InflaterFactory added

build.gradle

@@ -13,6 +13,7 @@ compileTestJava {
 }
 
 repositories {
+    maven { url uri('/home/gspowley/.m2/repository/')}
     mavenLocal()
     mavenCentral()
     maven { url "https://artifactory.broadinstitute.org/artifactory/libs-snapshot/" }
@@ -24,7 +25,6 @@ dependencies {
     compile 'org.apache.logging.log4j:log4j-api:2.5'
     compile 'org.apache.logging.log4j:log4j-core:2.5'
     compile 'com.github.samtools:htsjdk:2.7.0-18-g4d0070b-SNAPSHOT'
-
     testCompile 'org.testng:testng:6.9.9'
 }
 

src/main/java/com/intel/gkl/compression/IntelInflaterFactory.java

@@ -0,0 +1,37 @@
+package com.intel.gkl.compression;
+
+import htsjdk.samtools.util.zip.InflaterFactory;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.io.File;
+import java.util.zip.Inflater;
+
+/**
+ * Created by pnvaidya on 2/1/17.
+ */
+public class IntelInflaterFactory extends InflaterFactory {
+    private final static Logger logger = LogManager.getLogger(IntelDeflaterFactory.class);
+    private boolean intelInflaterSupported;
+
+    public IntelInflaterFactory(File tmpDir) {
+        intelInflaterSupported = new IntelInflater().load(tmpDir);
+    }
+
+    public IntelInflaterFactory() {
+        this(null);
+    }
+
+    public Inflater makeInflater(final boolean nowrap) {
+        if (intelInflaterSupported) {
+            return new IntelInflater(nowrap);
+        }
+        logger.warn("IntelInflater is not supported, using Java.util.zip.Inflater");
+        return new Inflater(nowrap);
+    }
+
+    public boolean usingIntelInflater() {
+        return intelInflaterSupported;
+    }
+}

src/main/native/compression/IntelInflater.cc

@@ -83,7 +83,7 @@ JNIEXPORT void JNICALL Java_com_intel_gkl_compression_IntelInflater_resetNative
 
 
 
-      fprintf(stdout,"%c",nowrap);
+
       isal_inflate_init(lz_stream);
 
       lz_stream->avail_in = 0;

src/test/java/com/intel/gkl/compression/InflaterUnitTest.java

@@ -0,0 +1,70 @@
+package com.intel.gkl.compression;
+
+import com.intel.gkl.IntelGKLUtils;
+import htsjdk.samtools.util.BlockCompressedInputStream;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.zip.Deflater;
+import java.util.zip.Inflater;
+
+/**
+ * Created by pnvaidya on 2/1/17.
+ */
+public class InflaterUnitTest {
+
+    private final static Logger log = LogManager.getLogger(InflaterUnitTest.class);
+    private final static String INPUT_FILE = IntelGKLUtils.pathToTestResource("HiSeq.1mb.1RG.2k_lines.bam");
+
+    @Test(enabled = true)
+    public void integrationTest() throws IOException {
+
+        final File inputFile = new File(INPUT_FILE);
+        long inputBytes = inputFile.length();
+        int compressedBytes = 0;
+        final byte[] inputbuffer = new byte[(int)inputBytes];
+        final byte[] outputbuffer = new byte[(int)inputBytes];
+        final byte[] finalbuffer = new byte[(int)inputBytes];
+
+        long totalTime = 0;
+
+        for (int i = 1; i < 10; i++) {
+
+            final IntelInflaterFactory intelInflaterFactory = new IntelInflaterFactory();
+            final Inflater inflater = intelInflaterFactory.makeInflater(true);
+
+            final IntelDeflaterFactory intelDeflaterFactory = new IntelDeflaterFactory();
+            final Deflater deflater = intelDeflaterFactory.makeDeflater(i, true);
+
+
+            final BlockCompressedInputStream inputStream = new BlockCompressedInputStream(inputFile);
+
+            inputBytes = inputStream.read(inputbuffer, 0, inputbuffer.length);
+            deflater.reset();
+            deflater.setInput(inputbuffer, 0, inputbuffer.length);
+            deflater.finish();
+            compressedBytes = deflater.deflate(outputbuffer, 0, outputbuffer.length);
+
+
+            try {
+                inflater.reset();
+                inflater.setInput(outputbuffer, 0, compressedBytes);
+                final long start = System.currentTimeMillis();
+                inflater.inflate(finalbuffer, 0, inputbuffer.length);
+                totalTime = System.currentTimeMillis() - start;
+                System.out.printf("Level: %d, time: %d\n", i, totalTime);
+
+
+            } catch (java.util.zip.DataFormatException e) {
+                e.printStackTrace();
+            }
+            Assert.assertEquals(inputbuffer, finalbuffer);
+            inflater.end();
+            deflater.end();
+        }
+    }
+}