Fix IndexFactory.writeIndex for tabix indexes

src/main/java/htsjdk/tribble/index/AbstractIndex.java

@@ -343,13 +343,16 @@ public void write(final LittleEndianOutputStream stream) throws IOException {
     }
 
     @Override
+    public void write(final File idxFile) throws IOException {
+        try(final LittleEndianOutputStream idxStream = new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(idxFile)))) {
+            write(idxStream);
+        }
+    }
+
+    @Override
     public void writeBasedOnFeatureFile(final File featureFile) throws IOException {
         if (!featureFile.isFile()) return;
-        final LittleEndianOutputStream idxStream =
-                new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(Tribble.indexFile(featureFile))));
-        write(idxStream);
-        idxStream.close();
-
+        write(Tribble.indexFile(featureFile));
     }
 
     public void read(final LittleEndianInputStream dis) throws IOException {

src/main/java/htsjdk/tribble/index/Index.java

@@ -70,6 +70,14 @@
     public void write(LittleEndianOutputStream stream) throws IOException;
 
     /**
+     * Writes the index into a file.
+     *
+     * @param idxFile Where to write the index.
+     * @throws IOException if the index is unable to write to the specified file
+     */
+    public void write(final File idxFile) throws IOException;
+
+    /**
      * Write an appropriately named and located Index file based on the name and location of the featureFile.
      * If featureFile is not a normal file, the index will silently not be written.
      * @param featureFile

src/main/java/htsjdk/tribble/index/IndexFactory.java

@@ -41,16 +41,13 @@
 import htsjdk.tribble.index.tabix.TabixIndexCreator;
 import htsjdk.tribble.readers.PositionalBufferedStream;
 import htsjdk.tribble.util.LittleEndianInputStream;
-import htsjdk.tribble.util.LittleEndianOutputStream;
 import htsjdk.tribble.util.ParsingUtils;
 import htsjdk.tribble.util.TabixUtils;
 
 import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.lang.reflect.Constructor;
@@ -288,18 +285,11 @@ public static LinearIndex createLinearIndex(final File inputFile, final FeatureC
      * @param idx
      * @param idxFile
      * @throws IOException
+     * @deprecated use {@link Index#write(File)} instead
      */
+    @Deprecated
     public static void writeIndex(final Index idx, final File idxFile) throws IOException {
-        LittleEndianOutputStream stream = null;
-        try {
-            stream = new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(idxFile)));
-            idx.write(stream);
-        }
-        finally {
-            if(stream != null) {
-                stream.close();
-            }
-        }
+        idx.write(idxFile);
     }
 
     /**

src/main/java/htsjdk/tribble/index/tabix/TabixIndex.java

@@ -201,13 +201,10 @@ public TabixFormat getFormatSpec() {
      *
      * @param tabixFile Where to write the index.
      */
-    public void write(final File tabixFile) {
-        final LittleEndianOutputStream los = new LittleEndianOutputStream(new BlockCompressedOutputStream(tabixFile));
-        try {
+    @Override
+    public void write(final File tabixFile) throws IOException {
+        try(final LittleEndianOutputStream los = new LittleEndianOutputStream(new BlockCompressedOutputStream(tabixFile))) {
             write(los);
-            los.close();
-        } catch (final IOException e) {
-            throw new TribbleException("Exception writing " + tabixFile.getAbsolutePath(), e);
         }
     }
 

src/test/java/htsjdk/tribble/FeatureReaderTest.java

@@ -134,7 +134,7 @@ public void testBedNames(final File featureFile, final IndexFactory.IndexType in
                 idxFile.delete();
             }
             final Index idx = IndexFactory.createIndex(featureFile, codec, indexType);
-            IndexFactory.writeIndex(idx, idxFile);
+            idx.write(idxFile);
 
             idxFile.deleteOnExit();
         } // else  let's just hope the index exists, and if so use it

src/test/java/htsjdk/tribble/index/IndexFactoryTest.java

@@ -25,18 +25,23 @@
 
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.samtools.util.IOUtil;
 import htsjdk.tribble.TestUtils;
 import htsjdk.tribble.TribbleException;
 import htsjdk.tribble.bed.BEDCodec;
+import htsjdk.tribble.index.linear.LinearIndex;
 import htsjdk.tribble.index.tabix.TabixFormat;
 import htsjdk.tribble.index.tabix.TabixIndex;
+import htsjdk.tribble.util.LittleEndianOutputStream;
 import htsjdk.variant.vcf.VCFCodec;
 import htsjdk.variant.vcf.VCFFileReader;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
 import java.util.List;
 
 /**

src/test/java/htsjdk/tribble/index/IndexTest.java

@@ -1,13 +1,23 @@
 package htsjdk.tribble.index;
 
+import htsjdk.samtools.util.IOUtil;
+import htsjdk.tribble.FeatureCodec;
 import htsjdk.tribble.TestUtils;
+import htsjdk.tribble.Tribble;
+import htsjdk.tribble.bed.BEDCodec;
 import htsjdk.tribble.index.linear.LinearIndex;
+import htsjdk.tribble.index.tabix.TabixFormat;
+import htsjdk.tribble.index.tabix.TabixIndex;
+import htsjdk.tribble.util.LittleEndianOutputStream;
+import htsjdk.tribble.util.TabixUtils;
+import htsjdk.variant.vcf.VCFCodec;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -47,4 +57,41 @@ public void testMassiveQuery(final int start, final int mid, final int mid2, fin
 
         Assert.assertTrue(allSize >= Math.max(leftSize,rightSize), "Expected size of joint query " + allSize + " to be at least >= max of left " + leftSize + " and right queries " + rightSize);
     }
+
+
+    @DataProvider(name = "writeIndexData")
+    public Object[][] writeIndexData() {
+        return new Object[][]{
+                {new File("src/test/resources/htsjdk/tribble/tabix/testTabixIndex.vcf"), IndexFactory.IndexType.LINEAR, new VCFCodec()},
+                {new File("src/test/resources/htsjdk/tribble/tabix/testTabixIndex.vcf.gz"), IndexFactory.IndexType.TABIX, new VCFCodec()},
+                {new File("src/test/resources/htsjdk/tribble/test.bed"), IndexFactory.IndexType.LINEAR, new BEDCodec()}
+        };
+    }
+
+    private final static OutputStream nullOutputStrem = new OutputStream() {
+        @Override
+        public void write(int b) throws IOException { }
+    };
+
+    @Test(dataProvider = "writeIndexData")
+    public void testWriteIndex(final File inputFile, final IndexFactory.IndexType type, final  FeatureCodec codec) throws Exception {
+        // temp index file for this test
+        final File tempIndex = File.createTempFile("index", (type == IndexFactory.IndexType.TABIX) ? TabixUtils.STANDARD_INDEX_EXTENSION : Tribble.STANDARD_INDEX_EXTENSION);
+        tempIndex.delete();
+        tempIndex.deleteOnExit();
+        // create the index
+        final Index index = IndexFactory.createIndex(inputFile, codec, type);
+        Assert.assertFalse(tempIndex.exists());
+        // write the index to a file
+        index.write(tempIndex);
+        Assert.assertTrue(tempIndex.exists());
+        // load the generated index
+        final Index loadedIndex = IndexFactory.loadIndex(tempIndex.getAbsolutePath());
+        // tess that the sequences and properties are the same
+        Assert.assertEquals(loadedIndex.getSequenceNames(), index.getSequenceNames());
+        Assert.assertEquals(loadedIndex.getProperties(), index.getProperties());
+        // test that write to a stream does not blows ip
+        index.write(new LittleEndianOutputStream(nullOutputStrem));
+    }
+
 }

src/test/java/htsjdk/tribble/index/tabix/TabixIndexTest.java

@@ -37,6 +37,7 @@
 import org.testng.annotations.Test;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Iterator;
 
 public class TabixIndexTest {
@@ -71,7 +72,7 @@ public void readWriteTest(final File tabixFile) throws Exception {
     }
 
     @Test
-    public void testQueryProvidedItemsAmount() {
+    public void testQueryProvidedItemsAmount() throws IOException {
         final String VCF = "src/test/resources/htsjdk/tribble/tabix/YRI.trio.2010_07.indel.sites.vcf";
         // Note that we store only compressed files
         final File plainTextVcfInputFile = new File(VCF);