Handling a BigWig file from Java+JNI : my notebook

In a previous post I've shown how to use a Java JNI interface to control a NCURSES panel from a java program.
I'll show here how to use java JNI to call the C methods developped by Jim Kent's team at UCSC to handle a BigWig file.

The Makefile for compiling the following sources is defined below:

	JAVA_HOME=/path/to/jdk
	JKENTSRC=path/to/jkentsrc
	CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I ${JKENTSRC}/src/inc -I ${JAVA_HOME}/include -I ${JAVA_HOME}/include/linux
	JAVACC=javacc
	test:libbigwig.so
	java BigWig wgEncodeCrgMapabilityAlign100mer.bigWig
	libbigwig.so:BigWig.h BigWig.c
	gcc ${CFLAGS} -fpic -c BigWig.c -o BigWig.o
	gcc -shared -o $@ BigWig.o ${JKENTSRC}/src/lib/jkent/jkweb.a -lm -lz
	BigWig.h:BigWig.java
	${JAVA_HOME}/bin/javac BigWig.java
	${JAVA_HOME}/bin/javah BigWig

view raw Makefile hosted with ❤ by GitHub

Export the LD_LIBRARY_PATH:

export LD_LIBRARY_PATH=/path/to/current/directory

Download Jim Kent's sources from http://hgdownload.cse.ucsc.edu/admin/jksrc.zip. See the README file to compile jksrc/lib and jksrc/jkOwnLib.

The java source BigWig.java declares seven natives JNI methods. They will call the C methods for opening and closing the bigWig file, and getting the summaries in a given genomic range.

	import java.io.*;
	public class BigWig
	{
	private long fd=0L;
	/** open the bigWig file */
	private native long open(String fname);
	/** close the big wig file */
	private native void close(long fid);
	/** get the summaries in the given genomic range */
	private native Double mean(long fid,String chrom,int start,int end);
	private native Double max(long fid,String chrom,int start,int end);
	private native Double min(long fid,String chrom,int start,int end);
	private native Double coverage(long fid,String chrom,int start,int end);
	private native Double stddev(long fid,String chrom,int start,int end);
	public BigWig(File f) throws IOException
	{
	if(!f.exists()) throw new FileNotFoundException(f.toString());
	this.fd = open(f.getAbsolutePath());
	if(this.fd==0L) throw new IOException("Cannot open bigwig "+f);
	}
	@Override
	protected void finalize() throws Throwable {
	try {
	close();
	} finally {
	super.finalize();
	}
	}
	public Double getMean(String chrom,int start,int end)
	{
	if(fd==0L) return null;
	return mean(fd,chrom,start,end);
	}
	public Double getMax(String chrom,int start,int end)
	{
	if(fd==0L) return null;
	return max(fd,chrom,start,end);
	}
	public Double getMin(String chrom,int start,int end)
	{
	if(fd==0L) return null;
	return min(fd,chrom,start,end);
	}
	public Double getCoverage(String chrom,int start,int end)
	{
	if(fd==0L) return null;
	return coverage(fd,chrom,start,end);
	}
	public Double getStdDev(String chrom,int start,int end)
	{
	if(fd==0L) return null;
	return stddev(fd,chrom,start,end);
	}
	public void close()
	{
	if(this.fd!=0L)
	{
	close(this.fd);
	}
	this.fd=0L;
	}
	public static void main(String args[]) throws IOException
	{
	System.loadLibrary("bigwig");
	BigWig big=new BigWig(new File(args[0]));
	System.err.println(big.getMean("chr1",0,1000000));
	System.err.println(big.getMax("chr1",0,1000000));
	System.err.println(big.getMin("chr1",0,1000000));
	System.err.println(big.getCoverage("chr1",0,1000000));
	System.err.println(big.getStdDev("chr1",0,1000000));
	System.err.println(big.getMean("chr2",0,1000000));
	System.err.println(big.getMean("chr1",0,10));
	big.close();
	}
	}

view raw BigWig.java hosted with ❤ by GitHub

After compiling the java source, the following C header is generated with javah:

	/* DO NOT EDIT THIS FILE - it is machine generated */
	#include <jni.h>
	/* Header for class BigWig */
	#ifndef _Included_BigWig
	#define _Included_BigWig
	#ifdef __cplusplus
	extern "C" {
	#endif
	/*
	* Class: BigWig
	* Method: open
	* Signature: (Ljava/lang/String;)J
	*/
	JNIEXPORT jlong JNICALL Java_BigWig_open
	(JNIEnv *, jobject, jstring);
	/*
	* Class: BigWig
	* Method: close
	* Signature: (J)V
	*/
	JNIEXPORT void JNICALL Java_BigWig_close
	(JNIEnv *, jobject, jlong);
	/*
	* Class: BigWig
	* Method: mean
	* Signature: (JLjava/lang/String;II)Ljava/lang/Double;
	*/
	JNIEXPORT jobject JNICALL Java_BigWig_mean
	(JNIEnv *, jobject, jlong, jstring, jint, jint);
	/*
	* Class: BigWig
	* Method: max
	* Signature: (JLjava/lang/String;II)Ljava/lang/Double;
	*/
	JNIEXPORT jobject JNICALL Java_BigWig_max
	(JNIEnv *, jobject, jlong, jstring, jint, jint);
	/*
	* Class: BigWig
	* Method: min
	* Signature: (JLjava/lang/String;II)Ljava/lang/Double;
	*/
	JNIEXPORT jobject JNICALL Java_BigWig_min
	(JNIEnv *, jobject, jlong, jstring, jint, jint);
	/*
	* Class: BigWig
	* Method: coverage
	* Signature: (JLjava/lang/String;II)Ljava/lang/Double;
	*/
	JNIEXPORT jobject JNICALL Java_BigWig_coverage
	(JNIEnv *, jobject, jlong, jstring, jint, jint);
	/*
	* Class: BigWig
	* Method: stddev
	* Signature: (JLjava/lang/String;II)Ljava/lang/Double;
	*/
	JNIEXPORT jobject JNICALL Java_BigWig_stddev
	(JNIEnv *, jobject, jlong, jstring, jint, jint);
	#ifdef __cplusplus
	}
	#endif
	#endif

view raw BigWig.h hosted with ❤ by GitHub

The C source implements the native methods defined in the java source. The code was inspired from ${JKENTSRC}/src/utils/bigWigSummary/bigWigSummary.c.

	#include "BigWig.h"
	#include "common.h"
	#include "linefile.h"
	#include "hash.h"
	#include "options.h"
	#include "sqlNum.h"
	#include "udc.h"
	#include "bigWig.h"
	JNIEXPORT jlong JNICALL Java_BigWig_open
	(JNIEnv *env, jobject o, jstring s)
	{
	const jbyte *fname = (*env)->GetStringUTFChars(env, s, NULL);
	if(fname==NULL) return 0L;
	struct bbiFile *bwf = bigWigFileOpen((char*)fname);
	(*env)->ReleaseStringUTFChars(env, s, fname);
	return (long)(bwf);
	}
	static jobject Java_BigWigSummary
	(JNIEnv *env, jobject o, jlong ptr, jstring chrom, jint start, jint end,enum bbiSummaryType type)
	{
	jobject ret=NULL;
	jbyte *reference ;
	struct bbiFile *bwf =(struct bbiFile*)ptr;
	double nan0 = strtod("NaN", NULL);
	double summaryValues[]={nan0};
	if(bwf==NULL) return NULL;
	if(chrom==NULL) return NULL;
	reference =(jbyte*) (*env)->GetStringUTFChars(env, chrom, NULL);
	if(reference==NULL) return NULL;
	if (bigWigSummaryArray(bwf, (char*)reference, start, end, type, 1, summaryValues))
	{
	if(!isnan(summaryValues[0]))
	{
	jclass clazz = (*env)->FindClass(env, "java/lang/Double");
	jmethodID constructor = (*env)->GetMethodID(env,clazz, "<init>", "(D)V");
	ret= (*env)->NewObject(env,clazz, constructor,(jdouble)summaryValues[0]);
	}
	}
	(*env)->ReleaseStringUTFChars(env, chrom, reference);
	return ret;
	}
	JNIEXPORT jobject JNICALL Java_BigWig_mean
	(JNIEnv *env, jobject o, jlong ptr, jstring chrom, jint start, jint end)
	{
	return Java_BigWigSummary(env,o,ptr,chrom,start,end,bbiSumMean);
	}
	JNIEXPORT jobject JNICALL Java_BigWig_min
	(JNIEnv *env, jobject o, jlong ptr, jstring chrom, jint start, jint end)
	{
	return Java_BigWigSummary(env,o,ptr,chrom,start,end,bbiSumMax);
	}
	JNIEXPORT jobject JNICALL Java_BigWig_max
	(JNIEnv *env, jobject o, jlong ptr, jstring chrom, jint start, jint end)
	{
	return Java_BigWigSummary(env,o,ptr,chrom,start,end,bbiSumMin);
	}
	JNIEXPORT jobject JNICALL Java_BigWig_coverage
	(JNIEnv *env, jobject o, jlong ptr, jstring chrom, jint start, jint end)
	{
	return Java_BigWigSummary(env,o,ptr,chrom,start,end,bbiSumCoverage);
	}
	JNIEXPORT jobject JNICALL Java_BigWig_stddev
	(JNIEnv *env, jobject o, jlong ptr, jstring chrom, jint start, jint end)
	{
	return Java_BigWigSummary(env,o,ptr,chrom,start,end,bbiSumStandardDeviation);
	}
	JNIEXPORT void JNICALL Java_BigWig_close
	(JNIEnv *env, jobject o, jlong ptr)
	{
	struct bbiFile *bwf =(struct bbiFile*)ptr;
	if(bwf==NULL) return;
	bigWigFileClose(&bwf);
	}

view raw BigWig.c hosted with ❤ by GitHub

Download a bigwig file for a test: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeCrgMapabilityAlign100mer.bigWig.

The main method in BigWig.java contains.a test:

java BigWig wgEncodeCrgMapabilityAlign100mer.bigWig
0.394749239542279

And here is the original output of the utility 'bigWigSummary':

bigWigSummary wgEncodeCrgMapabilityAlign100mer.bigWig -type=mean chr1 1 1000000 1
0.394749

That's it,

Piere