libBigWig是一個(gè)用于讀取/解析bigWig和bigBed文件的C語言庫(kù)。

github地址：https://github.com/dpryan79/libBigWig

libBigWig實(shí)現(xiàn)的功能和結(jié)構(gòu)在“bigWig.h”中阳仔。

# 例子：

https://github.com/dpryan79/libBigWig/test

#include "bigWig.h"
int main(int argc, char *argv[]) {
    bigWigFile_t *fp = NULL;
    bwOverlappingIntervals_t *intervals = NULL;
    double *stats = NULL;
    if(argc != 2) {
        fprintf(stderr, "Usage: %s {file.bw|URL://path/file.bw}\n", argv[0]);
        return 1;
    }

    //Initialize enough space to hold 128KiB (1<<17) of data at a time
    if(bwInit(1<<17) != 0) {
        fprintf(stderr, "Received an error in bwInit\n");
        return 1;
    }

    //Open the local/remote file
    fp = bwOpen(argv[1], NULL, "r");
    if(!fp) {
        fprintf(stderr, "An error occured while opening %s\n", argv[1]);
        return 1;
    }

    //Get values in a range (0-based, half open) without NAs
    intervals = bwGetValues(fp, "chr1", 10000000, 10000100, 0);
    bwDestroyOverlappingIntervals(intervals); //Free allocated memory

    //Get values in a range (0-based, half open) with NAs
    intervals = bwGetValues(fp, "chr1", 10000000, 10000100, 1);
    bwDestroyOverlappingIntervals(intervals); //Free allocated memory

    //Get the full intervals that overlap
    intervals = bwGetOverlappingIntervals(fp, "chr1", 10000000, 10000100);
    bwDestroyOverlappingIntervals(intervals);

    //Get an example statistic - standard deviation
    //We want ~4 bins in the range
    stats = bwStats(fp, "chr1", 10000000, 10000100, 4, dev);
    if(stats) {
        printf("chr1:10000000-10000100 std. dev.: %f %f %f %f\n", stats[0], stats[1], stats[2], stats[3]);
        free(stats);
    }

    bwClose(fp);
    bwCleanup();
    return 0;
}

# 對(duì)一個(gè)bigWig文件進(jìn)行寫入

https://github.com/dpryan79/libBigWig/blob/master/test/exampleWrite.c

#include "bigWig.h"

int main(int argc, char *argv[]) {
    bigWigFile_t *fp = NULL;
    char *chroms[] = {"1", "2"};
    char *chromsUse[] = {"1", "1", "1"};
    uint32_t chrLens[] = {1000000, 1500000};
    uint32_t starts[] = {0, 100, 125,
                         200, 220, 230,
                         500, 600, 625,
                         700, 800, 850};
    uint32_t ends[] = {5, 120, 126,
                       205, 226, 231};
    float values[] = {0.0f, 1.0f, 200.0f,
                      -2.0f, 150.0f, 25.0f,
                      0.0f, 1.0f, 200.0f,
                      -2.0f, 150.0f, 25.0f,
                      -5.0f, -20.0f, 25.0f,
                      -5.0f, -20.0f, 25.0f};
    
    if(bwInit(1<<17) != 0) {
        fprintf(stderr, "Received an error in bwInit\n");
        return 1;
    }

    fp = bwOpen("example_output.bw", NULL, "w");
    if(!fp) {
        fprintf(stderr, "An error occurred while opening example_output.bw for writingn\n");
        return 1;
    }

    //Allow up to 10 zoom levels, though fewer will be used in practice
    if(bwCreateHdr(fp, 10)) goto error;

    //Create the chromosome lists
    fp->cl = bwCreateChromList(chroms, chrLens, 2);
    if(!fp->cl) goto error;

    //Write the header
    if(bwWriteHdr(fp)) goto error;

    //Some example bedGraph-like entries
    if(bwAddIntervals(fp, chromsUse, starts, ends, values, 3)) goto error;
    //We can continue appending similarly formatted entries
    //N.B. you can't append a different chromosome (those always go into different
    if(bwAppendIntervals(fp, starts+3, ends+3, values+3, 3)) goto error;

    //Add a new block of entries with a span. Since bwAdd/AppendIntervals was just used we MUST create a new block
    if(bwAddIntervalSpans(fp, "1", starts+6, 20, values+6, 3)) goto error;
    //We can continue appending similarly formatted entries
    if(bwAppendIntervalSpans(fp, starts+9, values+9, 3)) goto error;

    //Add a new block of fixed-step entries
    if(bwAddIntervalSpanSteps(fp, "1", 900, 20, 30, values+12, 3)) goto error;
    //The start is then 760, since that's where the previous step ended
    if(bwAppendIntervalSpanSteps(fp, values+15, 3)) goto error;

    //Add a new chromosome
    chromsUse[0] = "2";
    chromsUse[1] = "2";
    chromsUse[2] = "2";
    if(bwAddIntervals(fp, chromsUse, starts, ends, values, 3)) goto error;

    //Closing the file causes the zoom levels to be created
    bwClose(fp);
    bwCleanup();

    return 0;

error:
    fprintf(stderr, "Received an error somewhere!\n");
    bwClose(fp);
    bwCleanup();
    return 1;
}

原文：

https://github.com/dpryan79/libBigWig