inflaterIntegrationTest

build.gradle

@@ -13,7 +13,7 @@ compileTestJava {
 }
 
 repositories {
-    maven { url uri('/home/gspowley/.m2/repository/')}
+   // maven { url uri('/home/gspowley/.m2/repository/')}
     mavenLocal()
     mavenCentral()
     maven { url "https://artifactory.broadinstitute.org/artifactory/libs-snapshot/" }
@@ -24,7 +24,7 @@ dependencies {
     compile 'org.broadinstitute:gatk-native-bindings:0.0.3'
     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'
+    compile 'com.github.samtools:htsjdk:2.8.1-28-g3a8fa8e-SNAPSHOT'
     testCompile 'org.testng:testng:6.9.9'
 }
 

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

@@ -79,6 +79,7 @@ public synchronized boolean load(File tempDir) {
     private int level;
     private int strategy;
     private boolean nowrap;
+
 
      /**
      * Creates a new compressor using the specified compression level.
@@ -119,6 +120,7 @@ public void reset() {
         resetNative(nowrap);
         inputBuffer = null;
         inputBufferLength = 0;
+
         endOfStream = false;
         finished = false;
     }
@@ -142,6 +144,8 @@ public void setInput(byte[] b, int off, int len) throws NullPointerException {
 
         inputBuffer = b;
         inputBufferLength = len;
+
+
     }
 
     /**
@@ -167,6 +171,7 @@ public void finish() {
      */
     @Override
     public int deflate(byte[] b, int off, int len ) {
+
         return deflateNative(b, len);
     }
 

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

@@ -24,7 +24,7 @@ public IntelInflaterFactory() {
     }
 
     public Inflater makeInflater(final boolean nowrap) {
-        if (intelInflaterSupported) {
+        if (intelInflaterSupported && nowrap) {
             return new IntelInflater(nowrap);
         }
         logger.warn("IntelInflater is not supported, using Java.util.zip.Inflater");

src/main/native/compression/IntelDeflater.cc

@@ -54,8 +54,8 @@ static jfieldID FID_inputBuffer;
 static jfieldID FID_inputBufferLength;
 static jfieldID FID_endOfStream;
 static jfieldID FID_finished;
-static jfieldID FID_finish;
 static jfieldID FID_level;
+//static jfieldID FID_inputBufferOffset;
 
 
 
@@ -69,8 +69,8 @@ JNIEXPORT void JNICALL Java_com_intel_gkl_compression_IntelDeflater_initNative
   FID_inputBufferLength = env->GetFieldID(cls, "inputBufferLength", "I");
   FID_endOfStream = env->GetFieldID(cls, "endOfStream", "Z");
   FID_finished = env->GetFieldID(cls, "finished", "Z");
-  FID_finish = env->GetFieldID(cls, "finish", "Z");
   FID_level = env->GetFieldID(cls,"level","I");
+//  FID_inputBufferOffset = env->GetFieldID(cls, "inputBufferOffset", "I");
 
 }
 
@@ -185,9 +185,10 @@ JNIEXPORT jint JNICALL Java_com_intel_gkl_compression_IntelDeflater_deflateNativ
 
   jbyteArray inputBuffer = (jbyteArray)env->GetObjectField(obj, FID_inputBuffer);
   jint inputBufferLength = env->GetIntField(obj, FID_inputBufferLength);
+  //jint inputBufferOffset = env->GetIntField(obj, FID_inputBufferOffset);
   jboolean endOfStream = env->GetBooleanField(obj, FID_endOfStream);
   jint level = env->GetIntField(obj, FID_level);
-  jboolean finish = env->GetBooleanField(obj, FID_finish);
+
 
   if(level == 1) {
 
@@ -198,11 +199,11 @@ JNIEXPORT jint JNICALL Java_com_intel_gkl_compression_IntelDeflater_deflateNativ
     jbyte* next_in = (jbyte*)env->GetPrimitiveArrayCritical(inputBuffer, 0);
     jbyte* next_out = (jbyte*)env->GetPrimitiveArrayCritical(outputBuffer, 0);
 
-    lz_stream->next_in = (UINT8*)next_in;
+    lz_stream->next_in = (UINT8*)(next_in);
     lz_stream->avail_in = inputBufferLength;
     lz_stream->end_of_stream = endOfStream;
-    lz_stream->next_out = (UINT8*)next_out;
-    lz_stream->avail_out = outputBufferLength;
+    lz_stream->next_out = (UINT8*) (next_out);
+    lz_stream->avail_out = outputBufferLength ;
 
     int bytes_in = inputBufferLength;
 
@@ -316,4 +317,5 @@ Java_com_intel_gkl_compression_IntelDeflater_endNative(JNIEnv *env, jobject obj)
   if (level != 1) {
     deflateEnd(lz_stream);
   }
+  else free(lz_stream);
 }

src/main/native/compression/IntelInflater.cc

@@ -83,16 +83,14 @@ JNIEXPORT void JNICALL Java_com_intel_gkl_compression_IntelInflater_resetNative
       }
       env->SetLongField(obj, FID_inf_lz_stream, (jlong)lz_stream);
 
-
+    }
       isal_inflate_init(lz_stream);
 
       lz_stream->avail_in = 0;
       lz_stream->next_in = Z_NULL;
       lz_stream->avail_out = 0;
       lz_stream->next_out = Z_NULL;
 
-     }
-
 }
 
 

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

@@ -21,9 +21,10 @@ public class InflaterUnitTest {
     private final static String INPUT_FILE = IntelGKLUtils.pathToTestResource("HiSeq.1mb.1RG.2k_lines.bam");
 
     @Test(enabled = true)
-    public void integrationTest() throws IOException {
+    public void inflaterUnitTest() throws IOException {
 
         final File inputFile = new File(INPUT_FILE);
+
         long inputBytes = inputFile.length();
         int compressedBytes = 0;
         final byte[] inputbuffer = new byte[(int)inputBytes];
@@ -66,5 +67,7 @@ public void integrationTest() throws IOException {
             inflater.end();
             deflater.end();
         }
+
+
     }
 }