settable deflater factory

.travis.yml

@@ -10,7 +10,7 @@ cache:
     - $HOME/.m2
 jdk:
   - oraclejdk8
-script: ./gradlew jacocoTestReport testSRA testIntelDeflater;
+script: ./gradlew jacocoTestReport testSRA;
 after_success:
   - echo "TRAVIS_BRANCH='$TRAVIS_BRANCH'";
     echo "JAVA_HOME='$JAVA_HOME'";

build.gradle

@@ -16,12 +16,6 @@ plugins {
 
 repositories {
     mavenCentral()
-
-    // Include the Broad artifactory for intel-gkl snapshots. This is temporary
-    // until intel-gkl is available on maven central.
-    //maven {
-    //    url "https://artifactory.broadinstitute.org/artifactory/libs-snapshot/"
-    //}
 }
 
 jacocoTestReport {
@@ -48,9 +42,6 @@ dependencies {
     compile "org.tukaani:xz:1.5"
     compile "gov.nih.nlm.ncbi:ngs-java:1.2.2"
 
-    // Disabled until intel-gkl is in maven central
-    // compile "com.intel:intel-gkl:0.0.1-20160525.160915-2"
-
     testCompile "org.testng:testng:6.9.9"
 }
 
@@ -126,22 +117,13 @@ test {
 
     useTestNG {
         if( OperatingSystem.current().isUnix() ){
-            excludeGroups "slow", "broken", "sra", "intel"
+            excludeGroups "slow", "broken", "sra"
         } else {
-            excludeGroups "slow", "broken", "unix", "sra", "intel"
+            excludeGroups "slow", "broken", "unix", "sra"
         }
     }
 }
 
-task testIntelDeflater(type: Test){
-    jvmArgs '-Dsamjdk.try_use_intel_deflater=true'
-
-    description "Run the Intel Deflater tests"
-    useTestNG {
-        includeGroups "intel"
-    }
-}
-
 task testSRA(type: Test){
     description "Run the SRA tests"
     useTestNG{

src/main/java/htsjdk/samtools/BAMFileWriter.java

@@ -26,6 +26,7 @@
 import htsjdk.samtools.util.BinaryCodec;
 import htsjdk.samtools.util.BlockCompressedOutputStream;
 import htsjdk.samtools.util.RuntimeIOException;
+import htsjdk.samtools.util.zip.DeflaterFactory;
 
 import java.io.DataOutputStream;
 import java.io.File;
@@ -68,6 +69,12 @@ protected BAMFileWriter(final OutputStream os, final File file, final int compre
         outputBinaryCodec.setOutputFileName(getPathString(file));
     }
 
+    protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
+        blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel, deflaterFactory);
+        outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
+        outputBinaryCodec.setOutputFileName(getPathString(file));
+    }
+
     private void prepareToWriteAlignments() {
         if (bamRecordCodec == null) {
             bamRecordCodec = new BAMRecordCodec(getFileHeader());

src/main/java/htsjdk/samtools/Defaults.java

@@ -54,9 +54,6 @@ public class Defaults {
      */
     public static final int NON_ZERO_BUFFER_SIZE;
 
-    /** Should BlockCompressedOutputStream attempt to load libIntelDeflater? */
-    public static final boolean TRY_USE_INTEL_DEFLATER;
-
     /**
      * The reference FASTA file.  If this is not set, the file is null.  This file may be required for reading
      * writing SAM files (ex. CRAM).
@@ -98,7 +95,6 @@ public class Defaults {
         }
         COMPRESSION_LEVEL = getIntProperty("compression_level", 5);
         BUFFER_SIZE = getIntProperty("buffer_size", 1024 * 128);
-        TRY_USE_INTEL_DEFLATER = getBooleanProperty("try_use_intel_deflater", false);
         if (BUFFER_SIZE == 0) {
             NON_ZERO_BUFFER_SIZE = 1024 * 128;
         } else {
@@ -124,7 +120,6 @@ public static SortedMap<String, Object> allDefaults(){
         result.put("USE_ASYNC_IO_FOR_TRIBBLE", USE_ASYNC_IO_FOR_TRIBBLE);
         result.put("COMPRESSION_LEVEL", COMPRESSION_LEVEL);
         result.put("BUFFER_SIZE", BUFFER_SIZE);
-        result.put("TRY_USE_INTEL_DEFLATER", TRY_USE_INTEL_DEFLATER);
         result.put("NON_ZERO_BUFFER_SIZE", NON_ZERO_BUFFER_SIZE);
         result.put("REFERENCE_FASTA", REFERENCE_FASTA);
         result.put("USE_CRAM_REF_DOWNLOAD", USE_CRAM_REF_DOWNLOAD);

src/main/java/htsjdk/samtools/SAMFileWriterFactory.java

@@ -29,11 +29,13 @@
 import htsjdk.samtools.util.Log;
 import htsjdk.samtools.util.Md5CalculatingOutputStream;
 import htsjdk.samtools.util.RuntimeIOException;
+import htsjdk.samtools.util.zip.DeflaterFactory;
 
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.util.zip.Deflater;
 
 /**
  * Create a writer for writing SAM, BAM, or CRAM files.
@@ -51,6 +53,7 @@ public class SAMFileWriterFactory implements Cloneable {
     /** compression level 0: min 9:max */
     private int compressionLevel = BlockCompressedOutputStream.getDefaultCompressionLevel();
     private Integer maxRecordsInRam = null;
+    private DeflaterFactory deflaterFactory = BlockCompressedOutputStream.getDefaultDeflaterFactory();
 
     /** simple constructor */
     public SAMFileWriterFactory() {
@@ -89,6 +92,18 @@ public SAMFileWriterFactory setCreateMd5File(final boolean createMd5File) {
         return this;
     }
 
+    /**
+     * Set the deflater factory used by BAM writers created by this writer factory. Must not be null.
+     * If this method is not called, the default  {@link DeflaterFactory} is used which creates the default JDK {@link Deflater}.
+     * This method returns the SAMFileWriterFactory itself. */
+    public SAMFileWriterFactory setDeflaterFactory(final DeflaterFactory deflaterFactory){
+        if (deflaterFactory == null){
+            throw new IllegalArgumentException("null deflater factory");
+        }
+        this.deflaterFactory = deflaterFactory;
+        return this;
+    }
+
     /** set compression level 0!none 9: max */
     public SAMFileWriterFactory setCompressionLevel(final int compressionLevel) {
         this.compressionLevel = Math.min(9, Math.max(0, compressionLevel));
@@ -206,7 +221,7 @@ public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean pre
             }
             OutputStream os = IOUtil.maybeBufferOutputStream(new FileOutputStream(outputFile, false), bufferSize);
             if (createMd5File) os = new Md5CalculatingOutputStream(os, new File(outputFile.getAbsolutePath() + ".md5"));
-            final BAMFileWriter ret = new BAMFileWriter(os, outputFile, compressionLevel);
+            final BAMFileWriter ret = new BAMFileWriter(os, outputFile, compressionLevel, deflaterFactory);
             final boolean createIndex = this.createIndex && IOUtil.isRegularPath(outputFile);
             if (this.createIndex && !createIndex) {
                 log.warn("Cannot create index for BAM because output file is not a regular file: " + outputFile.getAbsolutePath());
@@ -282,7 +297,7 @@ public SAMFileWriter makeSAMWriter(final SAMFileHeader header, final boolean pre
      */
 
     public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean presorted, final OutputStream stream) {
-        return initWriter(header, presorted, true, new BAMFileWriter(stream, null, this.getCompressionLevel()));
+        return initWriter(header, presorted, true, new BAMFileWriter(stream, null, this.getCompressionLevel(), this.deflaterFactory));
     }
 
     /**

src/main/java/htsjdk/samtools/SamReaderFactory.java

@@ -4,12 +4,7 @@
 import htsjdk.samtools.cram.ref.ReferenceSource;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.sra.SRAAccession;
-import htsjdk.samtools.util.BlockCompressedInputStream;
-import htsjdk.samtools.util.BlockCompressedStreamConstants;
-import htsjdk.samtools.util.CloserUtil;
-import htsjdk.samtools.util.IOUtil;
-import htsjdk.samtools.util.Log;
-import htsjdk.samtools.util.RuntimeIOException;
+import htsjdk.samtools.util.*;
 
 import java.io.File;
 import java.io.IOException;

src/main/java/htsjdk/samtools/example/PrintReadsExample.java

@@ -25,7 +25,6 @@
 import htsjdk.samtools.*;
 import htsjdk.samtools.util.Log;
 import htsjdk.samtools.util.ProgressLogger;
-import htsjdk.samtools.util.zip.DeflaterFactory;
 
 import java.io.File;
 import java.io.IOException;
@@ -39,11 +38,7 @@
  * This is a example program showing how to use SAM readers and (optionally) writers.
  * It's also useful for measuring time.
  * An example invocation is:
- * java -cp dist/htsjdk-2.1.1.jar htsjdk.samtools.example.PrintReadsExample in.bam false a.bam
- * <p>
- * or (to test the IntelDeflator)
- * java -Dsamjdk.intel_deflater_so_path=$PWD/lib/jni/libIntelDeflater.so -cp dist/htsjdk-2.1.1.jar htsjdk.samtools.example.PrintReadsExample in.bam false a.bam
- * <p>
+ * <code>java -cp dist/htsjdk-2.1.1.jar htsjdk.samtools.example.PrintReadsExample in.bam false a.bam</code>
  * Arguments:
  * - the first argument is the input file (SAM or BAM)
  * - the second argument is a boolean (true or false) that indicates whether reads are to be eagerly decoded (useful for benchmarking)
@@ -95,8 +90,7 @@ private static void printConfigurationInfo() throws IOException {
                 System.getProperty("user.name") + '@' + InetAddress.getLocalHost().getHostName() +
                 " on " + System.getProperty("os.name") + ' ' + System.getProperty("os.version") +
                 ' ' + System.getProperty("os.arch") + "; " + System.getProperty("java.vm.name") +
-                ' ' + System.getProperty("java.runtime.version") +
-                ' ' + (DeflaterFactory.usingIntelDeflater() ? "IntelDeflater loaded and available for Level 1 compression" : "Using JdkDeflater"));
+                ' ' + System.getProperty("java.runtime.version"));
 
         final List<String> list = Defaults.allDefaults().entrySet().stream().map(e -> e.getKey() + ':' + e.getValue()).collect(Collectors.toList());
         log.info(String.join(" ", list));

src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java

@@ -54,6 +54,7 @@ public class BlockCompressedOutputStream
     private static final Log log = Log.getInstance(BlockCompressedOutputStream.class);
 
     private static int defaultCompressionLevel = BlockCompressedStreamConstants.DEFAULT_COMPRESSION_LEVEL;
+    private static DeflaterFactory defaultDeflaterFactory = new DeflaterFactory();
 
     /**
      * Sets the GZip compression level for subsequent BlockCompressedOutputStream object creation
@@ -71,6 +72,22 @@ public static int getDefaultCompressionLevel() {
         return defaultCompressionLevel;
     }
 
+    /**
+     * Sets the default {@link DeflaterFactory} that will be used for all instances unless specified otherwise in the constructor.
+     * If this method is not called the default is a factory that will create the JDK {@link Deflater}.
+     * @param deflaterFactory non-null default factory.
+     */
+    public static void setDefaultDeflaterFactory(final DeflaterFactory deflaterFactory) {
+        if (deflaterFactory == null) {
+            throw new IllegalArgumentException("null deflaterFactory");
+        }
+        defaultDeflaterFactory = deflaterFactory;
+    }
+
+    public static DeflaterFactory getDefaultDeflaterFactory() {
+        return defaultDeflaterFactory;
+    }
+
     private final BinaryCodec codec;
     private final byte[] uncompressedBuffer = new byte[BlockCompressedStreamConstants.DEFAULT_UNCOMPRESSED_BLOCK_SIZE];
     private int numUncompressedBytes = 0;
@@ -102,20 +119,25 @@ public static int getDefaultCompressionLevel() {
 
     /**
      * Uses default compression level, which is 5 unless changed by setCompressionLevel
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(File, int, DeflaterFactory)} to specify a custom factory.
      */
     public BlockCompressedOutputStream(final String filename) {
         this(filename, defaultCompressionLevel);
     }
 
     /**
      * Uses default compression level, which is 5 unless changed by setCompressionLevel
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(File, int, DeflaterFactory)} to specify a custom factory.
      */
     public BlockCompressedOutputStream(final File file) {
         this(file, defaultCompressionLevel);
     }
 
     /**
      * Prepare to compress at the given compression level
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
      * @param compressionLevel 1 <= compressionLevel <= 9
      */
     public BlockCompressedOutputStream(final String filename, final int compressionLevel) {
@@ -125,29 +147,58 @@ public BlockCompressedOutputStream(final String filename, final int compressionL
     /**
      * Prepare to compress at the given compression level
      * @param compressionLevel 1 <= compressionLevel <= 9
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(File, int, DeflaterFactory)} to specify a custom factory.
      */
     public BlockCompressedOutputStream(final File file, final int compressionLevel) {
+        this(file, compressionLevel, defaultDeflaterFactory);
+    }
+
+    /**
+     * Prepare to compress at the given compression level
+     * @param compressionLevel 1 <= compressionLevel <= 9
+     * @param deflaterFactory custom factory to create deflaters (overrides the default)
+     */
+    public BlockCompressedOutputStream(final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
         this.file = file;
         codec = new BinaryCodec(file, true);
-        deflater = DeflaterFactory.makeDeflater(compressionLevel, true);
+        deflater = deflaterFactory.makeDeflater(compressionLevel, true);
         log.debug("Using deflater: " + deflater.getClass().getSimpleName());
     }
 
     /**
-     * Constructors that take output streams
-     * file may be null
+     * Uses default compression level, which is 5 unless changed by setCompressionLevel
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory)} to specify a custom factory.
+     *
+     * @param file may be null
      */
     public BlockCompressedOutputStream(final OutputStream os, final File file) {
         this(os, file, defaultCompressionLevel);
     }
 
+    /**
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory)} to specify a custom factory.
+     */
     public BlockCompressedOutputStream(final OutputStream os, final File file, final int compressionLevel) {
+        this(os, file, compressionLevel, defaultDeflaterFactory);
+    }
+
+    /**
+     * Creates the output stream.
+     * @param os output stream to create a BlockCompressedOutputStream from
+     * @param file file to which to write the output or null if not available
+     * @param compressionLevel the compression level (0-9)
+     * @param deflaterFactory custom factory to create deflaters (overrides the default)
+     */
+    public BlockCompressedOutputStream(final OutputStream os, final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
         this.file = file;
         codec = new BinaryCodec(os);
         if (file != null) {
             codec.setOutputFileName(file.getAbsolutePath());
         }
-        deflater = DeflaterFactory.makeDeflater(compressionLevel, true);
+        deflater = deflaterFactory.makeDeflater(compressionLevel, true);
         log.debug("Using deflater: " + deflater.getClass().getSimpleName());
     }
 
@@ -160,9 +211,9 @@ public BlockCompressedOutputStream(final OutputStream os, final File file, final
      */
     public static BlockCompressedOutputStream maybeBgzfWrapOutputStream(final File location, OutputStream output) {
         if (!(output instanceof BlockCompressedOutputStream)) {
-                return new BlockCompressedOutputStream(output, location);
+           return new BlockCompressedOutputStream(output, location);
         } else {
-        return (BlockCompressedOutputStream)output;
+           return (BlockCompressedOutputStream)output;
         }
     }