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Better configuration support. Now supports everything that people have expressed interest in except edit distance. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2021 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-11-11 20:54:49 +00:00
parent 6c9f86bb4d
commit 0c2a957ae0
8 changed files with 175 additions and 60 deletions
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8
c/bwa/bwa_gateway.cpp
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@ -76,6 +76,14 @@ 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_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_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; }
/**
* Create a sequence with a set of reasonable initial defaults.
* Will leave seq and rseq empty.

11
c/bwa/bwa_gateway.h
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@ -30,6 +30,17 @@ class BWA {
const char* reverse_bwt_filename,
const char* reverse_sa_filename);
~BWA();
// Parameterize the aligner.
void set_max_edit_distance(int 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);
void set_mismatch_penalty(int penalty);
void set_gap_open_penalty(int penalty);
void set_gap_extension_penalty(int penalty);
// Perform the alignment
void align(const char* bases, const unsigned read_length, Alignment*& alignments, unsigned& num_alignments);
};

64
c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp
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@ -12,23 +12,28 @@ static jclass java_alignment_array_class = NULL;
static jclass java_alignment_class = NULL;
static jmethodID java_alignment_constructor = NULL;
JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_create(JNIEnv* env,
jobject instance,
jstring java_ann,
jstring java_amb,
jstring java_pac,
jstring java_forward_bwt,
jstring java_forward_sa,
jstring java_reverse_bwt,
jstring java_reverse_sa)
typedef void (BWA::*int_setter)(int 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);
JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_create(JNIEnv* env, jobject instance, jobject configuration)
{
const char* ann_filename = env->GetStringUTFChars(java_ann, JNI_FALSE);
const char* amb_filename = env->GetStringUTFChars(java_amb, JNI_FALSE);
const char* pac_filename = env->GetStringUTFChars(java_pac, JNI_FALSE);
const char* forward_bwt_filename = env->GetStringUTFChars(java_forward_bwt, JNI_FALSE);
const char* forward_sa_filename = env->GetStringUTFChars(java_forward_sa, JNI_FALSE);
const char* reverse_bwt_filename = env->GetStringUTFChars(java_reverse_bwt, JNI_FALSE);
const char* reverse_sa_filename = env->GetStringUTFChars(java_reverse_sa, JNI_FALSE);
jstring java_ann = get_configuration_string(env,configuration,"annFileName");
jstring java_amb = get_configuration_string(env,configuration,"ambFileName");
jstring java_pac = get_configuration_string(env,configuration,"pacFileName");
jstring java_forward_bwt = get_configuration_string(env,configuration,"forwardBWTFileName");
jstring java_forward_sa = get_configuration_string(env,configuration,"forwardSAFileName");
jstring java_reverse_bwt = get_configuration_string(env,configuration,"reverseBWTFileName");
jstring java_reverse_sa = get_configuration_string(env,configuration,"reverseSAFileName");
const char* ann_filename = env->GetStringUTFChars(java_ann,JNI_FALSE);
const char* amb_filename = env->GetStringUTFChars(java_amb,JNI_FALSE);
const char* pac_filename = env->GetStringUTFChars(java_pac,JNI_FALSE);
const char* forward_bwt_filename = env->GetStringUTFChars(java_forward_bwt,JNI_FALSE);
const char* forward_sa_filename = env->GetStringUTFChars(java_forward_sa,JNI_FALSE);
const char* reverse_bwt_filename = env->GetStringUTFChars(java_reverse_bwt,JNI_FALSE);
const char* reverse_sa_filename = env->GetStringUTFChars(java_reverse_sa,JNI_FALSE);
BWA* bwa = new BWA(ann_filename,
amb_filename,
@ -38,6 +43,15 @@ 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_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);
env->ReleaseStringUTFChars(java_pac,pac_filename);
@ -120,3 +134,21 @@ JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACA
return java_alignments;
}
static jstring get_configuration_string(JNIEnv* env, jobject configuration, const char* field_name) {
jclass configuration_class = env->GetObjectClass(configuration);
jfieldID configuration_field = env->GetFieldID(configuration_class, field_name, "Ljava/lang/String;");
return (jstring)env->GetObjectField(configuration,configuration_field);
}
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);
jfieldID configuration_field = env->GetFieldID(configuration_class, field_name, "Ljava/lang/Integer;");
jobject boxed_value = env->GetObjectField(configuration,configuration_field);
if(boxed_value != NULL) {
jclass int_box_class = env->FindClass("java/lang/Integer");
jmethodID int_extractor = env->GetMethodID(int_box_class,"intValue", "()I");
jint value = env->CallIntMethod(boxed_value,int_extractor);
(bwa->*setter)(value);
}
}

4
c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.h
View File

@ -10,10 +10,10 @@ extern "C" {
/*
* Class: org_broadinstitute_sting_alignment_bwa_BWACAligner
* Method: create
* Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)J
* Signature: (Lorg/broadinstitute/sting/alignment/bwa/BWACConfiguration;)J
*/
JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACAligner_create
(JNIEnv *, jobject, jstring, jstring, jstring, jstring, jstring, jstring, jstring);
(JNIEnv *, jobject, jobject);
/*
* Class: org_broadinstitute_sting_alignment_bwa_BWACAligner

9
java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
View File

@ -40,13 +40,8 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
*/
@Override
public void initialize() {
aligner = new BWACAligner(prefix + ".ann",
prefix + ".amb",
prefix + ".pac",
prefix + ".bwt",
prefix + ".sa",
prefix + ".rbwt",
prefix + ".rsa");
BWACConfiguration configuration = new BWACConfiguration(prefix);
aligner = new BWACAligner(configuration);
}
/** Must return true for reads that need to be processed. Reads, for which this method return false will

9
java/src/org/broadinstitute/sting/alignment/bwa/AlignmentWalker.java
View File

@ -31,13 +31,8 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
*/
@Override
public void initialize() {
aligner = new BWACAligner(prefix + ".ann",
prefix + ".amb",
prefix + ".pac",
prefix + ".bwt",
prefix + ".sa",
prefix + ".rbwt",
prefix + ".rsa");
BWACConfiguration configuration = new BWACConfiguration(prefix);
aligner = new BWACAligner(configuration);
}
/**

32
java/src/org/broadinstitute/sting/alignment/bwa/BWACAligner.java
View File

@ -27,22 +27,10 @@ public class BWACAligner {
/**
* Create a pointer to the BWA/C thunk.
* @param annFileName Name of the ann file?
* @param ambFileName Name of the amb file?
* @param pacFileName Packed representation of the forward reference.
* @param forwardBWTFileName Name of the file where the forward BWT is stored.
* @param forwardSAFileName Name of te file where the forward suffix array is stored.
* @param reverseBWTFileName Name of the file where the reverse BWT is stored.
* @param reverseSAFileName Name of the file where the reverse SA is stored.
* @param configuration Configuration of the aligner.
* @return Pointer to the BWA/C thunk.
*/
protected native long create(String annFileName,
String ambFileName,
String pacFileName,
String forwardBWTFileName,
String forwardSAFileName,
String reverseBWTFileName,
String reverseSAFileName);
protected native long create(BWACConfiguration configuration);
/**
* Destroy the
@ -50,22 +38,10 @@ public class BWACAligner {
*/
protected native void destroy(long thunkPointer);
public BWACAligner(String annFileName,
String ambFileName,
String pacFileName,
String forwardBWTFileName,
String forwardSAFileName,
String reverseBWTFileName,
String reverseSAFileName) {
public BWACAligner(BWACConfiguration configuration) {
if(thunkPointer != 0)
throw new StingException("BWA/C attempting to reinitialize.");
thunkPointer = create(annFileName,
ambFileName,
pacFileName,
forwardBWTFileName,
forwardSAFileName,
reverseBWTFileName,
reverseSAFileName);
thunkPointer = create(configuration);
}
/**

98
java/src/org/broadinstitute/sting/alignment/bwa/BWACConfiguration.java 100644
View File

@ -0,0 +1,98 @@
package org.broadinstitute.sting.alignment.bwa;
import org.broadinstitute.sting.utils.StingException;
/**
* Configuration for the BWA/C aligner.
*
* @author mhanna
* @version 0.1
*/
public class BWACConfiguration {
/**
* ANN (?) file name.
*/
public String annFileName = null;
/**
* AMB (?) file name.
*/
public String ambFileName = null;
/**
* Packed reference sequence file.
*/
public String pacFileName = null;
/**
* Forward BWT file.
*/
public String forwardBWTFileName = null;
/**
* Forward suffix array file.
*/
public String forwardSAFileName = null;
/**
* Reverse BWT file.
*/
public String reverseBWTFileName = null;
/**
* Reverse suffix array file.
*/
public String reverseSAFileName = null;
/**
* The maximum edit distance used by BWA.
*/
public Float maximumEditDistance = null;
/**
* How many gap opens are acceptable within this alignment?
*/
public Integer maximumGapOpens = null;
/**
* How many gap extensions are acceptable within this alignment?
*/
public Integer maximumGapExtensions = null;
/**
* Do we disallow indels within a certain range from the start / end?
*/
public Integer disallowIndelWithinRange = null;
/**
* What is the scoring penalty for a mismatch?
*/
public Integer mismatchPenalty = null;
/**
* What is the scoring penalty for a gap open?
*/
public Integer gapOpenPenalty = null;
/**
* What is the scoring penalty for a gap extension?
*/
public Integer gapExtensionPenalty = null;
/**
* Create a new BWA configuration file using the given prefix.
* @param prefix Prefix to use when creating the configuration. Must not be null.
*/
public BWACConfiguration(String prefix) {
if(prefix == null)
throw new StingException("Prefix must not be null.");
annFileName = prefix + ".ann";
ambFileName = prefix + ".amb";
pacFileName = prefix + ".pac";
forwardBWTFileName = prefix + ".bwt";
forwardSAFileName = prefix + ".sa";
reverseBWTFileName = prefix + ".rbwt";
reverseSAFileName = prefix + ".rsa";
}
}