diff --git a/build.gradle b/build.gradle
index ec5ace94de..a05342a76a 100644
--- a/build.gradle
+++ b/build.gradle
@@ -16,6 +16,12 @@ 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 {
@@ -41,6 +47,7 @@ dependencies {
     compile "org.apache.commons:commons-compress:1.4.1"
     compile "org.tukaani:xz:1.5"
     compile "gov.nih.nlm.ncbi:ngs-java:1.2.2"
+    compile "com.intel:intel-gkl:0.0.1-20160525.160915-2"
 
     testCompile "org.testng:testng:6.9.9"
 }
@@ -65,12 +72,6 @@ jar {
     }
 }
 
-processResources {
-    into "lib/jni/", {
-        from ("lib/jni/libIntelDeflater.so")
-    }
-}
-
 import org.gradle.internal.os.OperatingSystem;
 
 tasks.withType(Test) {
@@ -83,7 +84,6 @@ tasks.withType(Test) {
 
     jvmArgs '-Djava.awt.headless=true'  //this prevents awt from displaying a java icon while the tests are running
 
-
     if (System.env.CI == "true") {  //if running under a CI output less into the logs
         int count = 0
 
@@ -121,6 +121,7 @@ tasks.withType(Test) {
 
 test {
     description = "Runs the unit tests other than the SRA tests"
+
     useTestNG {
         if( OperatingSystem.current().isUnix() ){
             excludeGroups "slow", "broken", "sra", "intel"
@@ -131,7 +132,7 @@ test {
 }
 
 task testIntelDeflater(type: Test){
-    jvmArgs '-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so'
+    jvmArgs '-Dsamjdk.try_use_intel_deflater=true'
 
     description "Run the Intel Deflater tests"
     useTestNG {
diff --git a/lib/jni/libIntelDeflater.so b/lib/jni/libIntelDeflater.so
deleted file mode 100755
index 5e8dd79870..0000000000
Binary files a/lib/jni/libIntelDeflater.so and /dev/null differ
diff --git a/scripts/build_intel_deflater.sh b/scripts/build_intel_deflater.sh
deleted file mode 100644
index f139cf0fb4..0000000000
--- a/scripts/build_intel_deflater.sh
+++ /dev/null
@@ -1,78 +0,0 @@
-#! /bin/bash
-#
-# The MIT License
-#
-# Copyright (c) 2013 The Broad Institute
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-
-# Build libIntelDeflater.so, the JNI library that wraps Intel IPP compression library and igzip.
-# Note that this is not built as part of standard release process.  Rather, it is built manually and then
-# copied to htsjdk/lib/jni.
-
-# Assumes OpenJDK exists at $OPENJDK.  I used openjdk-7-fcs-src-b147-27_jun_2011.zip
-# Assumes that Picard-public java sources have been compiled
-# Assumes IPP8_CODE_SAMPLES_DIR points to Intel IPP sample code built with -fPIC
-# Assumes IPP8_INSTALL_DIR points to composer_xe_2013_sp1 installation
-# Assumes IGZIP_LIB points to the directory containing libigzip0c.a
-source ${IPP8_INSTALL_DIR}/bin/ippvars.sh intel64
-
-set -e
-
-if [ "$OPENJDK" = "" ]
-then echo "ERROR: OPENJDK environment variable not defined." >&2
-     exit 1
-fi
-
-if [ "$IPP8_CODE_SAMPLES_DIR" = "" ]
-then echo "ERROR: IPP8_CODE_SAMPLES_DIR environment variable not defined." >&2
-     exit 1
-fi
-
-if [ "$IPP8_INSTALL_DIR" = "" ]
-then echo "ERROR: IPP8_INSTALL_DIR environment variable not defined." >&2
-     exit 1
-fi
-if [ "$IGZIP_LIB" = "" ]
-then echo "ERROR: IGZIP_LIB environment variable not defined." >&2
-     exit 1
-fi
-
-rootdir=$(dirname $(dirname $(dirname $0)))
-
-
-builddir=$rootdir/lib_build
-rm -rf $builddir
-mkdir -p $builddir
-
-echo $rootdir
-# Create JNI C header file
-javah -jni -classpath $rootdir/classes -d $builddir htsjdk.samtools.util.zip.IntelDeflater
-
-# Compile source and create library.
-gcc -I$builddir -I$rootdir/src/c/inteldeflater/ -I$JAVA_HOME/include/ -I$JAVA_HOME/include/linux/ -I$OPENJDK/jdk/src/share/native/common/ \
--I$OPENJDK/jdk/src/solaris/native/common/ -c -O3 -fPIC $rootdir/src/c/inteldeflater/IntelDeflater.c
-gcc  -z noexecstack -shared -o $builddir/libIntelDeflater.so IntelDeflater.o  -L${IPP8_CODE_SAMPLES_DIR}/__cmake/data-compression.intel64.make.static.release/__lib/release \
--lzlib  -lstdc++ -Wl,-Bstatic  -L$IGZIP_LIB -ligzip0c -lbfp754  -ldecimal  -liomp5  -liompstubs5  -lipgo  -lippac  -lippcc  -lippch  -lippcv  \
--lippdc  -lippdi  -lippgen  -lippi  -lippj  -lippm  -lippr  -lippsc  -lippvc  -lippvm  -lirng  -lmatmul  -lpdbx  \
--lpdbxinst  -lsvml  -lipps  -limf  -lirc  -lirc_s  -lippcore -Wl,-Bdynamic
-
-
-
diff --git a/src/main/c/inteldeflater/IntelDeflater.c b/src/main/c/inteldeflater/IntelDeflater.c
deleted file mode 100644
index 65f5d1d9e6..0000000000
--- a/src/main/c/inteldeflater/IntelDeflater.c
+++ /dev/null
@@ -1,392 +0,0 @@
-/*
- * Copyright (c) 1997, 2010, Oracle and/or its affiliates. All rights reserved.
- * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
- *
- * This code is free software; you can redistribute it and/or modify it
- * under the terms of the GNU General Public License version 2 only, as
- * published by the Free Software Foundation.  Oracle designates this
- * particular file as subject to the "Classpath" exception as provided
- * by Oracle in the LICENSE file that accompanied this code.
- *
- * This code is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
- * version 2 for more details (a copy is included in the LICENSE file that
- * accompanied this code).
- *
- * You should have received a copy of the GNU General Public License version
- * 2 along with this work; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
- * or visit www.oracle.com if you need additional information or have any
- * questions.
- */
-
-/*
- * Native method support for htsjdk.samtools.util.zip.IntelDeflater.
- * This is copied from OpenJDK native support for java.util.zip.Deflater, and modified to support igzip.
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <immintrin.h> 
-#include <emmintrin.h>
-#include <stdbool.h>
-#include <assert.h>
-#include "jlong.h"
-#include "jni.h"
-//#include "jni_util.h"
-
-#include "zlib.h"
-#include "htsjdk_samtools_util_zip_IntelDeflater.h"
-#include "igzip_lib.h"
-#define DEF_MEM_LEVEL 8
-#define FAST_COMPRESSION 1
-#define IGZIP_TRUE 1
-
-static jfieldID levelID;
-static jfieldID strategyID;
-static jfieldID setParamsID;
-static jfieldID finishID;
-static jfieldID finishedID;
-static jfieldID bufID, offID, lenID;
-
-typedef struct {
-    z_stream zStream;
-    LZ_Stream2 lz2Stream;
-    int useIGZIP;
-} Stream;
-
-
-bool is_cpuid_ecx_bit_set(int eax, int bitidx) 
-{ 
-  int ecx = 0, edx = 0, ebx = 0; 
-  __asm__ ("cpuid" 
-	   :"=b" (ebx), 
-	    "=c" (ecx), 
-	    "=d" (edx) 
-	   :"a" (eax) 
-	   ); 
-  return (((ecx >> bitidx)&1) == 1); 
-}
-
-bool is_sse42_supported() 
-{ 
-#ifdef __INTEL_COMPILER 
-  return  (_may_i_use_cpu_feature(_FEATURE_SSE4_2) > 0); 
-#else 
-  //  return  __builtin_cpu_supports("sse4.2"); 
-  return is_cpuid_ecx_bit_set(1, 20); 
-#endif 
-}
-//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-/**
- * Throw a Java exception by name. Similar to SignalError.
- */
-JNIEXPORT void JNICALL
-JNU_ThrowByName(JNIEnv *env, const char *name, const char *msg)
-{
-    jclass cls = (*env)->FindClass(env, name);
-
-    if (cls != 0) /* Otherwise an exception has already been thrown */
-        (*env)->ThrowNew(env, cls, msg);
-}
-
-/* JNU_Throw common exceptions */
-
-JNIEXPORT void JNICALL
-JNU_ThrowNullPointerException(JNIEnv *env, const char *msg)
-{
-    JNU_ThrowByName(env, "java/lang/NullPointerException", msg);
-}
-
-
-JNIEXPORT void JNICALL
-JNU_ThrowOutOfMemoryError(JNIEnv *env, const char *msg)
-{
-    JNU_ThrowByName(env, "java/lang/OutOfMemoryError", msg);
-}
-
-JNIEXPORT void JNICALL
-JNU_ThrowIllegalArgumentException(JNIEnv *env, const char *msg)
-{
-    JNU_ThrowByName(env, "java/lang/IllegalArgumentException", msg);
-}
-
-JNIEXPORT void JNICALL
-JNU_ThrowInternalError(JNIEnv *env, const char *msg)
-{
-    JNU_ThrowByName(env, "java/lang/InternalError", msg);
-}
-/////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-JNIEXPORT void JNICALL
-Java_htsjdk_samtools_util_zip_IntelDeflater_initIDs(JNIEnv *env, jclass cls)
-{
-    levelID = (*env)->GetFieldID(env, cls, "level", "I");
-    strategyID = (*env)->GetFieldID(env, cls, "strategy", "I");
-    setParamsID = (*env)->GetFieldID(env, cls, "setParams", "Z");
-    finishID = (*env)->GetFieldID(env, cls, "finish", "Z");
-    finishedID = (*env)->GetFieldID(env, cls, "finished", "Z");
-    bufID = (*env)->GetFieldID(env, cls, "buf", "[B");
-    offID = (*env)->GetFieldID(env, cls, "off", "I");
-    lenID = (*env)->GetFieldID(env, cls, "len", "I");
- 
-}
-
-JNIEXPORT jlong JNICALL
-Java_htsjdk_samtools_util_zip_IntelDeflater_init(JNIEnv *env, jclass cls, jint level,
-                                 jint strategy, jboolean nowrap)
-{
-    Stream *strm = calloc(1, sizeof(Stream));
-    if (level == FAST_COMPRESSION && is_sse42_supported()) { //Use igzip
-	printf("Using igzip\n");
-	strm->useIGZIP = IGZIP_TRUE;
-	if (strm == 0) {
-	    JNU_ThrowOutOfMemoryError(env, 0);
-	    return jlong_zero;
-	} else {
-	    init_stream(&strm->lz2Stream); //CHECK RETURN VALUE
-	    return ptr_to_jlong(strm);
-	}
-      
-    } else {
-
-	if (strm == 0) {
-	    JNU_ThrowOutOfMemoryError(env, 0);
-	    return jlong_zero;
-	} else {
-	    char *msg;
-	    switch (deflateInit2(&strm->zStream, level, Z_DEFLATED,
-				 nowrap ? -MAX_WBITS : MAX_WBITS,
-				 DEF_MEM_LEVEL, strategy)) {
-	    case Z_OK:
-		return ptr_to_jlong(&strm->zStream);
-	    case Z_MEM_ERROR:
-		free(strm);
-		JNU_ThrowOutOfMemoryError(env, 0);
-		return jlong_zero;
-	    case Z_STREAM_ERROR:
-		free(strm);
-		JNU_ThrowIllegalArgumentException(env, 0);
-		return jlong_zero;
-	    default:
-		msg = strm->zStream.msg;
-		free(strm);
-		JNU_ThrowInternalError(env, msg);
-		return jlong_zero;
-	    }
-	}
-    }
-}
-
-JNIEXPORT void JNICALL
-Java_htsjdk_samtools_util_zip_IntelDeflater_setDictionary(JNIEnv *env, jclass cls, jlong addr,
-                                          jarray b, jint off, jint len)
-{
-    Bytef *buf = (*env)->GetPrimitiveArrayCritical(env, b, 0);
-    int res;
-    if (buf == 0) {/* out of memory */
-        return;
-    }
-    res = deflateSetDictionary(&((Stream *)jlong_to_ptr(addr))->zStream, buf + off, len);
-    (*env)->ReleasePrimitiveArrayCritical(env, b, buf, 0);
-    switch (res) {
-    case Z_OK:
-        break;
-    case Z_STREAM_ERROR:
-        JNU_ThrowIllegalArgumentException(env, 0);
-        break;
-    default:
-        JNU_ThrowInternalError(env, ((Stream *)jlong_to_ptr(addr))->zStream.msg);
-        break;
-    }
-}
-
-JNIEXPORT jint JNICALL
-Java_htsjdk_samtools_util_zip_IntelDeflater_deflateBytes(JNIEnv *env, jobject this, jlong addr,
-                                         jarray b, jint off, jint len, jint flush)
-{
-    jarray this_buf = (*env)->GetObjectField(env, this, bufID);
-    jint this_off = (*env)->GetIntField(env, this, offID);
-    jint this_len = (*env)->GetIntField(env, this, lenID);
-    jbyte *in_buf;
-    jbyte *out_buf;
-    Stream *strm = jlong_to_ptr(addr);
-
-    //igzip only supports one compression level so setParamsID should not be set when using igzip 
-    //igzip does not support flush
-    if (((Stream *)jlong_to_ptr(addr))->useIGZIP && (((*env)->GetBooleanField(env, this, setParamsID) && strm->lz2Stream.total_in != 0)  || flush == 1)) {
-	JNU_ThrowInternalError(env, "igzip doesn't support this");
-    } else if (((Stream *)jlong_to_ptr(addr))->useIGZIP) {
-	in_buf = (*env)->GetPrimitiveArrayCritical(env, this_buf, 0);
-	if (in_buf == NULL) {
-	    // Throw OOME only when length is not zero
-	    if (this_len != 0) {
-		JNU_ThrowOutOfMemoryError(env, 0);
-	    }
-	    return 0;
-	}
-	out_buf = (*env)->GetPrimitiveArrayCritical(env, b, 0);
-	if (out_buf == NULL) {
-	    (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0);
-	    if (len != 0) {
-		JNU_ThrowOutOfMemoryError(env, 0);
-	    }
-	    return 0;
-	}
-	strm->lz2Stream.next_in = (Bytef *) (in_buf + this_off);
-	strm->lz2Stream.next_out = (Bytef *) (out_buf + off);
-	strm->lz2Stream.avail_in = this_len;
-	strm->lz2Stream.avail_out = len;
-	assert(strm->lz2Stream.avail_in != 0);
-	assert(strm->lz2Stream.avail_out != 0);
-	jboolean finish = (*env)->GetBooleanField(env, this, finishID);
-	if (finish) {
-	    strm->lz2Stream.end_of_stream = 1;
-	} else {
-	    strm->lz2Stream.end_of_stream = 0;
-	}
-	fast_lz(&strm->lz2Stream);
-
-	(*env)->ReleasePrimitiveArrayCritical(env, b, out_buf, 0);
-	(*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0);
-	if (finish) {
-	    (*env)->SetBooleanField(env, this, finishedID, JNI_TRUE);
-	}
-	this_off += this_len - strm->lz2Stream.avail_in;
-	(*env)->SetIntField(env, this, offID, this_off);
-	(*env)->SetIntField(env, this, lenID, strm->lz2Stream.avail_in);
-	return len - strm->lz2Stream.avail_out;
-    } else {
-
-	int res;
-	if ((*env)->GetBooleanField(env, this, setParamsID)) {
-	    int level = (*env)->GetIntField(env, this, levelID);
-	    int strategy = (*env)->GetIntField(env, this, strategyID);
-
-	    in_buf = (*env)->GetPrimitiveArrayCritical(env, this_buf, 0);
-	    if (in_buf == NULL) {
-		// Throw OOME only when length is not zero
-		if (this_len != 0)
-		    JNU_ThrowOutOfMemoryError(env, 0);
-		return 0;
-	    }
-	    out_buf = (*env)->GetPrimitiveArrayCritical(env, b, 0);
-	    if (out_buf == NULL) {
-		(*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0);
-		if (len != 0)
-		    JNU_ThrowOutOfMemoryError(env, 0);
-		return 0;
-	    }
-
-	    strm->zStream.next_in = (Bytef *) (in_buf + this_off);
-	    strm->zStream.next_out = (Bytef *) (out_buf + off);
-	    strm->zStream.avail_in = this_len;
-	    strm->zStream.avail_out = len;
-	    res = deflateParams(&strm->zStream, level, strategy);
-	    (*env)->ReleasePrimitiveArrayCritical(env, b, out_buf, 0);
-	    (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0);
-
-	    switch (res) {
-	    case Z_OK:
-		(*env)->SetBooleanField(env, this, setParamsID, JNI_FALSE);
-		this_off += this_len - strm->zStream.avail_in;
-		(*env)->SetIntField(env, this, offID, this_off);
-		(*env)->SetIntField(env, this, lenID, strm->zStream.avail_in);
-		return len - strm->zStream.avail_out;
-	    case Z_BUF_ERROR:
-		(*env)->SetBooleanField(env, this, setParamsID, JNI_FALSE);
-		return 0;
-	    default:
-		JNU_ThrowInternalError(env, strm->zStream.msg);
-		return 0;
-	    }
-	} else {
-	    jboolean finish = (*env)->GetBooleanField(env, this, finishID);
-	    in_buf = (*env)->GetPrimitiveArrayCritical(env, this_buf, 0);
-	    if (in_buf == NULL) {
-		if (this_len != 0)
-		    JNU_ThrowOutOfMemoryError(env, 0);
-		return 0;
-	    }
-	    out_buf = (*env)->GetPrimitiveArrayCritical(env, b, 0);
-	    if (out_buf == NULL) {
-		(*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0);
-		if (len != 0)
-		    JNU_ThrowOutOfMemoryError(env, 0);
-
-		return 0;
-	    }
-
-	    strm->zStream.next_in = (Bytef *) (in_buf + this_off);
-	    strm->zStream.next_out = (Bytef *) (out_buf + off);
-	    strm->zStream.avail_in = this_len;
-	    strm->zStream.avail_out = len;
-	    res = deflate(&strm->zStream, finish ? Z_FINISH : flush);
-	    (*env)->ReleasePrimitiveArrayCritical(env, b, out_buf, 0);
-	    (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0);
-
-	    switch (res) {
-	    case Z_STREAM_END:
-		(*env)->SetBooleanField(env, this, finishedID, JNI_TRUE);
-		/* fall through */
-	    case Z_OK:
-		this_off += this_len - strm->zStream.avail_in;
-		(*env)->SetIntField(env, this, offID, this_off);
-		(*env)->SetIntField(env, this, lenID, strm->zStream.avail_in);
-		return len - strm->zStream.avail_out;
-	    case Z_BUF_ERROR:
-		return 0;
-            default:
-		JNU_ThrowInternalError(env, strm->zStream.msg);
-		return 0;
-	    }
-	}
-    }
-}
-
-JNIEXPORT jint JNICALL
-Java_htsjdk_samtools_util_zip_IntelDeflater_getAdler(JNIEnv *env, jclass cls, jlong addr)
-{
-    if (((Stream *)jlong_to_ptr(addr))->useIGZIP)
-	JNU_ThrowInternalError(env, "igzip doesn't support getAdler function");
-    else
-	return ((Stream *)jlong_to_ptr(addr))->zStream.adler;
-}
-
-JNIEXPORT jlong JNICALL
-Java_htsjdk_samtools_util_zip_IntelDeflater_getBytesRead(JNIEnv *env, jclass cls, jlong addr)
-{
-    return ( ((Stream *)jlong_to_ptr(addr))->useIGZIP ? ((Stream *) jlong_to_ptr(addr))->lz2Stream.total_in : ((Stream *)jlong_to_ptr(addr))->zStream.total_in);
-}
-
-JNIEXPORT jlong JNICALL
-Java_htsjdk_samtools_util_zip_IntelDeflater_getBytesWritten(JNIEnv *env, jclass cls, jlong addr)
-{
-    return ( ((Stream *)jlong_to_ptr(addr))->useIGZIP ? ((Stream *) jlong_to_ptr(addr))->lz2Stream.total_out : ((Stream *)jlong_to_ptr(addr))->zStream.total_out);
-}
-
-JNIEXPORT void JNICALL
-Java_htsjdk_samtools_util_zip_IntelDeflater_reset(JNIEnv *env, jclass cls, jlong addr)
-{
-    if  (((Stream *)jlong_to_ptr(addr))->useIGZIP)
-	init_stream(&(((Stream *)jlong_to_ptr(addr))->lz2Stream));
-    else {
-    if (deflateReset(&(((Stream *)jlong_to_ptr(addr))->zStream)) != Z_OK) {
-	    JNU_ThrowInternalError(env, 0);
-	}
-    }
-}
-
-JNIEXPORT void JNICALL
-Java_htsjdk_samtools_util_zip_IntelDeflater_end(JNIEnv *env, jclass cls, jlong addr)
-{
-    if (!((Stream *)jlong_to_ptr(addr))->useIGZIP) {
-	if (deflateEnd(&(((Stream *)jlong_to_ptr(addr))->zStream)) == Z_STREAM_ERROR) {
-	    JNU_ThrowInternalError(env, 0);
-	} 
-    }
-    free((Stream *)jlong_to_ptr(addr));
-}
diff --git a/src/main/c/inteldeflater/README b/src/main/c/inteldeflater/README
deleted file mode 100644
index 31170d4b71..0000000000
--- a/src/main/c/inteldeflater/README
+++ /dev/null
@@ -1,7 +0,0 @@
-- IntelDeflater.c implements JNI for the IntelDeflater in htsjdk.samtools.util.zip.IntelDeflater
-- IntelDeflater uses Intel(R) Integrated  Performance Primitives (Intel(R) IPP) Samples and igzip to accelerate BAM compression.
-- Steps to build Intel Deflater using src/scripts/build_intel_deflater.sh:
-  - $OPENJDK should point to the OpenJDK directory
-  - $IPP8_INSTALL_DIR should point to the composer_xe_YEAR/ipp directory
-  - $IPP8_CODE_SAMPLES_DIR should point to ipp-samples.8.0.0.x directory
-  - $IGZIP_LIB should point to igzip_042/igzip directory, igzip should be built with ONLY_DEFLATE and GENOME_BAM defined. 
diff --git a/src/main/c/inteldeflater/igzip_lib.h b/src/main/c/inteldeflater/igzip_lib.h
deleted file mode 100644
index a27b334cc5..0000000000
--- a/src/main/c/inteldeflater/igzip_lib.h
+++ /dev/null
@@ -1,50 +0,0 @@
-/**********************************************************************
-The MIT License
-
-Copyright (c) 2014 Intel Corporation
-
-	Permission is hereby granted, free of charge, to any person
-	obtaining a copy of this software and associated documentation
-	files (the "Software"), to deal in the Software without
-	restriction, including without limitation the rights to use,
-	copy, modify, merge, publish, distribute, sublicense, and/or
-	sell copies of the Software, and to permit persons to whom the
-	Software is furnished to do so, subject to the following
-	conditions:
-
-	The above copyright notice and this permission notice shall be
-	included in all copies or substantial portions of the
-	Software.
-
-	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY
-	KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
-	WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
-	PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-	COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
-	OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-	SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-**********************************************************************/
-#include "internal_state_size.h"
-#include "types.h"
-
-typedef struct {
-    UINT8 opaque[INTERNAL_STATE_SIZE];
-} LZ_State2;
-
-typedef struct {
-    UINT8 *next_in;   // Next input byte
-    UINT32 avail_in;  // number of bytes available at next_in
-    UINT32 total_in;  // total number of bytes read so far
-
-    UINT8 *next_out;  // Next output byte
-    UINT32 avail_out; // number of bytes available at next_out
-    UINT32 total_out; // total number of bytes written so far
-    UINT32 end_of_stream; // non-zero if this is the last input buffer
-
-    LZ_State2 internal_state;
-} LZ_Stream2;
-
-
-void init_stream(LZ_Stream2 *stream);
-void fast_lz(LZ_Stream2 *stream);
diff --git a/src/main/c/inteldeflater/internal_state_size.h b/src/main/c/inteldeflater/internal_state_size.h
deleted file mode 100644
index 1823a33e00..0000000000
--- a/src/main/c/inteldeflater/internal_state_size.h
+++ /dev/null
@@ -1,32 +0,0 @@
-/**********************************************************************
-The MIT License
-
-Copyright (c) 2014 Intel Corporation
-
-	Permission is hereby granted, free of charge, to any person
-	obtaining a copy of this software and associated documentation
-	files (the "Software"), to deal in the Software without
-	restriction, including without limitation the rights to use,
-	copy, modify, merge, publish, distribute, sublicense, and/or
-	sell copies of the Software, and to permit persons to whom the
-	Software is furnished to do so, subject to the following
-	conditions:
-
-	The above copyright notice and this permission notice shall be
-	included in all copies or substantial portions of the
-	Software.
-
-	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY
-	KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
-	WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
-	PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-	COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
-	OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-	SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-**********************************************************************/
-//// for 8K
-#define INTERNAL_STATE_SIZE 82368+16
-
-// for 32K
-//#define INTERNAL_STATE_SIZE 328128+16
diff --git a/src/main/c/inteldeflater/types.h b/src/main/c/inteldeflater/types.h
deleted file mode 100644
index 83f7cc2667..0000000000
--- a/src/main/c/inteldeflater/types.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/**********************************************************************
-The MIT License
-
-Copyright (c) 2014 Intel Corporation
-
-	Permission is hereby granted, free of charge, to any person
-	obtaining a copy of this software and associated documentation
-	files (the "Software"), to deal in the Software without
-	restriction, including without limitation the rights to use,
-	copy, modify, merge, publish, distribute, sublicense, and/or
-	sell copies of the Software, and to permit persons to whom the
-	Software is furnished to do so, subject to the following
-	conditions:
-
-	The above copyright notice and this permission notice shall be
-	included in all copies or substantial portions of the
-	Software.
-
-	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY
-	KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
-	WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
-	PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-	COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
-	OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-	SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-**********************************************************************/
-
-#ifndef __TYPES_H
-#define __TYPES_H
-
-#include <stdint.h> // For standard integer types
-
-typedef struct {
-    uint64_t low;
-    uint64_t high;
-} uint128_t;
-
-typedef int64_t   INT64;
-typedef uint64_t  UINT64;
-typedef uint32_t  UINT32;
-typedef uint16_t  UINT16;
-typedef uint8_t   UINT8;
-typedef uint128_t UINT128;
-
-#endif
diff --git a/src/main/java/htsjdk/samtools/Defaults.java b/src/main/java/htsjdk/samtools/Defaults.java
index e6a2e1309e..e25d09aca4 100644
--- a/src/main/java/htsjdk/samtools/Defaults.java
+++ b/src/main/java/htsjdk/samtools/Defaults.java
@@ -57,12 +57,6 @@ public class Defaults {
     /** Should BlockCompressedOutputStream attempt to load libIntelDeflater? */
     public static final boolean TRY_USE_INTEL_DEFLATER;
 
-    /**
-     * Path to libIntelDeflater.so.  If this is not set, the library is looked for in the directory
-     * where the executable jar lives.
-     */
-    public static final String INTEL_DEFLATER_SHARED_LIBRARY_PATH;
-
     /**
      * 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).
@@ -104,8 +98,7 @@ 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", true);
-        INTEL_DEFLATER_SHARED_LIBRARY_PATH = getStringProperty("intel_deflater_so_path", null);
+        TRY_USE_INTEL_DEFLATER = getBooleanProperty("try_use_intel_deflater", false);
         if (BUFFER_SIZE == 0) {
             NON_ZERO_BUFFER_SIZE = 1024 * 128;
         } else {
@@ -132,7 +125,6 @@ public static SortedMap<String, Object> allDefaults(){
         result.put("COMPRESSION_LEVEL", COMPRESSION_LEVEL);
         result.put("BUFFER_SIZE", BUFFER_SIZE);
         result.put("TRY_USE_INTEL_DEFLATER", TRY_USE_INTEL_DEFLATER);
-        result.put("INTEL_DEFLATER_SHARED_LIBRARY_PATH", INTEL_DEFLATER_SHARED_LIBRARY_PATH);
         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);
diff --git a/src/main/java/htsjdk/samtools/example/PrintReadsExample.java b/src/main/java/htsjdk/samtools/example/PrintReadsExample.java
index b8b4106fc1..5b8f6b0067 100755
--- a/src/main/java/htsjdk/samtools/example/PrintReadsExample.java
+++ b/src/main/java/htsjdk/samtools/example/PrintReadsExample.java
@@ -96,7 +96,7 @@ private static void printConfigurationInfo() throws IOException {
                 " 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" : "JdkDeflater"));
+                ' ' + (DeflaterFactory.usingIntelDeflater() ? "IntelDeflater loaded and available for Level 1 compression" : "Using JdkDeflater"));
 
         final List<String> list = Defaults.allDefaults().entrySet().stream().map(e -> e.getKey() + ':' + e.getValue()).collect(Collectors.toList());
         log.info(String.join(" ", list));
diff --git a/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java b/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java
index 138a9754cf..3dde3e8e08 100644
--- a/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java
+++ b/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java
@@ -50,6 +50,9 @@ public class BlockCompressedOutputStream
         extends OutputStream
         implements LocationAware
 {
+
+    private static final Log log = Log.getInstance(BlockCompressedOutputStream.class);
+
     private static int defaultCompressionLevel = BlockCompressedStreamConstants.DEFAULT_COMPRESSION_LEVEL;
 
     /**
@@ -127,6 +130,7 @@ public BlockCompressedOutputStream(final File file, final int compressionLevel)
         this.file = file;
         codec = new BinaryCodec(file, true);
         deflater = DeflaterFactory.makeDeflater(compressionLevel, true);
+        log.debug("Using deflater: " + deflater.getClass().getSimpleName());
     }
 
     /**
@@ -144,6 +148,7 @@ public BlockCompressedOutputStream(final OutputStream os, final File file, final
             codec.setOutputFileName(file.getAbsolutePath());
         }
         deflater = DeflaterFactory.makeDeflater(compressionLevel, true);
+        log.debug("Using deflater: " + deflater.getClass().getSimpleName());
     }
 
     /**
diff --git a/src/main/java/htsjdk/samtools/util/zip/DeflaterFactory.java b/src/main/java/htsjdk/samtools/util/zip/DeflaterFactory.java
index 64bb8aab1b..368a9fd391 100644
--- a/src/main/java/htsjdk/samtools/util/zip/DeflaterFactory.java
+++ b/src/main/java/htsjdk/samtools/util/zip/DeflaterFactory.java
@@ -23,49 +23,66 @@
  */
 package htsjdk.samtools.util.zip;
 
+import com.intel.gkl.compression.IntelDeflater;
 import htsjdk.samtools.Defaults;
 import htsjdk.samtools.SAMException;
 
 import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
 import java.util.zip.Deflater;
 
 /**
- * Create zlib-based Deflater if JNI library and other require libraries are available, otherwise create standard
- * JDK Deflater.
- * Java 7 has its own Deflater implementation (libzip.so).  This is almost as fast as a zlib-based Deflater, so in general
- * there isn't a compelling reason to use zlib.  However, Intel has created a hardware-assisted zlib implementation
- * as part of their IPP (Integrated Performance Primitives) package that can run significantly faster on some Intel
- * hardware.  We have seen compression times reduced by 13% to 33% depending on particular hardware, and hope that
- * newer Intel processors will be even better.
+ * Create a hardware-accelerated Intel deflater if the required library is available on the classpath and
+ * {@link Defaults#TRY_USE_INTEL_DEFLATER} is true, otherwise create a standard JDK deflater.
  *
- * Note that this class will no longer be necessary once Java 8 is required, because JDK 8 will use zlib instead
- * of libzip implementation.
+ * The Intel deflater has been shown to significantly (by ~30%) outperform the standard JDK deflater
+ * at compression level 1, and to outperform the JDK deflater by smaller but still significant margins
+ * at higher compression levels.
+ *
+ * We use reflection to instantiate the IntelDeflater so that DeflaterFactory can be loaded
+ * and used at runtime even when the IntelDeflater is not on the classpath.
  */
 public class DeflaterFactory {
 
-    private static Constructor<IntelDeflater> intelDeflaterConstructor;
+    public static final String INTEL_DEFLATER_CLASS_NAME = "com.intel.gkl.compression.IntelDeflater";
+
+    private static final boolean usingIntelDeflater;
+    private static Constructor<? extends Deflater> intelDeflaterConstructor;
 
     static {
+        boolean intelDeflaterLibrarySuccessfullyLoaded = false;
+
         try {
             if (Defaults.TRY_USE_INTEL_DEFLATER) {
-                final Class<IntelDeflater> clazz = (Class<IntelDeflater>) Class.forName("htsjdk.samtools.util.zip.IntelDeflater");
+                @SuppressWarnings("unchecked")
+                final Class<IntelDeflater> clazz = (Class<IntelDeflater>)Class.forName(INTEL_DEFLATER_CLASS_NAME);
+
+                // Get the constructor we'll use to create new instances of IntelDeflater in makeDeflater()
                 intelDeflaterConstructor = clazz.getConstructor(Integer.TYPE, Boolean.TYPE);
+
+                // We also need to call load() on an IntelDeflater instance to actually load the native library
+                // (.so or .dylib) from a resource on the classpath. This should only be done once at startup.
+                final Constructor<IntelDeflater> zeroArgIntelDeflaterConstructor = clazz.getConstructor();
+                intelDeflaterLibrarySuccessfullyLoaded = zeroArgIntelDeflaterConstructor != null &&
+                                                         zeroArgIntelDeflaterConstructor.newInstance().load();
             }
-        } catch (ClassNotFoundException e) {
-            intelDeflaterConstructor = null;
-        } catch (NoSuchMethodException e) {
-            intelDeflaterConstructor = null;
-        } catch (UnsatisfiedLinkError e) {
+        }
+        catch ( ClassNotFoundException | NoSuchMethodException | UnsatisfiedLinkError |
+                IllegalAccessException | InstantiationException | InvocationTargetException e ) {
             intelDeflaterConstructor = null;
         }
+
+        usingIntelDeflater = intelDeflaterConstructor != null && intelDeflaterLibrarySuccessfullyLoaded;
     }
 
     public static Deflater makeDeflater(final int compressionLevel, final boolean nowrap) {
-        if (intelDeflaterConstructor != null) {
+        // The Intel Deflater currently only supports compression level 1
+        if ( usingIntelDeflater() && compressionLevel == 1 ) {
             try {
                 return intelDeflaterConstructor.newInstance(compressionLevel, nowrap);
-            } catch (Exception e) {
-                throw new SAMException("Exception constructing IntelDeflater", e);
+            }
+            catch ( IllegalAccessException | InstantiationException | InvocationTargetException e ) {
+                throw new SAMException("Error constructing IntelDeflater", e);
             }
         } else {
             return new Deflater(compressionLevel, nowrap);
@@ -73,6 +90,6 @@ public static Deflater makeDeflater(final int compressionLevel, final boolean no
     }
 
     public static boolean usingIntelDeflater() {
-        return intelDeflaterConstructor != null;
+        return usingIntelDeflater;
     }
 }
diff --git a/src/main/java/htsjdk/samtools/util/zip/IntelDeflater.java b/src/main/java/htsjdk/samtools/util/zip/IntelDeflater.java
deleted file mode 100644
index 30cb698ffb..0000000000
--- a/src/main/java/htsjdk/samtools/util/zip/IntelDeflater.java
+++ /dev/null
@@ -1,567 +0,0 @@
-/*
- * Copyright (c) 1996, 2010, Oracle and/or its affiliates. All rights reserved.
- * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
- *
- * This code is free software; you can redistribute it and/or modify it
- * under the terms of the GNU General Public License version 2 only, as
- * published by the Free Software Foundation.  Oracle designates this
- * particular file as subject to the "Classpath" exception as provided
- * by Oracle in the LICENSE file that accompanied this code.
- *
- * This code is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
- * version 2 for more details (a copy is included in the LICENSE file that
- * accompanied this code).
- *
- * You should have received a copy of the GNU General Public License version
- * 2 along with this work; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
- * or visit www.oracle.com if you need additional information or have any
- * questions.
- */
-package htsjdk.samtools.util.zip;
-
-import htsjdk.samtools.Defaults;
-
-import java.io.File;
-import java.net.URL;
-import java.util.zip.Deflater;
-
-/**
- * This is a copy of java.util.zip.Deflater from OpenJDK 7, with the following changes:
- * - package and class name changed
- * - static block to load libIntelDeflater library
- * - extends java.util.zip.Deflater so that IntelDeflater object can be used as regular Deflater object.
- *   Note however that all methods of Deflater are overridden.
- *
- * The shared library is found via one of the following mechanisms:
- * 1. if samjdk.intel_deflater_so_path system property is set, this is assumed to be the path of libIntelDeflater.so
- * 2. If system property is not set, directory where the jarfile that this class came from lives is tried as location
- *    of libIntelDeflater.so
- * 3. If either of the above fails to find the library, regular LD_LIBRARY_PATH is used to find the library.
- * 4. If that doesn't work, class fails to load and code falls back to regular Java Deflater class.
- *
- *
- * The rest of this document is copied verbatim from the original OpenJDK file.
- *
- * This class provides support for general purpose compression using the
- * popular ZLIB compression library. The ZLIB compression library was
- * initially developed as part of the PNG graphics standard and is not
- * protected by patents. It is fully described in the specifications at
- * the <a href="package-summary.html#package_description">java.util.zip
- * package description</a>.
- *
- * <p>The following code fragment demonstrates a trivial compression
- * and decompression of a string using <tt>IntelDeflater</tt> and
- * <tt>Inflater</tt>.
- *
- * <blockquote><pre>
- * try {
- *     // Encode a String into bytes
- *     String inputString = "blahblahblah";
- *     byte[] input = inputString.getBytes("UTF-8");
- *
- *     // Compress the bytes
- *     byte[] output = new byte[100];
- *     IntelDeflater compresser = new IntelDeflater();
- *     compresser.setInput(input);
- *     compresser.finish();
- *     int compressedDataLength = compresser.deflate(output);
- *     compresser.end();
- *
- *     // Decompress the bytes
- *     Inflater decompresser = new Inflater();
- *     decompresser.setInput(output, 0, compressedDataLength);
- *     byte[] result = new byte[100];
- *     int resultLength = decompresser.inflate(result);
- *     decompresser.end();
- *
- *     // Decode the bytes into a String
- *     String outputString = new String(result, 0, resultLength, "UTF-8");
- * } catch(java.io.UnsupportedEncodingException ex) {
- *     // handle
- * } catch (java.util.zip.DataFormatException ex) {
- *     // handle
- * }
- * </pre></blockquote>
- *
- * @see         java.util.zip.Inflater
- * @author      David Connelly
- */
-public
-class IntelDeflater extends Deflater {
-
-    private final ZStreamRef zsRef;
-    private byte[] buf = new byte[0];
-    private int off, len;
-    private int level, strategy;
-    private boolean setParams;
-    private boolean finish, finished;
-
-    /**
-     * Compression flush mode used to achieve best compression result.
-     *
-     * @see IntelDeflater#deflate(byte[], int, int, int)
-     * @since 1.7
-     */
-    public static final int NO_FLUSH = 0;
-
-    /**
-     * Compression flush mode used to flush out all pending output; may
-     * degrade compression for some compression algorithms.
-     *
-     * @see IntelDeflater#deflate(byte[], int, int, int)
-     * @since 1.7
-     */
-    public static final int SYNC_FLUSH = 2;
-
-    /**
-     * Compression flush mode used to flush out all pending output and
-     * reset the deflater. Using this mode too often can seriously degrade
-     * compression.
-     *
-     * @see IntelDeflater#deflate(byte[], int, int, int)
-     * @since 1.7
-     */
-    public static final int FULL_FLUSH = 3;
-
-    static {
-        try {
-            final File sharedLibrary;
-            if (Defaults.INTEL_DEFLATER_SHARED_LIBRARY_PATH != null) {
-                // Load via path set by -Dsamjdk.intel_deflater_so_path=<path>
-                sharedLibrary = new File(Defaults.INTEL_DEFLATER_SHARED_LIBRARY_PATH);
-            } else {
-                // Look in directory containing this class for the library
-                URL jarUrl = IntelDeflater.class.getProtectionDomain().getCodeSource().getLocation();
-                sharedLibrary = new File(new File(jarUrl.getPath()).getParentFile(), "libIntelDeflater.so");
-            }
-            System.load(sharedLibrary.getAbsolutePath());
-        } catch (Throwable e) {
-            // Possible exceptions:
-            // System.load: UnsatisfiedLinkError
-            // getProtectionDomain: SecurityException
-            // NullPointerException due to getCodeSource returning null
-
-            // Try to find via LD_LIBRARY_PATH
-            System.loadLibrary("IntelDeflater");
-        }
-        initIDs();
-    }
-
-    /**
-     * Creates a new compressor using the specified compression level.
-     * If 'nowrap' is true then the ZLIB header and checksum fields will
-     * not be used in order to support the compression format used in
-     * both GZIP and PKZIP.
-     * @param level the compression level (0-9)
-     * @param nowrap if true then use GZIP compatible compression
-     */
-    public IntelDeflater(int level, boolean nowrap) {
-        this.level = level;
-        this.strategy = DEFAULT_STRATEGY;
-        this.zsRef = new ZStreamRef(init(level, DEFAULT_STRATEGY, nowrap));
-    }
-
-    /**
-     * Creates a new compressor using the specified compression level.
-     * Compressed data will be generated in ZLIB format.
-     * @param level the compression level (0-9)
-     */
-    public IntelDeflater(int level) {
-        this(level, false);
-    }
-
-    /**
-     * Creates a new compressor with the default compression level.
-     * Compressed data will be generated in ZLIB format.
-     */
-    public IntelDeflater() {
-        this(DEFAULT_COMPRESSION, false);
-    }
-
-    /**
-     * Sets input data for compression. This should be called whenever
-     * needsInput() returns true indicating that more input data is required.
-     * @param b the input data bytes
-     * @param off the start offset of the data
-     * @param len the length of the data
-     * @see IntelDeflater#needsInput
-     */
-    @Override
-    public void setInput(byte[] b, int off, int len) {
-        if (b== null) {
-            throw new NullPointerException();
-        }
-        if (off < 0 || len < 0 || off > b.length - len) {
-            throw new ArrayIndexOutOfBoundsException();
-        }
-        synchronized (zsRef) {
-            this.buf = b;
-            this.off = off;
-            this.len = len;
-        }
-    }
-
-    /**
-     * Sets input data for compression. This should be called whenever
-     * needsInput() returns true indicating that more input data is required.
-     * @param b the input data bytes
-     * @see IntelDeflater#needsInput
-     */
-    @Override
-    public void setInput(byte[] b) {
-        setInput(b, 0, b.length);
-    }
-
-    /**
-     * Sets preset dictionary for compression. A preset dictionary is used
-     * when the history buffer can be predetermined. When the data is later
-     * uncompressed with Inflater.inflate(), Inflater.getAdler() can be called
-     * in order to get the Adler-32 value of the dictionary required for
-     * decompression.
-     * @param b the dictionary data bytes
-     * @param off the start offset of the data
-     * @param len the length of the data
-     * @see java.util.zip.Inflater#inflate
-     * @see java.util.zip.Inflater#getAdler
-     */
-    @Override
-    public void setDictionary(byte[] b, int off, int len) {
-        if (b == null) {
-            throw new NullPointerException();
-        }
-        if (off < 0 || len < 0 || off > b.length - len) {
-            throw new ArrayIndexOutOfBoundsException();
-        }
-        synchronized (zsRef) {
-            ensureOpen();
-            setDictionary(zsRef.address(), b, off, len);
-        }
-    }
-
-    /**
-     * Sets preset dictionary for compression. A preset dictionary is used
-     * when the history buffer can be predetermined. When the data is later
-     * uncompressed with Inflater.inflate(), Inflater.getAdler() can be called
-     * in order to get the Adler-32 value of the dictionary required for
-     * decompression.
-     * @param b the dictionary data bytes
-     * @see java.util.zip.Inflater#inflate
-     * @see java.util.zip.Inflater#getAdler
-     */
-    @Override
-    public void setDictionary(byte[] b) {
-        setDictionary(b, 0, b.length);
-    }
-
-    /**
-     * Sets the compression strategy to the specified value.
-     * @param strategy the new compression strategy
-     * @exception IllegalArgumentException if the compression strategy is
-     *                                     invalid
-     */
-    @Override
-    public void setStrategy(int strategy) {
-        switch (strategy) {
-            case DEFAULT_STRATEGY:
-            case FILTERED:
-            case HUFFMAN_ONLY:
-                break;
-            default:
-                throw new IllegalArgumentException();
-        }
-        synchronized (zsRef) {
-            if (this.strategy != strategy) {
-                this.strategy = strategy;
-                setParams = true;
-            }
-        }
-    }
-
-    /**
-     * Sets the current compression level to the specified value.
-     * @param level the new compression level (0-9)
-     * @exception IllegalArgumentException if the compression level is invalid
-     */
-    @Override
-    public void setLevel(int level) {
-        if ((level < 0 || level > 9) && level != DEFAULT_COMPRESSION) {
-            throw new IllegalArgumentException("invalid compression level");
-        }
-        synchronized (zsRef) {
-            if (this.level != level) {
-                this.level = level;
-                setParams = true;
-            }
-        }
-    }
-
-    /**
-     * Returns true if the input data buffer is empty and setInput()
-     * should be called in order to provide more input.
-     * @return true if the input data buffer is empty and setInput()
-     * should be called in order to provide more input
-     */
-    @Override
-    public boolean needsInput() {
-        return len <= 0;
-    }
-
-    /**
-     * When called, indicates that compression should end with the current
-     * contents of the input buffer.
-     */
-    @Override
-    public void finish() {
-        synchronized (zsRef) {
-            finish = true;
-        }
-    }
-
-    /**
-     * Returns true if the end of the compressed data output stream has
-     * been reached.
-     * @return true if the end of the compressed data output stream has
-     * been reached
-     */
-    @Override
-    public boolean finished() {
-        synchronized (zsRef) {
-            return finished;
-        }
-    }
-
-    /**
-     * Compresses the input data and fills specified buffer with compressed
-     * data. Returns actual number of bytes of compressed data. A return value
-     * of 0 indicates that {@link #needsInput() needsInput} should be called
-     * in order to determine if more input data is required.
-     *
-     * <p>This method uses {@link #NO_FLUSH} as its compression flush mode.
-     * An invocation of this method of the form {@code deflater.deflate(b, off, len)}
-     * yields the same result as the invocation of
-     * {@code deflater.deflate(b, off, len, IntelDeflater.NO_FLUSH)}.
-     *
-     * @param b the buffer for the compressed data
-     * @param off the start offset of the data
-     * @param len the maximum number of bytes of compressed data
-     * @return the actual number of bytes of compressed data written to the
-     *         output buffer
-     */
-    @Override
-    public int deflate(byte[] b, int off, int len) {
-        return deflate(b, off, len, NO_FLUSH);
-    }
-
-    /**
-     * Compresses the input data and fills specified buffer with compressed
-     * data. Returns actual number of bytes of compressed data. A return value
-     * of 0 indicates that {@link #needsInput() needsInput} should be called
-     * in order to determine if more input data is required.
-     *
-     * <p>This method uses {@link #NO_FLUSH} as its compression flush mode.
-     * An invocation of this method of the form {@code deflater.deflate(b)}
-     * yields the same result as the invocation of
-     * {@code deflater.deflate(b, 0, b.length, IntelDeflater.NO_FLUSH)}.
-     *
-     * @param b the buffer for the compressed data
-     * @return the actual number of bytes of compressed data written to the
-     *         output buffer
-     */
-    @Override
-    public int deflate(byte[] b) {
-        return deflate(b, 0, b.length, NO_FLUSH);
-    }
-
-    /**
-     * Compresses the input data and fills the specified buffer with compressed
-     * data. Returns actual number of bytes of data compressed.
-     *
-     * <p>Compression flush mode is one of the following three modes:
-     *
-     * <ul>
-     * <li>{@link #NO_FLUSH}: allows the deflater to decide how much data
-     * to accumulate, before producing output, in order to achieve the best
-     * compression (should be used in normal use scenario). A return value
-     * of 0 in this flush mode indicates that {@link #needsInput()} should
-     * be called in order to determine if more input data is required.
-     *
-     * <li>{@link #SYNC_FLUSH}: all pending output in the deflater is flushed,
-     * to the specified output buffer, so that an inflater that works on
-     * compressed data can get all input data available so far (In particular
-     * the {@link #needsInput()} returns {@code true} after this invocation
-     * if enough output space is provided). Flushing with {@link #SYNC_FLUSH}
-     * may degrade compression for some compression algorithms and so it
-     * should be used only when necessary.
-     *
-     * <li>{@link #FULL_FLUSH}: all pending output is flushed out as with
-     * {@link #SYNC_FLUSH}. The compression state is reset so that the inflater
-     * that works on the compressed output data can restart from this point
-     * if previous compressed data has been damaged or if random access is
-     * desired. Using {@link #FULL_FLUSH} too often can seriously degrade
-     * compression.
-     * </ul>
-     *
-     * <p>In the case of {@link #FULL_FLUSH} or {@link #SYNC_FLUSH}, if
-     * the return value is {@code len}, the space available in output
-     * buffer {@code b}, this method should be invoked again with the same
-     * {@code flush} parameter and more output space.
-     *
-     * @param b the buffer for the compressed data
-     * @param off the start offset of the data
-     * @param len the maximum number of bytes of compressed data
-     * @param flush the compression flush mode
-     * @return the actual number of bytes of compressed data written to
-     *         the output buffer
-     *
-     * @throws IllegalArgumentException if the flush mode is invalid
-     * @since 1.7
-     */
-    public int deflate(byte[] b, int off, int len, int flush) {
-        //System.out.println("Inside IntelDeflater\n");
-        if (b == null) {
-            throw new NullPointerException();
-        }
-        if (off < 0 || len < 0 || off > b.length - len) {
-            throw new ArrayIndexOutOfBoundsException();
-        }
-        synchronized (zsRef) {
-            ensureOpen();
-            if (flush == NO_FLUSH || flush == SYNC_FLUSH ||
-                    flush == FULL_FLUSH)
-                return deflateBytes(zsRef.address(), b, off, len, flush);
-            throw new IllegalArgumentException();
-        }
-    }
-
-    /**
-     * Returns the ADLER-32 value of the uncompressed data.
-     * @return the ADLER-32 value of the uncompressed data
-     */
-    @Override
-    public int getAdler() {
-        synchronized (zsRef) {
-            ensureOpen();
-            return getAdler(zsRef.address());
-        }
-    }
-
-    /**
-     * Returns the total number of uncompressed bytes input so far.
-     *
-     * <p>Since the number of bytes may be greater than
-     * Integer.MAX_VALUE, the {@link #getBytesRead()} method is now
-     * the preferred means of obtaining this information.</p>
-     *
-     * @return the total number of uncompressed bytes input so far
-     */
-    @Override
-    public int getTotalIn() {
-        return (int) getBytesRead();
-    }
-
-    /**
-     * Returns the total number of uncompressed bytes input so far.</p>
-     *
-     * @return the total (non-negative) number of uncompressed bytes input so far
-     * @since 1.5
-     */
-    @Override
-    public long getBytesRead() {
-        synchronized (zsRef) {
-            ensureOpen();
-            return getBytesRead(zsRef.address());
-        }
-    }
-
-    /**
-     * Returns the total number of compressed bytes output so far.
-     *
-     * <p>Since the number of bytes may be greater than
-     * Integer.MAX_VALUE, the {@link #getBytesWritten()} method is now
-     * the preferred means of obtaining this information.</p>
-     *
-     * @return the total number of compressed bytes output so far
-     */
-    @Override
-    public int getTotalOut() {
-        return (int) getBytesWritten();
-    }
-
-    /**
-     * Returns the total number of compressed bytes output so far.</p>
-     *
-     * @return the total (non-negative) number of compressed bytes output so far
-     * @since 1.5
-     */
-    @Override
-    public long getBytesWritten() {
-        synchronized (zsRef) {
-            ensureOpen();
-            return getBytesWritten(zsRef.address());
-        }
-    }
-
-    /**
-     * Resets deflater so that a new set of input data can be processed.
-     * Keeps current compression level and strategy settings.
-     */
-    @Override
-    public void reset() {
-        synchronized (zsRef) {
-            ensureOpen();
-            reset(zsRef.address());
-            finish = false;
-            finished = false;
-            off = len = 0;
-        }
-    }
-
-    /**
-     * Closes the compressor and discards any unprocessed input.
-     * This method should be called when the compressor is no longer
-     * being used, but will also be called automatically by the
-     * finalize() method. Once this method is called, the behavior
-     * of the IntelDeflater object is undefined.
-     */
-    @Override
-    public void end() {
-        synchronized (zsRef) {
-            long addr = zsRef.address();
-            zsRef.clear();
-            if (addr != 0) {
-                end(addr);
-                buf = null;
-            }
-        }
-    }
-
-    /**
-     * Closes the compressor when garbage is collected.
-     */
-    protected void finalize() {
-        end();
-    }
-
-    private void ensureOpen() {
-        assert Thread.holdsLock(zsRef);
-        if (zsRef.address() == 0)
-            throw new NullPointerException("IntelDeflater has been closed");
-    }
-
-    private static native void initIDs();
-    private native static long init(int level, int strategy, boolean nowrap);
-    private native static void setDictionary(long addr, byte[] b, int off, int len);
-    private native int deflateBytes(long addr, byte[] b, int off, int len,
-                                    int flush);
-    private native static int getAdler(long addr);
-    private native static long getBytesRead(long addr);
-    private native static long getBytesWritten(long addr);
-    private native static void reset(long addr);
-    private native static void end(long addr);
-}
-
diff --git a/src/main/java/htsjdk/samtools/util/zip/ZStreamRef.java b/src/main/java/htsjdk/samtools/util/zip/ZStreamRef.java
deleted file mode 100644
index 8fa5f78e55..0000000000
--- a/src/main/java/htsjdk/samtools/util/zip/ZStreamRef.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Copyright (c) 2009, Oracle and/or its affiliates. All rights reserved.
- * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
- *
- * This code is free software; you can redistribute it and/or modify it
- * under the terms of the GNU General Public License version 2 only, as
- * published by the Free Software Foundation.  Oracle designates this
- * particular file as subject to the "Classpath" exception as provided
- * by Oracle in the LICENSE file that accompanied this code.
- *
- * This code is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
- * version 2 for more details (a copy is included in the LICENSE file that
- * accompanied this code).
- *
- * You should have received a copy of the GNU General Public License version
- * 2 along with this work; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
- * or visit www.oracle.com if you need additional information or have any
- * questions.
- */
-package htsjdk.samtools.util.zip;
-
-/**
- * Copied from OpenJDK 7.  Only change is package name, because IntelDeflater needs this and
- * the original class is private to java.util.zip package.
- *
- * A reference to the native zlib's z_stream structure.
- */
-
-class ZStreamRef {
-
-    private long address;
-    ZStreamRef (long address) {
-        this.address = address;
-    }
-
-    long address() {
-        return address;
-    }
-
-    void clear() {
-        address = 0;
-    }
-}
diff --git a/src/main/java/htsjdk/variant/example/PrintVariantsExample.java b/src/main/java/htsjdk/variant/example/PrintVariantsExample.java
index 997f0ee6b7..7810ad731c 100755
--- a/src/main/java/htsjdk/variant/example/PrintVariantsExample.java
+++ b/src/main/java/htsjdk/variant/example/PrintVariantsExample.java
@@ -98,7 +98,7 @@ private static void printConfigurationInfo() throws IOException {
                 " 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" : "JdkDeflater"));
+                ' ' + (DeflaterFactory.usingIntelDeflater() ? "IntelDeflater loaded and available for Level 1 compression" : "Using JdkDeflater"));
 
         log.info(Defaults.allDefaults().entrySet().stream().map(e -> e.getKey() + ':' + e.getValue()).collect(Collectors.<String>joining(" ")));
     }
diff --git a/src/test/java/htsjdk/samtools/util/IntelDeflaterTest.java b/src/test/java/htsjdk/samtools/util/IntelDeflaterTest.java
index 00fb0ba4b0..747597e186 100755
--- a/src/test/java/htsjdk/samtools/util/IntelDeflaterTest.java
+++ b/src/test/java/htsjdk/samtools/util/IntelDeflaterTest.java
@@ -72,7 +72,7 @@ Iterator<Object[]> TestIntelDeflaterIsLoadedData(){
         return retVal.iterator();
     }
 
-    @Test(dataProvider = "TestIntelDeflaterIsLoadedData", groups={"unix", "intel"},expectedExceptions = IllegalAccessError.class)
+    @Test(dataProvider = "TestIntelDeflaterIsLoadedData", groups={"intel"}, expectedExceptions = IllegalAccessError.class)
     public void TestIntelDeflatorIsLoaded(final File inputFile, final Boolean eagerlyDecode,final Integer compressionLevel) throws IOException,IllegalAccessError {
         Log log = Log.getInstance(IntelDeflaterTest.class);
         Log.setGlobalLogLevel(Log.LogLevel.INFO);