aligner: create file/folder structure to the hpg-aligner and add the …

…jni functions. #8

build.sh

@@ -17,11 +17,11 @@ mkdir -p build/libs
 if [[ "Darwin" == "$PLATFORM" ]]; then
 	cp hpg-bigdata-core/native/third-party/htslib/libhts.*dylib build/libs/
 	cp hpg-bigdata-core/native/third-party/avro-c-1.7.7/build/src/libavro.*dylib build/libs/
-	cp hpg-bigdata-core/native/libhpgbigdata.dylib build/libs/
+	cp hpg-bigdata-core/native/*.dylib build/libs/
 else
 	cp hpg-bigdata-core/native/third-party/htslib/libhts.so* build/libs/
 	cp hpg-bigdata-core/native/third-party/avro-c-1.7.7/build/src/libavro.so* build/libs/
-    cp hpg-bigdata-core/native/libhpgbigdata.so build/libs/
+    cp hpg-bigdata-core/native/*.so build/libs/
 fi
 
 cp README.md build/

hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/ConvertCommandExecutor.java

@@ -64,7 +64,7 @@
 import org.opencb.biodata.models.sequence.Read;
 import org.opencb.commons.io.DataReader;
 import org.opencb.commons.run.ParallelTaskRunner;
-import org.opencb.hpg.bigdata.core.NativeSupport;
+import org.opencb.hpg.bigdata.core.NativeConverter;
 import org.opencb.hpg.bigdata.core.converters.FastqRecord2ReadConverter;
 import org.opencb.hpg.bigdata.core.converters.FullVcfCodec;
 import org.opencb.hpg.bigdata.core.converters.SAMRecord2ReadAlignmentConverter;
@@ -83,8 +83,6 @@
 import org.opencb.hpg.bigdata.core.utils.PathUtils;
 import org.opencb.hpg.bigdata.core.utils.ReadUtils;
 
-import static org.opencb.hpg.bigdata.tools.converters.mr.Fastq2AvroMR.*;
-
 /**
  * Created by imedina on 16/03/15.
  */
@@ -352,7 +350,7 @@ private void sam2avro(String input, String output, String codecName) throws IOEx
             System.out.println("\tjava.libary.path = " + System.getProperty("java.library.path"));
             System.loadLibrary("hpgbigdata");
             System.out.println("...done!");
-			new NativeSupport().bam2ga(in, out, convertCommandOptions.compression == null ? "snappy" : convertCommandOptions.compression);
+			new NativeConverter().bam2ga(in, out, convertCommandOptions.compression == null ? "snappy" : convertCommandOptions.compression);
 			return;
 		}
 

hpg-bigdata-core/native/build.sh

@@ -34,4 +34,14 @@ fi
 echo 
 echo "Building the dynamic library $olib"
 
-gcc -O3 -std=gnu99 ./converters/bam2ga.c jni/org_opencb_hpg_bigdata_core_NativeSupport.c -o $olib -shared -fPIC -I third-party/avro-c-1.7.7/src/ -I $JAVA_HOME/include -I $JAVA_HOME/include/linux -I $JAVA_HOME/include/darwin -I third-party/ -I third-party/htslib/ -L third-party/avro-c-1.7.7/build/src/ -L third-party/htslib/ -lhts -lavro -lpthread
+gcc -O3 -std=gnu99 ./converters/bam2ga.c jni/org_opencb_hpg_bigdata_core_NativeConverter.c -o $olib -shared -fPIC -I third-party/avro-c-1.7.7/src/ -I jni/ -I $JAVA_HOME/include -I $JAVA_HOME/include/linux -I $JAVA_HOME/include/darwin -I third-party/ -I third-party/htslib/ -L third-party/avro-c-1.7.7/build/src/ -L third-party/htslib/ -lhts -lavro -lpthread
+
+olib="libhpgaligner.so"
+if [[ "Darwin" == "$PLATFORM" ]]; then
+  olib="libhpgaligner.dylib"
+fi
+
+echo
+echo "Building the dynamic library $olib"
+
+gcc -O3 -std=gnu99 ./third-party/hpg-aligner/index.c ./third-party/hpg-aligner/mapper.c -o $olib -shared -fPIC -I jni/

hpg-bigdata-core/native/jni/org_opencb_hpg_bigdata_core_NativeAligner.c

@@ -0,0 +1,46 @@
+#include "org_opencb_hpg_bigdata_core_NativeAligner.h"
+
+//------------------------------------------------------------------------------//
+
+void *load_index(char *index_path);
+void free_index(void *index);
+
+char *map(char *fastq, void *index);
+
+//------------------------------------------------------------------------------//
+
+JNIEXPORT jlong JNICALL Java_org_opencb_hpg_bigdata_core_NativeAligner_load_1index
+  (JNIEnv *env, jobject this, jstring index_path) {
+
+  const char *path = (*env)->GetStringUTFChars(env, index_path, NULL);
+  void *index = load_index(path);
+  return ((long) index);
+}
+
+//------------------------------------------------------------------------------//
+
+JNIEXPORT void JNICALL Java_org_opencb_hpg_bigdata_core_NativeAligner_free_1index
+  (JNIEnv *env, jobject this, jlong index) {
+
+  free_index((void *) index);
+}
+
+//------------------------------------------------------------------------------//
+
+JNIEXPORT jstring JNICALL Java_org_opencb_hpg_bigdata_core_NativeAligner_map
+  (JNIEnv *env, jobject this, jstring fastq, jlong index) {
+
+    const char *reads = (*env)->GetStringUTFChars(env, fastq, NULL);
+    char *sam = map(reads, (void *)index);
+
+    jstring res = (*env)->NewStringUTF(env, sam);
+
+    // free memory
+    if (sam) free(sam);
+
+    // return
+	return res;
+}
+
+//------------------------------------------------------------------------------//
+//------------------------------------------------------------------------------//

hpg-bigdata-core/native/jni/org_opencb_hpg_bigdata_core_NativeSupport.c → hpg-bigdata-core/native/jni/org_opencb_hpg_bigdata_core_NativeConverter.c

@@ -1,11 +1,12 @@
-#include "org_opencb_hpg_bigdata_core_NativeSupport.h"
+#include "org_opencb_hpg_bigdata_core_NativeConverter.h"
 
 //------------------------------------------------------------------------------//
 
 void bam2ga(const char *bam_filename, const char *avro_filename, const char *codec_name);
 
-JNIEXPORT void JNICALL Java_org_opencb_hpg_bigdata_core_NativeSupport_bam2ga(JNIEnv *env, jobject this,
-																			 jstring bamFilename, jstring gaFilename, jstring compression) {
+JNIEXPORT void JNICALL Java_org_opencb_hpg_bigdata_core_NativeConverter_bam2ga(JNIEnv *env, jobject this,
+																			   jstring bamFilename, jstring gaFilename,
+																			   jstring compression) {
 
   const char *bam_filename = (*env)->GetStringUTFChars(env, bamFilename, NULL);
   const char *ga_filename = (*env)->GetStringUTFChars(env, gaFilename, NULL);

hpg-bigdata-core/native/third-party/hpg-aligner/comp.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+#gcc -O3 -std=gnu99 ./converters/bam2ga.c jni/org_opencb_hpg_bigdata_core_NativeSupport.c -o $olib -shared -fPIC -I third-party/avro-c-1.7.7/src/ -I $JAVA_HOME/include -I $JAVA_HOME/include/linux -I $JAVA_HOME/include/darwin -I third-party/ -I third-party/htslib/ -L third-party/avro-c-1.7.7/build/src/ -L third-party/htslib/ -lhts -lavro -lpthread
+gcc -O3 -std=gnu99 hpg-aligner.c index.c mapper.c -o hpg-aligner
+
+olib="libhpgaligner.so"
+gcc -O3 -std=gnu99 hpg-aligner.c index.c mapper.c -o $olib -shared -fPIC

hpg-bigdata-core/native/third-party/hpg-aligner/hpg-aligner.c

@@ -0,0 +1,30 @@
+
+//----------------------------------------------------------------------------------------------------------------------
+//
+//----------------------------------------------------------------------------------------------------------------------
+
+void *load_index(char *index_path);
+void free_index(void *index);
+
+char *map(char *fastq, void *index);
+
+//----------------------------------------------------------------------------------------------------------------------
+// main
+//----------------------------------------------------------------------------------------------------------------------
+
+void main() {
+    // load index
+    char *index_path = "/toto/index.sa";
+    void *index = load_index(index_path);
+
+    // mapping
+    char *fastq = "@read1\nACTACTACTACTGG\n+\n22222222222222\n@read2\nGAGTTCCAAAGGGG\n+\n22222222222222\n";
+    char *sam = map(fastq, index);
+
+    printf("fastq:\n%s\n", fastq);
+    printf("sam:\n%s\n", sam);
+
+    // free memory
+    free(sam);
+    free_index(index);
+}

hpg-bigdata-core/native/third-party/hpg-aligner/index.c

@@ -0,0 +1,24 @@
+#include <stdio.h>
+#include <stdlib.h>
+
+//----------------------------------------------------------------------------------------------------------------------
+//
+//----------------------------------------------------------------------------------------------------------------------
+
+void *load_index(char *index_path) {
+    char *index = (char *) calloc(100, sizeof(char));
+    sprintf(index, "index located at %s", index_path);
+    printf("Loading index...\n\t%s\n...done!\n", index);
+    return (void *) index;
+}
+
+//----------------------------------------------------------------------------------------------------------------------
+//
+//----------------------------------------------------------------------------------------------------------------------
+
+void free_index(void *index) {
+    if (index) {
+        printf("Freeing index...\n\t%s\n...done!\n", (char *) index);
+        free((char *) index);
+    }
+}

hpg-bigdata-core/native/third-party/hpg-aligner/mapper.c

@@ -0,0 +1,13 @@
+#include <stdio.h>
+#include <stdlib.h>
+
+//----------------------------------------------------------------------------------------------------------------------
+//
+//----------------------------------------------------------------------------------------------------------------------
+
+char *map(char *fastq, char *index_path) {
+    char *sam = (char *) calloc(100, sizeof(char));
+    sprintf(sam, "read1\t10\t20\t100M\tATAAATTACGGGGGAGA\nread2\t10\t20\t100M\tATAAATTACGGGGGAGA\n");
+    //printf("Mapping...\n%s\n%s\n...done!\n", fastq, sam);
+    return sam;
+}

hpg-bigdata-core/src/main/java/org/opencb/hpg/bigdata/core/NativeAligner.java

@@ -0,0 +1,26 @@
+/*
+ * Copyright 2015 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.opencb.hpg.bigdata.core;
+
+public class NativeAligner {
+	// index
+	public native long load_index(String indexPath);
+	public native void free_index(long index);
+
+	// map
+	public native String map(String sequences, long index);
+}

hpg-bigdata-core/src/main/java/org/opencb/hpg/bigdata/core/NativeSupport.java → hpg-bigdata-core/src/main/java/org/opencb/hpg/bigdata/core/NativeConverter.java

@@ -16,6 +16,6 @@
 
 package org.opencb.hpg.bigdata.core;
 
-public class NativeSupport {
+public class NativeConverter {
 	public native void bam2ga(String bamFilename, String gaFilename, String compression);	
 }