1. Added support for building the PairHMM vector library into build.xml.

The library is compiled using  makefile and copied into the directory:
build/java/classes/org/broadinstitute/sting/utils/pairhmm/
2. Bundled the library into StingUtils.jar. Unpacked and loaded at
runtime without the need to set java.library.path

Caveats:
Platform independence has probably been thrown out of the window.
Assumptions:
a. make command exists at /usr/bin/make
b. rsync command exists at /usr/bin/rsync
c. icc is in the PATH of the user

build.xml

@@ -64,6 +64,7 @@
     <property name="R.private.scripts.dir" value="${private.dir}/R/scripts" />
     <property name="R.protected.scripts.dir" value="${protected.dir}/R/scripts" />
     <property name="R.public.src.dir" value="${public.dir}/R/src" />
+    <property name="vector.pairhmm.library.source.dir" value="${public.dir}/c++/VectorPairHMM" />
 
     <!-- Build directories -->
     <property name="java.classes" value="${build.dir}/java/classes" />
@@ -648,9 +649,23 @@
         </copy>
     </target>
 
-    <target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage">
+    <target name="build.vector.pairhmm.library">
+         <exec dir="${vector.pairhmm.library.source.dir}" executable="/usr/bin/make">
+         </exec>
+    </target>
+
+    <target name="copy.vector.pairhmm.library" depends="build.vector.pairhmm.library">
+      <exec executable="/usr/bin/rsync">
+          <arg value="-a"/>
+          <arg value="${vector.pairhmm.library.source.dir}/libVectorLoglessPairHMM.so"/>
+          <arg value="${java.classes}/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so"/> 
+        </exec>
+    </target>
+
+    <target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage, copy.vector.pairhmm.library">
         <jar jarfile="${dist.dir}/StingUtils.jar">
             <fileset dir="${java.classes}" includes="**/sting/utils/**/*.class"/>
+            <fileset dir="${java.classes}" includes="**/sting/utils/**/*.so"/>
             <fileset dir="${java.classes}" includes="**/sting/commandline/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/>

protected/java/src/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java

@@ -59,6 +59,15 @@ import java.util.List;
 import java.util.Map;
 import java.util.HashMap;
 
+//For loading library from jar
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+
 
 /**
  * Created with IntelliJ IDEA.
@@ -111,7 +120,28 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
         synchronized(isVectorLoglessPairHMMLibraryLoaded) {
             //Load the library and initialize the FieldIDs
             if(!isVectorLoglessPairHMMLibraryLoaded) {
+                try
+                {
+                    //Try loading from Java's library path first
+                    //Useful if someone builds his/her own library and wants to override the bundled
+                    //implementation without modifying the Java code
                     System.loadLibrary("VectorLoglessPairHMM");
+                }
+                catch(UnsatisfiedLinkError ule)
+                {
+                    //Could not load from Java's library path - try unpacking from jar
+                    try
+                    {
+                        logger.info("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from StingUtils.jar");
+                        loadLibraryFromJar("/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so");
+                    }
+                    catch(IOException ioe)
+                    {
+                        //Throw the UnsatisfiedLinkError to make it clear to the user what failed
+                        throw ule;
+                    }
+                }
+
                 isVectorLoglessPairHMMLibraryLoaded = true;
                 jniInitializeClassFieldsAndMachineMask(JNIReadDataHolderClass.class, JNIHaplotypeDataHolderClass.class, enableAll);        //need to do this only once
             }
@@ -229,4 +259,75 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
         super.close();
         jniClose();
     }
+   
+    //Copied from http://frommyplayground.com/how-to-load-native-jni-library-from-jar 
+    /**
+     * Loads library from current JAR archive
+     * 
+     * The file from JAR is copied into system temporary directory and then loaded. The temporary file is deleted after exiting.
+     * Method uses String as filename because the pathname is "abstract", not system-dependent.
+     * 
+     * @param filename The filename inside JAR as absolute path (beginning with '/'), e.g. /package/File.ext
+     * @throws IOException If temporary file creation or read/write operation fails
+     * @throws IllegalArgumentException If source file (param path) does not exist
+     * @throws IllegalArgumentException If the path is not absolute or if the filename is shorter than three characters (restriction of {@see File#createTempFile(java.lang.String, java.lang.String)}).
+     */
+    public static void loadLibraryFromJar(String path) throws IOException {
+
+        if (!path.startsWith("/")) {
+            throw new IllegalArgumentException("The path to be absolute (start with '/').");
+        }
+
+        // Obtain filename from path
+        String[] parts = path.split("/");
+        String filename = (parts.length > 1) ? parts[parts.length - 1] : null;
+
+        // Split filename to prexif and suffix (extension)
+        String prefix = "";
+        String suffix = null;
+        if (filename != null) {
+            parts = filename.split("\\.", 2);
+            prefix = parts[0];
+            suffix = (parts.length > 1) ? "."+parts[parts.length - 1] : null; // Thanks, davs! :-)
+        }
+
+        // Check if the filename is okay
+        if (filename == null || prefix.length() < 3) {
+            throw new IllegalArgumentException("The filename has to be at least 3 characters long.");
+        }
+
+        // Prepare temporary file
+        File temp = File.createTempFile(prefix, suffix);
+        //System.out.println("Temp lib file "+temp.getAbsolutePath());
+        temp.deleteOnExit();
+
+        if (!temp.exists()) {
+            throw new FileNotFoundException("File " + temp.getAbsolutePath() + " does not exist.");
+        }
+
+        // Prepare buffer for data copying
+        byte[] buffer = new byte[1024];
+        int readBytes;
+
+        // Open and check input stream
+        InputStream is = VectorLoglessPairHMM.class.getResourceAsStream(path);
+        if (is == null) {
+            throw new FileNotFoundException("File " + path + " was not found inside JAR.");
+        }
+
+        // Open output stream and copy data between source file in JAR and the temporary file
+        OutputStream os = new FileOutputStream(temp);
+        try {
+            while ((readBytes = is.read(buffer)) != -1) {
+                os.write(buffer, 0, readBytes);
+            }
+        } finally {
+            // If read/write fails, close streams safely before throwing an exception
+            os.close();
+            is.close();
+        }
+
+        // Finally, load the library
+        System.load(temp.getAbsolutePath());
+    }
 }