Cytoband implements IGVNamedFeature {
     String chromosome;
     String name;
     String longName;

src/main/java/org/broad/igv/feature/FeatureDB.java

@@ -53,11 +53,11 @@ public class FeatureDB {
     /**
      * Map for all features other than genes.
      */
-    //private static Map<String, NamedFeature> featureMap = new HashMap(10000);
-    private static Map<String, List<NamedFeature>> featureMap = Collections.synchronizedSortedMap(new TreeMap<String, List<NamedFeature>>());
+    //private static Map<String, IGVNamedFeature> featureMap = new HashMap(10000);
+    private static Map<String, List<IGVNamedFeature>> featureMap = Collections.synchronizedSortedMap(new TreeMap<String, List<IGVNamedFeature>>());
     private static final int MAX_DUPLICATE_COUNT = 20;
 
-    public static void addFeature(NamedFeature feature, Genome genome) {
+    public static void addFeature(IGVNamedFeature feature, Genome genome) {
 
         final String name = feature.getName();
         if (name != null && name.length() > 0 && !name.equals(".")) {
@@ -81,7 +81,7 @@ public static void addFeature(NamedFeature feature, Genome genome) {
         }
     }
 
-    public static void removeFeature(NamedFeature feature, Genome genome) {
+    public static void removeFeature(IGVNamedFeature feature, Genome genome) {
 
         final String name = feature.getName();
         if (name != null && name.length() > 0 && !name.equals(".")) {
@@ -134,7 +134,7 @@ private static void removeByAttributes(IGVFeature igvFeature, Genome genome) {
      * @param genome  The genome which these features belong to. Used for checking chromosomes
      * @return true if successfully added, false if not
      */
-    static boolean put(String name, NamedFeature feature, Genome genome) {
+    static boolean put(String name, IGVNamedFeature feature, Genome genome) {
         String key = name.toUpperCase();
         if (!Globals.isHeadless()) {
             Genome currentGenome = genome != null ? genome : GenomeManager.getInstance().getCurrentGenome();
@@ -144,9 +144,9 @@ static boolean put(String name, NamedFeature feature, Genome genome) {
         }
 
         synchronized (featureMap) {
-            List<NamedFeature> currentList = featureMap.get(key);
+            List<IGVNamedFeature> currentList = featureMap.get(key);
             if (currentList == null) {
-                List<NamedFeature> newList = new SortedList<NamedFeature>(
+                List<IGVNamedFeature> newList = new SortedList<IGVNamedFeature>(
                         new ArrayList<>(), FeatureComparator.get(true));
                 boolean added = newList.add(feature);
                 if (added) {
@@ -170,7 +170,7 @@ static boolean put(String name, NamedFeature feature, Genome genome) {
 
         Genome currentGenome = GenomeManager.getInstance().getCurrentGenome();
         if (currentGenome == null || currentGenome.getChromosome(feature.getChr()) != null) {
-            NamedFeature currentFeature = featureMap.get(key);
+            IGVNamedFeature currentFeature = featureMap.get(key);
             if (currentFeature == null) {
                 featureMap.put(key, feature);
             } else {
@@ -200,7 +200,7 @@ static boolean put(String name, NamedFeature feature, Genome genome) {
      */
 
 
-    public static void addFeature(String name, NamedFeature feature, Genome genome) {
+    public static void addFeature(String name, IGVNamedFeature feature, Genome genome) {
         put(name.toUpperCase(), feature, genome);
     }
 
@@ -228,9 +228,9 @@ static int size() {
     /**
      * Return a feature with the given name.
      */
-    public static NamedFeature getFeature(String name) {
+    public static IGVNamedFeature getFeature(String name) {
         String nm = name.trim().toUpperCase();
-        List<NamedFeature> features = featureMap.get(nm);
+        List<IGVNamedFeature> features = featureMap.get(nm);
 
         if (features != null) {
             return features.get(0);
@@ -255,9 +255,9 @@ public static NamedFeature getFeature(String name) {
      *             string will be found.
      * @return
      */
-    static Map<String, List<NamedFeature>> getFeaturesMap(String name) {
+    static Map<String, List<IGVNamedFeature>> getFeaturesMap(String name) {
         String nm = name.trim().toUpperCase();
-        SortedMap<String, List<NamedFeature>> treeMap = (SortedMap) featureMap;
+        SortedMap<String, List<IGVNamedFeature>> treeMap = (SortedMap) featureMap;
         //Search is inclusive to first argument, exclusive to second
         return treeMap.subMap(nm, nm + Character.MAX_VALUE);
     }
@@ -270,7 +270,7 @@ static Map<String, List<NamedFeature>> getFeaturesMap(String name) {
      * @return
      * @see #getFeaturesList(String, int, boolean)
      */
-    public static List<NamedFeature> getFeaturesList(String name, int limit) {
+    public static List<IGVNamedFeature> getFeaturesList(String name, int limit) {
         return getFeaturesList(name, limit, true);
     }
 
@@ -283,18 +283,18 @@ public static List<NamedFeature> getFeaturesList(String name, int limit) {
      * @param longestOnly Whether to take only the longest feature for each name
      * @return
      */
-    public static List<NamedFeature> getFeaturesList(String name, int limit, boolean longestOnly) {
+    public static List<IGVNamedFeature> getFeaturesList(String name, int limit, boolean longestOnly) {
 
         //Note: We are iterating over submap, this needs
         //to be synchronized over the main map.
         synchronized (featureMap) {
-            Map<String, List<NamedFeature>> resultMap = getFeaturesMap(name);
+            Map<String, List<IGVNamedFeature>> resultMap = getFeaturesMap(name);
             Set<String> names = resultMap.keySet();
             Iterator<String> nameIter = names.iterator();
-            ArrayList<NamedFeature> features = new ArrayList<NamedFeature>((Math.min(limit, names.size())));
+            ArrayList<IGVNamedFeature> features = new ArrayList<IGVNamedFeature>((Math.min(limit, names.size())));
             int ii = 0;
             while (nameIter.hasNext() && ii < limit) {
-                List<NamedFeature> subFeats = resultMap.get(nameIter.next());
+                List<IGVNamedFeature> subFeats = resultMap.get(nameIter.next());
                 if (longestOnly) {
                     features.add(subFeats.get(0));
                 } else {
@@ -328,11 +328,11 @@ public static Map<Integer, BasicFeature> getMutationAA(String name, int proteinP
         }
 
         Map<Integer, BasicFeature> results = new HashMap<Integer, BasicFeature>();
-        List<NamedFeature> possibles = featureMap.get(nm);
+        List<IGVNamedFeature> possibles = featureMap.get(nm);
 
         if (possibles != null) {
             synchronized (featureMap) {
-                for (NamedFeature f : possibles) {
+                for (IGVNamedFeature f : possibles) {
                     if (!(f instanceof BasicFeature)) {
                         continue;
                     }
@@ -381,13 +381,13 @@ public static Map<Integer, BasicFeature> getMutationNT(String name, int startPos
         }
 
         Map<Integer, BasicFeature> results = new HashMap<Integer, BasicFeature>();
-        List<NamedFeature> possibles = featureMap.get(nm);
+        List<IGVNamedFeature> possibles = featureMap.get(nm);
         String tempNT;
         String brefNT = refNT.toUpperCase();
 
         if (possibles != null) {
             synchronized (featureMap) {
-                for (NamedFeature f : possibles) {
+                for (IGVNamedFeature f : possibles) {
                     if (!(f instanceof BasicFeature)) {
                         continue;
                     }

src/main/java/org/broad/igv/feature/IGVFeature.java

@@ -29,13 +29,12 @@
 import java.awt.*;
 import java.util.Collections;
 import java.util.List;
-import java.util.Map;
 
 /**
  * Interface for features in IGV annotation tracks  (FeatureTrack and derived classes).
  */
 
-public interface IGVFeature extends LocusScore, NamedFeature {
+public interface IGVFeature extends LocusScore, IGVNamedFeature {
 
     default String getIdentifier() {
         return null;

src/main/java/org/broad/igv/feature/NamedFeature.java → src/main/java/org/broad/igv/feature/IGVNamedFeature.java

@@ -25,13 +25,11 @@
 
 package org.broad.igv.feature;
 
-import htsjdk.tribble.Feature;
-
 /**
  * @author jrobinso
  * @date Sep 16, 2010
  */
-public interface  NamedFeature extends Feature {
+public interface IGVNamedFeature extends htsjdk.tribble.NamedFeature {
 
     String getName();
 

src/main/java/org/broad/igv/feature/Locus.java

@@ -35,7 +35,7 @@
 /**
  * @author jrobinso
  */
-public class Locus extends Range implements NamedFeature {
+public class Locus extends Range implements IGVNamedFeature {
 
     private static NumberFormat NUMBER_FORMAT = NumberFormat.getInstance(Locale.US);
 

src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java

@@ -7,11 +7,11 @@
 import htsjdk.tribble.CloseableTribbleIterator;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.FeatureReader;
+import org.broad.igv.feature.IGVNamedFeature;
 import org.broad.igv.logging.*;
 import org.broad.igv.Globals;
 import org.broad.igv.feature.CytoBandFileParser;
 import org.broad.igv.feature.FeatureDB;
-import org.broad.igv.feature.NamedFeature;
 import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequence;
 import org.broad.igv.feature.genome.fasta.FastaIndexedSequence;
@@ -26,8 +26,6 @@
 
 import java.io.BufferedReader;
 import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
 import java.util.*;
 
 public class JsonGenomeLoader extends GenomeLoader {
@@ -288,8 +286,8 @@ private void addToFeatureDB(List<ResourceLocator> locators, Genome genome) {
                 CloseableTribbleIterator<Feature> iter = featureReader.iterator();
                 while (iter.hasNext()) {
                     Feature f = iter.next();
-                    if (f instanceof NamedFeature) {
-                        FeatureDB.addFeature((NamedFeature) f, genome);
+                    if (f instanceof IGVNamedFeature) {
+                        FeatureDB.addFeature((IGVNamedFeature) f, genome);
                     }
                 }
             } catch (IOException e) {

src/main/java/org/broad/igv/feature/tribble/IGVFeatureReader.java

@@ -28,6 +28,7 @@
 
 
 
+import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.index.Index;
 
@@ -49,7 +50,7 @@ public interface IGVFeatureReader {
 
     public Iterator<Feature> query(final String chr, final int start, final int end) throws IOException;
 
-    public Iterator<Feature> iterator() throws IOException;
+    public CloseableIterator<Feature> iterator() throws IOException;
 
     public List<String> getSequenceNames();
 

src/main/java/org/broad/igv/feature/tribble/TribbleReaderWrapper.java

@@ -25,6 +25,7 @@
 
 package org.broad.igv.feature.tribble;
 
+import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.tribble.*;
 import htsjdk.tribble.index.Index;
 import htsjdk.tribble.index.IndexFactory;
@@ -54,9 +55,7 @@ public TribbleReaderWrapper(FeatureReader<Feature> wrappedReader) {
     public synchronized Iterator<Feature> query(String chr, int start, int end) throws IOException {
 
         // Tribble iterators must be closed, so we need to copy the features and insure closure before exiting.
-        CloseableTribbleIterator<Feature> iter = null;
-        try {
-            iter = wrappedReader.query(chr, start + 1, end);
+        try (CloseableTribbleIterator<Feature> iter = wrappedReader.query(chr, start + 1, end)) {
             List<Feature> featureList = new ArrayList<Feature>();
             while (iter.hasNext()) {
                 Feature f = iter.next();
@@ -69,13 +68,11 @@ public synchronized Iterator<Feature> query(String chr, int start, int end) thro
                 }
             }
             return featureList.iterator();
-        } finally {
-            if(iter != null) iter.close();
         }
     }
 
     @Override
-    public Iterator<Feature> iterator() throws IOException {
+    public CloseableIterator<Feature> iterator() throws IOException {
         // Note: Technically this is a file handle leak as the "close" method of the tribble iterator is not called.
         // In practice this is not a problem as the iterator() method is only called by batch programs transversing
         // the entire file.   It is none-the-less a file handle leak that should be addressed at some point.

src/main/java/org/broad/igv/track/TribbleFeatureSource.java

@@ -25,6 +25,7 @@
 
 package org.broad.igv.track;
 
+import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.tribble.*;
 import htsjdk.tribble.index.Index;
 import org.broad.igv.Globals;
@@ -332,45 +333,30 @@ private NonIndexedFeatureSource(AbstractFeatureReader basicReader, FeatureCodec
             super(basicReader, codec, genome);
 
             featureMap = new HashMap<>(25);
-            Iterator<Feature> iter = null;
 
-            try {
-                iter = reader.iterator();
+            try (CloseableIterator<Feature> iter = reader.iterator()) {
                 while (iter.hasNext()) {
                     Feature f = iter.next();
                     if (f == null) continue;
 
                     String seqName = f.getChr();
                     String igvChr = genome == null ? seqName : genome.getCanonicalChrName(seqName);
 
-                    List<Feature> featureList = featureMap.get(igvChr);
-                    if (featureList == null) {
-                        featureList = new ArrayList();
-                        featureMap.put(igvChr, featureList);
-                    }
+                    List<Feature> featureList = featureMap.computeIfAbsent(igvChr, k -> new ArrayList<>());
                     featureList.add(f);
-                    if (f instanceof org.broad.igv.feature.NamedFeature) FeatureDB.addFeature((org.broad.igv.feature.NamedFeature) f, genome);
+                    if (f instanceof IGVNamedFeature named) FeatureDB.addFeature(named, genome);
 
-                    if (this.isVCF && f instanceof Variant) {
-                        Variant v = (Variant) f;
+                    if (this.isVCF && f instanceof Variant v) {
                         String chr2 = v.getAttributeAsString("CHR2");
                         String pos2 = v.getAttributeAsString("END");
                         if (chr2 != null && pos2 != null) {
                             String mateChr = genome == null ? chr2 : genome.getCanonicalChrName(chr2);
                             MateVariant mate = new MateVariant(mateChr, Integer.parseInt(pos2), v);
-                            featureList = featureMap.get(mateChr);
-                            if (featureList == null) {
-                                featureList = new ArrayList();
-                                featureMap.put(mateChr, featureList);
-                            }
+                            featureList = featureMap.computeIfAbsent(mateChr, k -> new ArrayList<>());
                             featureList.add(mate);
                         }
                     }
                 }
-            } finally {
-                if (iter instanceof CloseableTribbleIterator) {
-                    ((CloseableTribbleIterator) iter).close();
-                }
             }
 
             for (List<Feature> featureList : featureMap.values()) {