From f5818c0cda2e218eaf1c1bd815dc719e00194014 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 13 Nov 2009 22:18:56 +0000
Subject: [PATCH] Fix max edit distance to ensure interface similarity between
 our aligner and 'bwa aln'.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2043 348d0f76-0448-11de-a6fe-93d51630548a
---
 c/bwa/bwa_gateway.cpp                          | 14 ++++++++++++--
 c/bwa/bwa_gateway.h                            |  2 +-
 ...stitute_sting_alignment_bwa_BWACAligner.cpp | 18 ++++++++++++++++--
 3 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/c/bwa/bwa_gateway.cpp b/c/bwa/bwa_gateway.cpp
index ec2ae2da0..45e28b6d7 100644
--- a/c/bwa/bwa_gateway.cpp
+++ b/c/bwa/bwa_gateway.cpp
@@ -76,10 +76,20 @@ void BWA::load_default_options()
   options.trim_qual = 0;
 }
 
-void BWA::set_max_edit_distance(int edit_distance) { options.max_diff = edit_distance; }
+void BWA::set_max_edit_distance(float edit_distance) { 
+  if(edit_distance < 1) {
+    options.fnr = edit_distance;
+    options.max_diff = -1;
+  }
+  else {
+    options.fnr = -1.0;
+    options.max_diff = (int)edit_distance;
+  }
+}
+
 void BWA::set_max_gap_opens(int max_gap_opens) { options.max_gapo = max_gap_opens; }
 void BWA::set_max_gap_extensions(int max_gap_extensions) { options.max_gape = max_gap_extensions; }
-void BWA::set_disallow_indel_within_range(int indel_range) { options.indel_end_skip = indel_range; printf("set indel end skip to %d\n", options.indel_end_skip);}
+void BWA::set_disallow_indel_within_range(int indel_range) { options.indel_end_skip = indel_range; }
 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; }
diff --git a/c/bwa/bwa_gateway.h b/c/bwa/bwa_gateway.h
index 7a933ad82..f559cd9e2 100644
--- a/c/bwa/bwa_gateway.h
+++ b/c/bwa/bwa_gateway.h
@@ -32,7 +32,7 @@ class BWA {
   ~BWA();
 
   // Parameterize the aligner.
-  void set_max_edit_distance(int edit_distance);
+  void set_max_edit_distance(float edit_distance);
   void set_max_gap_opens(int max_gap_opens);
   void set_max_gap_extensions(int max_gap_extensions);
   void set_disallow_indel_within_range(int indel_range);
diff --git a/c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp b/c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp
index b24919950..ddb614062 100644
--- a/c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp
+++ b/c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp
@@ -13,9 +13,12 @@ static jclass java_alignment_class = NULL;
 static jmethodID java_alignment_constructor = NULL;
 
 typedef void (BWA::*int_setter)(int value);
+typedef void (BWA::*float_setter)(float value);
 
 static jstring get_configuration_string(JNIEnv* env, jobject configuration, const char* field_name);
+
 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);
 
 JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_create(JNIEnv* env, jobject instance, jobject configuration)
 {
@@ -43,14 +46,13 @@ JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_
 		     reverse_bwt_filename,
 		     reverse_sa_filename);
 
-  //set_int_configuration_param(env, configuration, "maximumEditDistance", bwa, &BWA::set_max_edit_distance);
+  set_float_configuration_param(env, configuration, "maximumEditDistance", bwa, &BWA::set_max_edit_distance);
   set_int_configuration_param(env, configuration, "maximumGapOpens", bwa, &BWA::set_max_gap_opens);
   set_int_configuration_param(env, configuration, "maximumGapExtensions", bwa, &BWA::set_max_gap_extensions);
   set_int_configuration_param(env, configuration, "disallowIndelWithinRange", bwa, &BWA::set_disallow_indel_within_range);
   set_int_configuration_param(env, configuration, "mismatchPenalty", bwa, &BWA::set_mismatch_penalty);
   set_int_configuration_param(env, configuration, "gapOpenPenalty", bwa, &BWA::set_gap_open_penalty);
   set_int_configuration_param(env, configuration, "gapExtensionPenalty", bwa, &BWA::set_gap_extension_penalty);
-  
 
   env->ReleaseStringUTFChars(java_ann,ann_filename);
   env->ReleaseStringUTFChars(java_amb,amb_filename);
@@ -152,3 +154,15 @@ static void set_int_configuration_param(JNIEnv* env, jobject configuration, cons
     (bwa->*setter)(value);
   }
 }
+
+static void set_float_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, float_setter setter) {
+  jclass configuration_class = env->GetObjectClass(configuration);
+  jfieldID configuration_field = env->GetFieldID(configuration_class, field_name, "Ljava/lang/Float;");
+  jobject boxed_value = env->GetObjectField(configuration,configuration_field);
+  if(boxed_value != NULL) {
+    jclass float_box_class = env->FindClass("java/lang/Float");
+    jmethodID float_extractor = env->GetMethodID(float_box_class,"floatValue", "()F");
+    jfloat value = env->CallFloatMethod(boxed_value,float_extractor);
+    (bwa->*setter)(value);
+  }
+}