From 21dc05138a243e153faa2ef5507fff8af28c097e Mon Sep 17 00:00:00 2001
From: handsake <handsake@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 17 Dec 2010 14:49:15 +0000
Subject: [PATCH] Bug fixes for the bwa aligner and changes to support
 compiling against newer releases of the bwa code base.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4863 348d0f76-0448-11de-a6fe-93d51630548a
---
 c/bwa/bwa_gateway.cpp                                        | 5 ++++-
 .../broadinstitute/sting/alignment/bwa/c/BWACAligner.java    | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/c/bwa/bwa_gateway.cpp b/c/bwa/bwa_gateway.cpp
index 9d7b70117..3f6850e37 100644
--- a/c/bwa/bwa_gateway.cpp
+++ b/c/bwa/bwa_gateway.cpp
@@ -208,7 +208,7 @@ void BWA::load_default_options()
 }
 
 void BWA::set_max_edit_distance(float edit_distance) { 
-  if(edit_distance < 1) {
+  if(edit_distance > 0 && edit_distance < 1) {
     options.fnr = edit_distance;
     options.max_diff = -1;
   }
@@ -246,6 +246,9 @@ bwa_seq_t* BWA::create_sequence(const char* bases, const unsigned read_length)
   sequence->cigar = NULL;
   sequence->n_cigar = 0;
 
+  sequence->multi = NULL;
+  sequence->n_multi = 0;
+
   return sequence;
 }
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
index 322dd01b6..8631c42d8 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
@@ -59,7 +59,7 @@ public class BWACAligner extends BWAAligner {
      */
     @Override
     public void updateConfiguration(BWAConfiguration configuration) {
-        if(thunkPointer != 0)
+        if(thunkPointer == 0)
             throw new ReviewedStingException("BWA/C: attempting to update configuration of uninitialized aligner.");
         updateConfiguration(thunkPointer,configuration);
     }