updating to htsjdk 2.14.1

build.gradle

@@ -56,7 +56,7 @@ repositories {
     mavenLocal()
 }
 
-final htsjdkVersion = System.getProperty('htsjdk.version','2.13.2')
+final htsjdkVersion = System.getProperty('htsjdk.version','2.14.1')
 final picardVersion = System.getProperty('picard.version','2.17.2')
 final sparkVersion = System.getProperty('spark.version', '2.0.2')
 final hadoopBamVersion = System.getProperty('hadoopBam.version','7.9.1')

src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/UpdateVCFSequenceDictionary.java

@@ -18,6 +18,7 @@
 import org.broadinstitute.hellbender.engine.ReadsContext;
 import org.broadinstitute.hellbender.engine.ReferenceContext;
 import org.broadinstitute.hellbender.engine.VariantWalker;
+import org.broadinstitute.hellbender.utils.io.IOUtils;
 
 import java.io.File;
 
@@ -178,7 +179,7 @@ private SAMSequenceDictionary getSequenceDictionaryFromInput(final String source
             }
 
         } else {
-            dictionary = SAMSequenceDictionaryExtractor.extractDictionary(new File(dictionarySource));
+            dictionary = SAMSequenceDictionaryExtractor.extractDictionary(IOUtils.getPath(dictionarySource));
             if (dictionary == null || dictionary.getSequences().isEmpty()) {
                 throw new CommandLineException.BadArgumentValue(
                         String.format(

src/main/java/org/broadinstitute/hellbender/utils/test/SimpleIntervalTestFactory.java

@@ -6,6 +6,7 @@
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 
 import java.io.File;
+import java.nio.file.Path;
 
 /**
  * Some common elements for target collection analysis tool unit and integration tests.
@@ -15,15 +16,15 @@
 public final class SimpleIntervalTestFactory {
 
     /** Initialize the reference file and dictionary to use for creating intervals. */
-    public SimpleIntervalTestFactory(final File referenceFile){
+    public SimpleIntervalTestFactory(final Path referenceFile){
         this.REFERENCE_FILE = referenceFile;
-        this.REFERENCE_DICTIONARY = SAMSequenceDictionaryExtractor.extractDictionary(REFERENCE_FILE);;
+        this.REFERENCE_DICTIONARY = SAMSequenceDictionaryExtractor.extractDictionary(REFERENCE_FILE);
     }
 
     /**
      * {@link File} pointing to the test toy reference used in targets analysis tool tests.
      */
-    public final File REFERENCE_FILE;
+    public final Path REFERENCE_FILE;
 
     /**
      * Sequence dictionary extracted from {@link #REFERENCE_FILE}.

src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/UpdateVCFSequenceDictionaryIntegrationTest.java

@@ -50,7 +50,7 @@ private void testGoodUpdateSequenceDictionary(
         SAMSequenceDictionary sourceDictionary =
                 SAMSequenceDictionaryExtractor.extractDictionary(
                         inputSourceFile == null ?
-                                inputReferenceFile : inputSourceFile
+                                inputReferenceFile.toPath() : inputSourceFile.toPath()
                 );
 
         // Some sequence dictionary sources will contain optional attributes (i.e., if the source is a .dict file,

src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java

@@ -1973,7 +1973,7 @@ private void assertCreateOverlapMap(List<Locatable> locatables1, List<Locatable>
     @Test(dataProvider = "genomicSortingTests")
     public void testBasicGenomicSortOfLocatable(final List<Locatable> testList, final List<Locatable> gtList) throws IOException {
 
-        final SAMSequenceDictionary dictionary = SAMSequenceDictionaryExtractor.extractDictionary(new File(FULL_HG19_DICT));
+        final SAMSequenceDictionary dictionary = SAMSequenceDictionaryExtractor.extractDictionary(new File(FULL_HG19_DICT).toPath());
         testList.sort(IntervalUtils.getDictionaryOrderComparator(dictionary));
         Assert.assertEquals(testList, gtList);
     }
@@ -1996,7 +1996,7 @@ public void testBasicGenomicSortOfLocatableErrorContigNotInDictionary() throws I
                new SimpleInterval("GL1234.123NOT_IN_DICT", 3500, 4000)
         );
 
-        final SAMSequenceDictionary dictionary = SAMSequenceDictionaryExtractor.extractDictionary(new File(FULL_HG19_DICT));
+        final SAMSequenceDictionary dictionary = SAMSequenceDictionaryExtractor.extractDictionary(new File(FULL_HG19_DICT).toPath());
         testList.sort(IntervalUtils.getDictionaryOrderComparator(dictionary));
     }