Add setter for file name to BlockCompressedOutputStream

samtools · Mar 9, 2017 · 1f23883 · 1f23883
1 parent ce693cd
commit 1f23883
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Showing 2 changed files with 20 additions and 3 deletions.
diff --git a/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java b/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java
@@ -111,6 +111,7 @@ public static DeflaterFactory getDefaultDeflaterFactory() {
     private final Deflater noCompressionDeflater = new Deflater(Deflater.NO_COMPRESSION, true);
     private final CRC32 crc32 = new CRC32();
     private File file = null;
+    private String fileName = null;
     private long mBlockAddress = 0;
 
 
@@ -161,6 +162,7 @@ public BlockCompressedOutputStream(final File file, final int compressionLevel)
      */
     public BlockCompressedOutputStream(final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
         this.file = file;
+        this.fileName = file.getAbsolutePath();
         codec = new BinaryCodec(file, true);
         deflater = deflaterFactory.makeDeflater(compressionLevel, true);
         log.debug("Using deflater: " + deflater.getClass().getSimpleName());
@@ -196,7 +198,8 @@ public BlockCompressedOutputStream(final OutputStream os, final File file, final
         this.file = file;
         codec = new BinaryCodec(os);
         if (file != null) {
-            codec.setOutputFileName(file.getAbsolutePath());
+            fileName = file.getAbsolutePath();
+            codec.setOutputFileName(fileName);
         }
         deflater = deflaterFactory.makeDeflater(compressionLevel, true);
         log.debug("Using deflater: " + deflater.getClass().getSimpleName());
@@ -217,6 +220,19 @@ public static BlockCompressedOutputStream maybeBgzfWrapOutputStream(final File l
         }
     }
 
+    /**
+     * Sets the file name if it is not already set.
+     * @throws IllegalStateException if the file name was already set.
+     * @param fileName the filename.
+     */
+    public void setFileName(final String fileName) {
+        if (this.fileName != null) {
+            throw new IllegalStateException("File name is already set: " + this.fileName);
+        }
+        this.fileName = fileName;
+        codec.setOutputFileName(fileName);
+    }
+
     /**
      * Writes b.length bytes from the specified byte array to this output stream. The general contract for write(b)
      * is that it should have exactly the same effect as the call write(b, 0, b.length).

diff --git a/src/main/java/htsjdk/tribble/index/tabix/TabixIndex.java b/src/main/java/htsjdk/tribble/index/tabix/TabixIndex.java
@@ -207,8 +207,9 @@ public TabixFormat getFormatSpec() {
      */
     @Override
     public void write(final Path tabixPath) throws IOException {
-        try(final LittleEndianOutputStream los = new LittleEndianOutputStream(new BlockCompressedOutputStream(Files.newOutputStream(tabixPath), null))) {
-            write(los);
+        try(final BlockCompressedOutputStream bcos = new BlockCompressedOutputStream(Files.newOutputStream(tabixPath), null)) {
+            bcos.setFileName(tabixPath.toUri().toString());
+            write(new LittleEndianOutputStream(bcos));
         }
     }