diff --git a/public/c/bwa/build_linux.sh b/public/c/bwa/build_linux.sh
index c713f3963..b3631a28d 100755
--- a/public/c/bwa/build_linux.sh
+++ b/public/c/bwa/build_linux.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
-export BWA_HOME="/humgen/gsa-scr1/hanna/src/bwa"
+export BWA_HOME="/humgen/gsa-scr1/hanna/src/bwa-trunk/bwa"
 export JAVA_INCLUDE="/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/include -I/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/include/linux"
 export TARGET_LIB="libbwa.so"
 export EXTRA_LIBS="-lc -lz -lstdc++ -lpthread"
diff --git a/public/c/bwa/bwa_gateway.cpp b/public/c/bwa/bwa_gateway.cpp
index 3f6850e37..00f5aa5bc 100644
--- a/public/c/bwa/bwa_gateway.cpp
+++ b/public/c/bwa/bwa_gateway.cpp
@@ -1,5 +1,6 @@
 #include <cstdio>
 #include <cstring>
+#include <cstdlib>
 
 #include "bwase.h"
 #include "bwa_gateway.h"
@@ -27,6 +28,9 @@ BWA::BWA(const char* ann_filename,
   bwt_restore_sa(reverse_sa_filename, bwts[1]);
   load_default_options();
 
+  // Always reinitialize the random seed whenever a new set of files are loaded.
+  initialize_random_seed();
+
   // initialize the bwase subsystem
   bwase_initialize();
 }
@@ -207,6 +211,11 @@ void BWA::load_default_options()
   options.trim_qual = 0;
 }
 
+void BWA::initialize_random_seed()
+{
+  srand48(bns->seed);  
+}
+
 void BWA::set_max_edit_distance(float edit_distance) { 
   if(edit_distance > 0 && edit_distance < 1) {
     options.fnr = edit_distance;
diff --git a/public/c/bwa/bwa_gateway.h b/public/c/bwa/bwa_gateway.h
index 0ef0a129b..2d26ec650 100644
--- a/public/c/bwa/bwa_gateway.h
+++ b/public/c/bwa/bwa_gateway.h
@@ -37,6 +37,7 @@ class BWA {
   gap_opt_t options;
 
   void load_default_options();
+  void initialize_random_seed();
   bwa_seq_t* create_sequence(const char* bases, const unsigned read_length);
   void copy_bases_into_sequence(bwa_seq_t* sequence, const char* bases, const unsigned read_length);
   Alignment generate_final_alignment_from_sequence(bwa_seq_t* sequence);
diff --git a/public/c/bwa/libbwa.so.1 b/public/c/bwa/libbwa.so.1
deleted file mode 100755
index bfa3c2847..000000000
Binary files a/public/c/bwa/libbwa.so.1 and /dev/null differ
diff --git a/public/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java
index dafaf3ffe..a6af034cb 100644
--- a/public/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java
@@ -14,7 +14,7 @@ import java.util.Arrays;
 public class AlignerIntegrationTest extends WalkerTest {
     @Test
     public void testBasicAlignment() {
-        String md5 = "34eb4323742999d6d250a0aaa803c6d5";
+        String md5 = "a2bdf907b18114a86ca47f9fc23791bf";
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + GATKDataLocation + "bwa/human_b36_both.fasta" +
                         " -T Align" +