At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.

public/c/bwa/build_linux.sh

@@ -1,5 +1,5 @@
 #!/bin/sh
-export BWA_HOME="/humgen/gsa-scr1/hanna/src/bwa-trunk/bwa"
+export BWA_HOME="/humgen/gsa-scr1/hanna/src/bio-bwa/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"

public/c/bwa/bwa_gateway.cpp

@@ -233,6 +233,8 @@ void BWA::set_disallow_indel_within_range(int indel_range) { options.indel_end_s
 void BWA::set_mismatch_penalty(int penalty) { options.s_mm = penalty; }
 void BWA::set_gap_open_penalty(int penalty) { options.s_gapo = penalty; }
 void BWA::set_gap_extension_penalty(int penalty) { options.s_gape = penalty; }
+void BWA::set_mode_nonstop() { options.mode |= BWA_MODE_NONSTOP; options.max_top2 = 0x7fffffff; }
+void BWA::set_max_entries_in_queue(int max_entries) { options.max_entries = max_entries; }
 
 /**
  * Create a sequence with a set of reasonable initial defaults.  

public/c/bwa/bwa_gateway.h

@@ -60,6 +60,8 @@ class BWA {
   void set_mismatch_penalty(int penalty);
   void set_gap_open_penalty(int penalty);
   void set_gap_extension_penalty(int penalty);
+  void set_mode_nonstop();
+  void set_max_entries_in_queue(int max_entries);
 
   // Perform the alignment
   Alignment* generate_single_alignment(const char* bases, 

public/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp

@@ -8,11 +8,13 @@
 #include "bwa_gateway.h"
 #include "org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h"
 
+typedef void (BWA::*boolean_setter)();
 typedef void (BWA::*int_setter)(int value);
 typedef void (BWA::*float_setter)(float value);
 
 static jobject convert_to_java_alignment(JNIEnv* env, const jbyte* read_bases, const jsize read_length, const Alignment& alignment);
 static jstring get_configuration_file(JNIEnv* env, jobject configuration, const char* field_name);
+static void set_boolean_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, boolean_setter setter);
 static void set_int_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, int_setter setter);
 static void set_float_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, float_setter setter);
 static void throw_config_value_exception(JNIEnv* env, const char* field_name, const char* message);
@@ -100,6 +102,10 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner
   if(env->ExceptionCheck()) return; 
   set_int_configuration_param(env, configuration, "gapExtensionPenalty", bwa, &BWA::set_gap_extension_penalty);
   if(env->ExceptionCheck()) return;
+  set_boolean_configuration_param(env, configuration, "nonStopMode", bwa, &BWA::set_mode_nonstop);
+  if(env->ExceptionCheck()) return;
+  set_int_configuration_param(env, configuration, "maxEntriesInQueue", bwa, &BWA::set_max_entries_in_queue);
+  if(env->ExceptionCheck()) return;
 }
 
 JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getPaths(JNIEnv *env, jobject instance, jlong java_bwa, jbyteArray java_bases) 
@@ -357,6 +363,36 @@ static jstring get_configuration_file(JNIEnv* env, jobject configuration, const
   return path;
 }
 
+static void set_boolean_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, boolean_setter setter) {
+  jclass configuration_class = env->GetObjectClass(configuration);
+  if(configuration_class == NULL) return;
+
+  jfieldID configuration_field = env->GetFieldID(configuration_class, field_name, "Ljava/lang/Boolean;");
+  if(configuration_field == NULL) return;
+
+  jobject boxed_value = env->GetObjectField(configuration,configuration_field);
+  if(env->ExceptionCheck()) return;
+
+  if(boxed_value != NULL) {
+    jclass boolean_box_class = env->FindClass("java/lang/Boolean");
+    if(boolean_box_class == NULL) return;
+
+    jmethodID boolean_extractor = env->GetMethodID(boolean_box_class,"booleanValue", "()Z");
+    if(boolean_extractor == NULL) return;
+
+    jboolean value = env->CallBooleanMethod(boxed_value,boolean_extractor);
+    if(env->ExceptionCheck()) return;
+
+    if(value)
+      (bwa->*setter)();
+
+    env->DeleteLocalRef(boolean_box_class);
+  }
+
+  env->DeleteLocalRef(boxed_value);
+  env->DeleteLocalRef(configuration_class);
+}
+
 static void set_int_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, int_setter setter) {
   jclass configuration_class = env->GetObjectClass(configuration);
   if(configuration_class == NULL) return;

public/java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java

@@ -41,4 +41,14 @@ public class BWAConfiguration {
      * What is the scoring penalty for a gap extension?
      */
     public Integer gapExtensionPenalty = null;
+
+    /**
+     * Enter bwa's 'non-stop' mode (equivalent to bwa aln -N parameter).
+     */
+    public Boolean nonStopMode = false;
+
+    /**
+     * Set the max queue size that bwa will use when searching for matches (equivalent to bwa aln -m parameter).
+     */
+    public Integer maxEntriesInQueue = null;
 }