From 15c14add4deb44f97ac6310637d80d662e5e8997 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 13 Nov 2009 22:55:27 +0000
Subject: [PATCH] Repackage the aligner for better partitioning.  The C
 aligner, for example, is now partitioned from the Java aligner, and both are
 partitioned from the more general- purpose BWT reader.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2045 348d0f76-0448-11de-a6fe-93d51630548a
---
 c/bwa/Makefile                                |  8 +++++---
 ...ute_sting_alignment_bwa_c_BWACAligner.cpp} |  8 ++++----
 ...itute_sting_alignment_bwa_c_BWACAligner.h} | 20 +++++++++----------
 .../{bwa => }/AlignmentValidationWalker.java  |  6 ++++--
 .../alignment/{bwa => }/AlignmentWalker.java  |  6 ++++--
 .../alignment/bwa/{ => c}/BWACAligner.java    |  7 ++-----
 .../bwa/{ => c}/BWACConfiguration.java        |  2 +-
 .../bwa/{ => java}/AlignerTestHarness.java    |  5 ++++-
 .../{ => java}/AlignmentMatchSequence.java    |  3 ++-
 .../bwa/{ => java}/AlignmentState.java        |  2 +-
 .../alignment/bwa/{ => java}/BWAAligner.java  |  7 +++++--
 .../bwa/{ => java}/BWAAlignment.java          |  5 ++++-
 .../alignment/bwa/{ => java}/LowerBound.java  |  4 ++--
 .../alignment/{bwa => reference}/bwt/BWT.java |  4 ++--
 .../{bwa => reference}/bwt/BWTReader.java     |  8 ++++----
 .../{bwa => reference}/bwt/BWTWriter.java     |  6 +++---
 .../{bwa => reference}/bwt/Bases.java         |  2 +-
 .../{bwa => reference}/bwt/Counts.java        |  2 +-
 .../bwt/CreateBWTFromReference.java           |  4 ++--
 .../{bwa => reference}/bwt/SequenceBlock.java |  2 +-
 .../{bwa => reference}/bwt/SuffixArray.java   |  2 +-
 .../bwt/SuffixArrayReader.java                |  6 +++---
 .../bwt/SuffixArrayWriter.java                |  4 ++--
 .../packing/BasePackedInputStream.java        |  2 +-
 .../packing/BasePackedOutputStream.java       |  2 +-
 .../packing/CreatePACFromReference.java       |  2 +-
 .../{bwa => reference}/packing/PackUtils.java |  2 +-
 .../packing/UnsignedIntPackedInputStream.java |  2 +-
 .../UnsignedIntPackedOutputStream.java        |  2 +-
 29 files changed, 74 insertions(+), 61 deletions(-)
 rename c/bwa/{org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp => org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp} (96%)
 rename c/bwa/{org_broadinstitute_sting_alignment_bwa_BWACAligner.h => org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h} (51%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => }/AlignmentValidationWalker.java (96%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => }/AlignmentWalker.java (91%)
 rename java/src/org/broadinstitute/sting/alignment/bwa/{ => c}/BWACAligner.java (96%)
 rename java/src/org/broadinstitute/sting/alignment/bwa/{ => c}/BWACConfiguration.java (97%)
 rename java/src/org/broadinstitute/sting/alignment/bwa/{ => java}/AlignerTestHarness.java (96%)
 rename java/src/org/broadinstitute/sting/alignment/bwa/{ => java}/AlignmentMatchSequence.java (97%)
 rename java/src/org/broadinstitute/sting/alignment/bwa/{ => java}/AlignmentState.java (76%)
 rename java/src/org/broadinstitute/sting/alignment/bwa/{ => java}/BWAAligner.java (97%)
 rename java/src/org/broadinstitute/sting/alignment/bwa/{ => java}/BWAAlignment.java (95%)
 rename java/src/org/broadinstitute/sting/alignment/bwa/{ => java}/LowerBound.java (95%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/bwt/BWT.java (97%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/bwt/BWTReader.java (89%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/bwt/BWTWriter.java (89%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/bwt/Bases.java (97%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/bwt/Counts.java (98%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/bwt/CreateBWTFromReference.java (98%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/bwt/SequenceBlock.java (94%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/bwt/SuffixArray.java (97%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/bwt/SuffixArrayReader.java (91%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/bwt/SuffixArrayWriter.java (92%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/packing/BasePackedInputStream.java (98%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/packing/BasePackedOutputStream.java (98%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/packing/CreatePACFromReference.java (97%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/packing/PackUtils.java (98%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/packing/UnsignedIntPackedInputStream.java (98%)
 rename java/src/org/broadinstitute/sting/alignment/{bwa => reference}/packing/UnsignedIntPackedOutputStream.java (98%)

diff --git a/c/bwa/Makefile b/c/bwa/Makefile
index 5b888fac8..6399a0e6d 100644
--- a/c/bwa/Makefile
+++ b/c/bwa/Makefile
@@ -4,8 +4,7 @@ CXXFLAGS=-g -Wall -O2 -m64 -fPIC
 .cpp.o:
 	$(CXX) -c $(CXXFLAGS) -I$(BWA_HOME) -I$(JAVA_INCLUDE) $< -o $@
 
-all: init org_broadinstitute_sting_alignment_bwa_BWACAligner.o bwa_gateway.o 
-	$(LIBTOOL_COMMAND) org_broadinstitute_sting_alignment_bwa_BWACAligner.o bwa_gateway.o -o $(TARGET_LIB) -L$(BWA_HOME) -lbwacore $(EXTRA_LIBS)
+all: init lib
 
 init:
 	@echo Please make sure the following platforms are set correctly on your machine.
@@ -13,7 +12,10 @@ init:
 	@echo JAVA_INCLUDE=$(JAVA_INCLUDE)
 	@echo TARGET_LIB=$(TARGET_LIB)
 	@echo EXTRA_LIBS=$(EXTRA_LIBS)
-	@echo LIBTOOL_COMMAND=$(LIBTOOL_COMMAND)x
+	@echo LIBTOOL_COMMAND=$(LIBTOOL_COMMAND)
+
+lib: org_broadinstitute_sting_alignment_bwa_c_BWACAligner.o bwa_gateway.o 
+	$(LIBTOOL_COMMAND) $? -o $(TARGET_LIB) -L$(BWA_HOME) -lbwacore $(EXTRA_LIBS)
 
 clean:
 	rm *.o libbwa.*
diff --git a/c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp b/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp
similarity index 96%
rename from c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp
rename to c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp
index ddb614062..3e07a623a 100644
--- a/c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp
+++ b/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp
@@ -6,7 +6,7 @@
 #include "bwt.h"
 #include "bwtaln.h"
 #include "bwa_gateway.h"
-#include "org_broadinstitute_sting_alignment_bwa_BWACAligner.h"
+#include "org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h"
 
 static jclass java_alignment_array_class = NULL;
 static jclass java_alignment_class = NULL;
@@ -20,7 +20,7 @@ static jstring get_configuration_string(JNIEnv* env, jobject configuration, cons
 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)
+JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_create(JNIEnv* env, jobject instance, jobject configuration)
 {
   jstring java_ann = get_configuration_string(env,configuration,"annFileName");
   jstring java_amb = get_configuration_string(env,configuration,"ambFileName");
@@ -70,13 +70,13 @@ JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_
   return (jlong)bwa;
 }
 
-JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_destroy(JNIEnv* env, jobject instance, jlong java_bwa) 
+JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_destroy(JNIEnv* env, jobject instance, jlong java_bwa) 
 {
   BWA* bwa = (BWA*)java_bwa;
   delete bwa;
 }
 
-JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_getAlignments(JNIEnv* env, jobject object, jlong java_bwa, jbyteArray java_bases) {
+JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getAlignments(JNIEnv* env, jobject object, jlong java_bwa, jbyteArray java_bases) {
   BWA* bwa = (BWA*)java_bwa;
 
   const jsize read_length = env->GetArrayLength(java_bases);
diff --git a/c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.h b/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h
similarity index 51%
rename from c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.h
rename to c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h
index 4288e8ace..c2c081e16 100644
--- a/c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.h
+++ b/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h
@@ -1,34 +1,34 @@
 /* DO NOT EDIT THIS FILE - it is machine generated */
 #include <jni.h>
-/* Header for class org_broadinstitute_sting_alignment_bwa_BWACAligner */
+/* Header for class org_broadinstitute_sting_alignment_bwa_c_BWACAligner */
 
-#ifndef _Included_org_broadinstitute_sting_alignment_bwa_BWACAligner
-#define _Included_org_broadinstitute_sting_alignment_bwa_BWACAligner
+#ifndef _Included_org_broadinstitute_sting_alignment_bwa_c_BWACAligner
+#define _Included_org_broadinstitute_sting_alignment_bwa_c_BWACAligner
 #ifdef __cplusplus
 extern "C" {
 #endif
 /*
- * Class:     org_broadinstitute_sting_alignment_bwa_BWACAligner
+ * Class:     org_broadinstitute_sting_alignment_bwa_c_BWACAligner
  * Method:    create
- * Signature: (Lorg/broadinstitute/sting/alignment/bwa/BWACConfiguration;)J
+ * Signature: (Lorg/broadinstitute/sting/alignment/bwa/c/BWACConfiguration;)J
  */
-JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_create
+JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_create
   (JNIEnv *, jobject, jobject);
 
 /*
- * Class:     org_broadinstitute_sting_alignment_bwa_BWACAligner
+ * Class:     org_broadinstitute_sting_alignment_bwa_c_BWACAligner
  * Method:    destroy
  * Signature: (J)V
  */
-JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_destroy
+JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_destroy
   (JNIEnv *, jobject, jlong);
 
 /*
- * Class:     org_broadinstitute_sting_alignment_bwa_BWACAligner
+ * Class:     org_broadinstitute_sting_alignment_bwa_c_BWACAligner
  * Method:    getAlignments
  * Signature: (J[B)[Lorg/broadinstitute/sting/alignment/Alignment;
  */
-JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_getAlignments
+JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getAlignments
   (JNIEnv *, jobject, jlong, jbyteArray);
 
 #ifdef __cplusplus
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
similarity index 96%
rename from java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
rename to java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
index cde68f272..36e4f39de 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
@@ -1,10 +1,12 @@
-package org.broadinstitute.sting.alignment.bwa;
+package org.broadinstitute.sting.alignment;
 
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.alignment.Alignment;
+import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+import org.broadinstitute.sting.alignment.bwa.c.BWACConfiguration;
 import net.sf.samtools.SAMRecord;
 
 /**
@@ -41,7 +43,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
     @Override
     public void initialize() {
         BWACConfiguration configuration = new BWACConfiguration(prefix);
-        aligner = new BWACAligner(configuration);        
+        aligner = new BWACAligner(configuration);
     }
 
     /** Must return true for reads that need to be processed. Reads, for which this method return false will
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
similarity index 91%
rename from java/src/org/broadinstitute/sting/alignment/bwa/AlignmentWalker.java
rename to java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
index 1b36b6788..aacf8bc04 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
@@ -1,7 +1,9 @@
-package org.broadinstitute.sting.alignment.bwa;
+package org.broadinstitute.sting.alignment;
 
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+import org.broadinstitute.sting.alignment.bwa.c.BWACConfiguration;
 import net.sf.samtools.SAMRecord;
 
 import java.util.Random;
@@ -32,7 +34,7 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
     @Override
     public void initialize() {
         BWACConfiguration configuration = new BWACConfiguration(prefix);
-        aligner = new BWACAligner(configuration);        
+        aligner = new BWACAligner(configuration);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/BWACAligner.java b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
similarity index 96%
rename from java/src/org/broadinstitute/sting/alignment/bwa/BWACAligner.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
index 6ceffbc8e..34b4d096c 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/BWACAligner.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
@@ -1,13 +1,10 @@
-package org.broadinstitute.sting.alignment.bwa;
+package org.broadinstitute.sting.alignment.bwa.c;
 
-import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.alignment.Alignment;
-
-import java.io.File;
-import java.util.Scanner;
+import org.broadinstitute.sting.alignment.bwa.c.BWACConfiguration;
 
 /**
  * An aligner using the BWA/C implementation.
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/BWACConfiguration.java b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACConfiguration.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/alignment/bwa/BWACConfiguration.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/c/BWACConfiguration.java
index 7b9269ff2..96eee7b64 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/BWACConfiguration.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACConfiguration.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.alignment.bwa;
+package org.broadinstitute.sting.alignment.bwa.c;
 
 import org.broadinstitute.sting.utils.StingException;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
similarity index 96%
rename from java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
index a1875a389..c3499ca8c 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
@@ -1,7 +1,10 @@
-package org.broadinstitute.sting.alignment.bwa;
+package org.broadinstitute.sting.alignment.bwa.java;
 
 import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.alignment.Alignment;
+import org.broadinstitute.sting.alignment.bwa.java.BWAAligner;
+import org.broadinstitute.sting.alignment.bwa.java.BWAAlignment;
+import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentMatchSequence.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/alignment/bwa/AlignmentMatchSequence.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
index 026669246..f05ce48b1 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentMatchSequence.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
@@ -1,5 +1,6 @@
-package org.broadinstitute.sting.alignment.bwa;
+package org.broadinstitute.sting.alignment.bwa.java;
 
+import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Deque;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentState.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentState.java
similarity index 76%
rename from java/src/org/broadinstitute/sting/alignment/bwa/AlignmentState.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentState.java
index fb8d5004f..92c603335 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentState.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentState.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.alignment.bwa;
+package org.broadinstitute.sting.alignment.bwa.java;
 
 /**
  * The state of a given base in the alignment.
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAligner.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAligner.java
index a47ffd459..c5c43ceca 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAligner.java
@@ -1,6 +1,9 @@
-package org.broadinstitute.sting.alignment.bwa;
+package org.broadinstitute.sting.alignment.bwa.java;
 
-import org.broadinstitute.sting.alignment.bwa.bwt.*;
+import org.broadinstitute.sting.alignment.reference.bwt.*;
+import org.broadinstitute.sting.alignment.bwa.java.LowerBound;
+import org.broadinstitute.sting.alignment.bwa.java.BWAAlignment;
+import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.utils.BaseUtils;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/BWAAlignment.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
similarity index 95%
rename from java/src/org/broadinstitute/sting/alignment/bwa/BWAAlignment.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
index 19bbce0d4..cc912dd82 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/BWAAlignment.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
@@ -1,6 +1,9 @@
-package org.broadinstitute.sting.alignment.bwa;
+package org.broadinstitute.sting.alignment.bwa.java;
 
 import org.broadinstitute.sting.alignment.Alignment;
+import org.broadinstitute.sting.alignment.bwa.java.BWAAligner;
+import org.broadinstitute.sting.alignment.bwa.java.AlignmentMatchSequence;
+import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.Cigar;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java
similarity index 95%
rename from java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java
index 7e4510128..3784643c0 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java
@@ -1,9 +1,9 @@
-package org.broadinstitute.sting.alignment.bwa;
+package org.broadinstitute.sting.alignment.bwa.java;
 
 import java.util.List;
 import java.util.ArrayList;
 
-import org.broadinstitute.sting.alignment.bwa.bwt.BWT;
+import org.broadinstitute.sting.alignment.reference.bwt.BWT;
 
 /**
  * At any point along the given read, what is a good lower bound for the
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWT.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWT.java
rename to java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
index db708797f..dac8f1523 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWT.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.alignment.bwa.bwt;
+package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.alignment.bwa.packing.PackUtils;
+import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 import org.broadinstitute.sting.utils.StingException;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTReader.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
similarity index 89%
rename from java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTReader.java
rename to java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
index 9b0d70840..1205b8589 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTReader.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
@@ -1,9 +1,9 @@
-package org.broadinstitute.sting.alignment.bwa.bwt;
+package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.alignment.bwa.packing.UnsignedIntPackedInputStream;
-import org.broadinstitute.sting.alignment.bwa.packing.BasePackedInputStream;
-import org.broadinstitute.sting.alignment.bwa.packing.PackUtils;
+import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
+import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream;
+import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 
 import java.io.*;
 import java.nio.ByteOrder;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTWriter.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
similarity index 89%
rename from java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTWriter.java
rename to java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
index 32b94acf2..772a194bb 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTWriter.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
@@ -1,8 +1,8 @@
-package org.broadinstitute.sting.alignment.bwa.bwt;
+package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.alignment.bwa.packing.UnsignedIntPackedOutputStream;
-import org.broadinstitute.sting.alignment.bwa.packing.BasePackedOutputStream;
+import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
+import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream;
 
 import java.io.*;
 import java.nio.ByteOrder;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/Bases.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/alignment/bwa/bwt/Bases.java
rename to java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
index 9ea69de52..b348ad547 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/Bases.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.alignment.bwa.bwt;
+package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/Counts.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/alignment/bwa/bwt/Counts.java
rename to java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
index e2d0d92b9..cf07cb173 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/Counts.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.alignment.bwa.bwt;
+package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/CreateBWTFromReference.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/alignment/bwa/bwt/CreateBWTFromReference.java
rename to java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
index dfebe0258..29ac6e790 100755
--- a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/CreateBWTFromReference.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
@@ -23,7 +23,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.alignment.bwa.bwt;
+package org.broadinstitute.sting.alignment.reference.bwt;
 
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
@@ -35,7 +35,7 @@ import java.util.TreeSet;
 import java.util.Comparator;
 
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.alignment.bwa.packing.PackUtils;
+import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 
 /**
  * Create a suffix array data structure.
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SequenceBlock.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java
similarity index 94%
rename from java/src/org/broadinstitute/sting/alignment/bwa/bwt/SequenceBlock.java
rename to java/src/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java
index ba41d92f3..13714de1e 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SequenceBlock.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.alignment.bwa.bwt;
+package org.broadinstitute.sting.alignment.reference.bwt;
 
 /**
  * Models a block of bases within the BWT.
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArray.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArray.java
rename to java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
index 65696fa92..0f808be2a 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArray.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.alignment.bwa.bwt;
+package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayReader.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
similarity index 91%
rename from java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayReader.java
rename to java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
index d7d92dfa5..afec6890f 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayReader.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
@@ -1,8 +1,8 @@
-package org.broadinstitute.sting.alignment.bwa.bwt;
+package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.alignment.bwa.packing.UnsignedIntPackedInputStream;
-import org.broadinstitute.sting.alignment.bwa.packing.PackUtils;
+import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
+import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 
 import java.io.*;
 import java.nio.ByteOrder;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayWriter.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
similarity index 92%
rename from java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayWriter.java
rename to java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
index d05f576b7..84469cc21 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayWriter.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
@@ -1,7 +1,7 @@
-package org.broadinstitute.sting.alignment.bwa.bwt;
+package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.alignment.bwa.packing.UnsignedIntPackedOutputStream;
+import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 
 import java.io.*;
 import java.nio.ByteOrder;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedInputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedInputStream.java
rename to java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
index ad1df8fe4..7bf446693 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedInputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.alignment.bwa.packing;
+package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.StingException;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedOutputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedOutputStream.java
rename to java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
index cc6294a99..a6296bf40 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedOutputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.alignment.bwa.packing;
+package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.StingException;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/packing/CreatePACFromReference.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/alignment/bwa/packing/CreatePACFromReference.java
rename to java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java
index 05bc1fe61..06c822955 100755
--- a/java/src/org/broadinstitute/sting/alignment/bwa/packing/CreatePACFromReference.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java
@@ -23,7 +23,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.alignment.bwa.packing;
+package org.broadinstitute.sting.alignment.reference.packing;
 
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/packing/PackUtils.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/alignment/bwa/packing/PackUtils.java
rename to java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
index 297bd3012..0c5d29fd6 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/packing/PackUtils.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.alignment.bwa.packing;
+package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.StingException;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/packing/UnsignedIntPackedInputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/alignment/bwa/packing/UnsignedIntPackedInputStream.java
rename to java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java
index e04f55e87..c07766ee1 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/packing/UnsignedIntPackedInputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.alignment.bwa.packing;
+package org.broadinstitute.sting.alignment.reference.packing;
 
 import java.io.*;
 import java.nio.ByteBuffer;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/packing/UnsignedIntPackedOutputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/alignment/bwa/packing/UnsignedIntPackedOutputStream.java
rename to java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java
index 700fe141f..9d7853695 100755
--- a/java/src/org/broadinstitute/sting/alignment/bwa/packing/UnsignedIntPackedOutputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java
@@ -23,7 +23,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.alignment.bwa.packing;
+package org.broadinstitute.sting.alignment.reference.packing;
 
 import java.io.*;
 import java.nio.ByteBuffer;