Merge pull request #48 from Intel-HLS/pv_updates

fix API issues
IntelLabs · Feb 24, 2017 · d4f0a10 · d4f0a10
2 parents e3187f8 + d7290fa
commit d4f0a10
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Showing 3 changed files with 17 additions and 6 deletions.
diff --git a/src/main/java/com/intel/gkl/compression/IntelDeflater.java b/src/main/java/com/intel/gkl/compression/IntelDeflater.java
@@ -96,6 +96,7 @@ public IntelDeflater(int level, boolean nowrap) {
         this.level = level;
         this.nowrap = nowrap;
         strategy = DEFAULT_STRATEGY;
+
     }
 
      /**
@@ -135,6 +136,7 @@ public void reset() {
      */
     @Override
     public void setInput(byte[] b, int off, int len) throws NullPointerException {
+        if(lz_stream == 0) reset();
         if(b == null) {
             throw new NullPointerException("Input is null");
         }
@@ -144,8 +146,6 @@ public void setInput(byte[] b, int off, int len) throws NullPointerException {
 
         inputBuffer = b;
         inputBufferLength = len;
-
-
     }
 
     /**

diff --git a/src/main/java/com/intel/gkl/compression/IntelInflater.java b/src/main/java/com/intel/gkl/compression/IntelInflater.java
@@ -88,6 +88,7 @@ public synchronized boolean load(File tempDir) {
     public IntelInflater(boolean nowrap) {
       //  initFieldsNative();
         this.nowrap = nowrap;
+
     }
 
     /**
@@ -116,6 +117,7 @@ public void reset() {
      */
     @Override
     public void setInput(byte[] b, int off, int len) throws NullPointerException {
+        if(lz_stream == 0) reset();
         if(b == null) {
             throw new NullPointerException("Input is null");
         }
@@ -125,6 +127,7 @@ public void setInput(byte[] b, int off, int len) throws NullPointerException {
         inputBuffer = b;
         inputBufferOffset = off;
         inputBufferLength = len;
+
     }
 
     /**
@@ -152,7 +155,7 @@ public int inflate (byte[] b, int off, int len ) {
      */
     @Override
     public int inflate (byte[] b ) {
-        return inflateNative( b, 0, 0);
+        return inflateNative( b, 0, b.length);
     }
 
     /**
@@ -175,6 +178,15 @@ public boolean finished() {
      */
     @Override
     public void end() {
-        endNative();
+
+        if(lz_stream !=0)
+        {
+            endNative();
+            lz_stream=0;
+        }
     }
+
+    @Override
+    protected void finalize() {}
+
 }
diff --git a/src/test/java/com/intel/gkl/compression/DeflaterUnitTest.java b/src/test/java/com/intel/gkl/compression/DeflaterUnitTest.java
@@ -82,7 +82,6 @@ public void randomDNATest() {
 
 
                 randomDNA(input);
-                deflater.reset();
                 deflater.setInput(input, 0, input.length);
                 deflater.finish();
 
@@ -98,7 +97,7 @@ public void randomDNATest() {
 
 
                 try {
-                    inflater.reset();
+
                     inflater.setInput(compressed, 0, compressedBytes);
                     final long start = System.currentTimeMillis();
                     inflater.inflate(result, 0, LEN);