Merge pull request #533 from bpow/bzip2-fixes

Bzip2 fixes in cram.io.ExternalCompression

build.gradle

@@ -40,7 +40,6 @@ dependencies {
     compile "org.xerial.snappy:snappy-java:1.0.3-rc3"
     compile "org.apache.commons:commons-compress:1.4.1"
     compile "org.tukaani:xz:1.5"
-    compile "org.apache.ant:ant:1.8.2"
     compile "gov.nih.nlm.ncbi:ngs-java:1.2.2"
 
     testCompile "org.testng:testng:6.9.9"

src/main/java/htsjdk/samtools/cram/io/ExternalCompression.java

@@ -3,9 +3,9 @@
 import htsjdk.samtools.cram.encoding.rans.RANS;
 import htsjdk.samtools.util.IOUtil;
 import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
+import org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream;
 import org.apache.commons.compress.compressors.xz.XZCompressorInputStream;
 import org.apache.commons.compress.compressors.xz.XZCompressorOutputStream;
-import org.apache.tools.bzip2.CBZip2InputStream;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
@@ -58,7 +58,11 @@ public static byte[] gunzip(final byte[] data) throws IOException {
      * @return compressed blob
      */
     public static byte[] bzip2(final byte[] data) throws IOException {
-        return InputStreamUtils.readFully(new BZip2CompressorInputStream(new ByteArrayInputStream(data)));
+        final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+        final BZip2CompressorOutputStream bos = new BZip2CompressorOutputStream(byteArrayOutputStream);
+        IOUtil.copyStream(new ByteArrayInputStream(data), bos);
+        bos.close();
+        return byteArrayOutputStream.toByteArray();
     }
 
     /**
@@ -71,10 +75,7 @@ public static byte[] bzip2(final byte[] data) throws IOException {
     @SuppressWarnings("ResultOfMethodCallIgnored")
     public static byte[] unbzip2(final byte[] data) throws IOException {
         final ByteArrayInputStream byteArrayInputStream = new ByteArrayInputStream(data);
-        // hello, apache!
-        byteArrayInputStream.read();
-        byteArrayInputStream.read();
-        return InputStreamUtils.readFully(new CBZip2InputStream(byteArrayInputStream));
+        return InputStreamUtils.readFully(new BZip2CompressorInputStream(byteArrayInputStream));
     }
 
     /**

src/tests/java/htsjdk/samtools/cram/io/ExternalCompressionTest.java

@@ -0,0 +1,30 @@
+package htsjdk.samtools.cram.io;
+
+import org.apache.commons.compress.utils.IOUtils;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.nio.file.Files;
+
+public class ExternalCompressionTest {
+    public static final File BZIP2_FILE = new File("testdata/htsjdk/samtools/io/bzip2-test.bz2");
+    public static final byte [] TEST_BYTES = "This is a simple string to test BZip2".getBytes();
+
+    @Test
+    public void testBZip2Decompression() throws IOException {
+        final byte [] input = Files.readAllBytes(BZIP2_FILE.toPath());
+        final byte [] output = ExternalCompression.unbzip2(input);
+        Assert.assertEquals(output, "BZip2 worked".getBytes());
+    }
+
+    @Test
+    public void testBZip2Roundtrip() throws IOException {
+        final byte [] compressed = ExternalCompression.bzip2(TEST_BYTES);
+        final byte [] restored = ExternalCompression.unbzip2(compressed);
+        Assert.assertEquals(TEST_BYTES, restored);
+    }
+}