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#include "bigWig.h"
#include <stdio.h>
#include <inttypes.h>
#include <stdlib.h>
#include <assert.h>
//Print overly verbose header information
void bwPrintHdr(bigWigFile_t *bw) {
uint64_t i;
int64_t i64;
printf("Version: %"PRIu16"\n", bw->hdr->version);
printf("Levels: %"PRIu16"\n", bw->hdr->nLevels);
printf("ctOffset: 0x%"PRIx64"\n", bw->hdr->ctOffset);
printf("dataOffset: 0x%"PRIx64"\n", bw->hdr->dataOffset);
printf("indexOffset: 0x%"PRIx64"\n", bw->hdr->indexOffset);
printf("sqlOffset: 0x%"PRIx64"\n", bw->hdr->sqlOffset);
printf("summaryOffset: 0x%"PRIx64"\n", bw->hdr->summaryOffset);
printf("bufSize: %"PRIu32"\n", bw->hdr->bufSize);
printf("extensionOffset: 0x%"PRIx64"\n", bw->hdr->extensionOffset);
if(bw->hdr->nLevels) {
printf(" i level data index\n");
}
for(i=0; i<bw->hdr->nLevels; i++) {
printf("\t%"PRIu64"\t%"PRIu32"\t%"PRIx64"\t%"PRIx64"\n", i, bw->hdr->zoomHdrs->level[i], bw->hdr->zoomHdrs->dataOffset[i], bw->hdr->zoomHdrs->indexOffset[i]);
}
printf("nBasesCovered: %"PRIu64"\n", bw->hdr->nBasesCovered);
printf("minVal: %f\n", bw->hdr->minVal);
printf("maxVal: %f\n", bw->hdr->maxVal);
printf("sumData: %f\n", bw->hdr->sumData);
printf("sumSquared: %f\n", bw->hdr->sumSquared);
//Chromosome idx/name/length
if(bw->cl) {
printf("Chromosome List\n");
printf(" idx\tChrom\tLength (bases)\n");
for(i64=0; i64<bw->cl->nKeys; i64++) {
printf(" %"PRIu64"\t%s\t%"PRIu32"\n", i64, bw->cl->chrom[i64], bw->cl->len[i64]);
}
}
}
void bwPrintIndexNode(bwRTreeNode_t *node, int level) {
uint16_t i;
if(!node) return;
for(i=0; i<node->nChildren; i++) {
if(node->isLeaf) {
printf(" %i\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t0x%"PRIx64"\t%"PRIu64"\n", level,\
node->chrIdxStart[i], \
node->baseStart[i], \
node->chrIdxEnd[i], \
node->baseEnd[i], \
node->dataOffset[i], \
node->x.size[i]);
} else {
printf(" %i\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t0x%"PRIx64"\tNA\n", level,\
node->chrIdxStart[i], \
node->baseStart[i], \
node->chrIdxEnd[i], \
node->baseEnd[i], \
node->dataOffset[i]);
bwPrintIndexNode(node->x.child[i], level+1);
}
}
}
void bwPrintIndexTree(bigWigFile_t *fp) {
printf("\nIndex tree:\n");
printf("nItems:\t%"PRIu64"\n", fp->idx->nItems);
printf("chrIdxStart:\t%"PRIu32"\n", fp->idx->chrIdxStart);
printf("baseStart:\t%"PRIu32"\n", fp->idx->baseStart);
printf("chrIdxEnd:\t%"PRIu32"\n", fp->idx->chrIdxEnd);
printf("baseEnd:\t%"PRIu32"\n", fp->idx->baseEnd);
printf("idxSize:\t%"PRIu64"\n", fp->idx->idxSize);
printf(" level\tchrIdxStart\tbaseStart\tchrIdxEnd\tbaseEnd\tchild\tsize\n");
bwPrintIndexNode(fp->idx->root, 0);
}
void printIntervals(bwOverlappingIntervals_t *ints, uint32_t start) {
uint32_t i;
if(!ints) return;
for(i=0; i<ints->l; i++) {
if(ints->start && ints->end) {
printf("Interval %"PRIu32"\t%"PRIu32"-%"PRIu32": %f\n",i, ints->start[i], ints->end[i], ints->value[i]);
} else if(ints->start) {
printf("Interval %"PRIu32"\t%"PRIu32"-%"PRIu32": %f\n",i, ints->start[i], ints->start[i]+1, ints->value[i]);
} else {
printf("Interval %"PRIu32"\t%"PRIu32"-%"PRIu32": %f\n",i, start+i, start+i+1, ints->value[i]);
}
}
}
//This is an example call back function
CURLcode callBack(CURL *curl) {
CURLcode rv;
rv = curl_easy_setopt(curl, CURLOPT_USERNAME, "anonymous");
if(rv != CURLE_OK) return rv;
rv = curl_easy_setopt(curl, CURLOPT_PASSWORD, "libBigWig@github.com");
return rv;
}
int main(int argc, char *argv[]) {
bigWigFile_t *fp = NULL;
bwOverlappingIntervals_t *intervals = NULL;
double *stats = NULL;
char chrom[] = "chr1";
if(argc != 2) {
fprintf(stderr, "Usage: %s {file.bw|URL://path/file.bw}\n", argv[0]);
return 1;
}
if(bwInit(1<<17) != 0) {
fprintf(stderr, "Received an error in bwInit\n");
return 1;
}
fp = bwOpen(argv[1], callBack, "r");
if(!fp) {
fprintf(stderr, "An error occured while opening %s\n", argv[1]);
return 1;
}
bwPrintHdr(fp);
bwPrintIndexTree(fp);
//Try to get some blocks
printf("%s:10000000-10000100 Intervals\n", chrom);
intervals = bwGetOverlappingIntervals(fp, chrom, 10000000, 10000100);
printIntervals(intervals,0);
bwDestroyOverlappingIntervals(intervals);
printf("%s:10000000-10000100 Values\n", chrom);
intervals = bwGetValues(fp, chrom, 10000000, 10000100, 0);
printIntervals(intervals,0);
bwDestroyOverlappingIntervals(intervals);
stats = bwStats(fp, chrom, 10000000, 10000100, 1, mean);
if(stats) {
printf("%s:10000000-10000100 mean: %f\n", chrom, stats[0]);
free(stats);
}
stats = bwStats(fp, chrom, 10000000, 10000100, 2, mean);
if(stats) {
printf("%s:10000000-10000100 mean: %f %f\n", chrom, stats[0], stats[1]);
free(stats);
}
stats = bwStats(fp, chrom, 10000000, 10000100, 1, dev);
if(stats) {
printf("%s:10000000-10000100 std. dev.: %f\n", chrom, stats[0]);
free(stats);
}
stats = bwStats(fp, chrom, 10000000, 10000100, 2, dev);
if(stats) {
printf("%s:10000000-10000100 std. dev.: %f %f\n", chrom, stats[0], stats[1]);
free(stats);
}
stats = bwStats(fp, chrom, 10000000, 10000100, 1, min);
if(stats) {
printf("%s:10000000-10000100 min: %f\n", chrom, stats[0]);
free(stats);
}
stats = bwStats(fp, chrom, 10000000, 10000100, 2, min);
if(stats) {
printf("%s:10000000-10000100 min: %f %f\n", chrom, stats[0], stats[1]);
free(stats);
}
stats = bwStats(fp, chrom, 10000000, 10000100, 1, max);
if(stats) {
printf("%s:10000000-10000100 max: %f\n", chrom, stats[0]);
free(stats);
}
stats = bwStats(fp, chrom, 10000000, 10000100, 2, max);
if(stats) {
printf("%s:10000000-10000100 max: %f %f\n", chrom, stats[0], stats[1]);
free(stats);
}
stats = bwStats(fp, chrom, 10000000, 10000100, 1, cov);
if(stats) {
printf("%s:10000000-10000100 coverage: %f\n", chrom, stats[0]);
free(stats);
}
stats = bwStats(fp, chrom, 10000000, 10000100, 2, cov);
if(stats) {
printf("%s:10000000-10000100 coverage: %f %f\n", chrom, stats[0], stats[1]);
free(stats);
}
bwClose(fp);
bwCleanup();
return 0;
}
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