bio-bigwig 0.0.1
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- checksums.yaml +7 -0
- data/LICENSE.txt +21 -0
- data/README.md +131 -0
- data/ext/bio/bigwig/bigwigext.c +747 -0
- data/ext/bio/bigwig/bigwigext.h +9 -0
- data/ext/bio/bigwig/extconf.rb +30 -0
- data/ext/bio/bigwig/libBigWig/LICENSE +22 -0
- data/ext/bio/bigwig/libBigWig/bigWig.h +606 -0
- data/ext/bio/bigwig/libBigWig/bigWigIO.h +110 -0
- data/ext/bio/bigwig/libBigWig/bwCommon.h +70 -0
- data/ext/bio/bigwig/libBigWig/bwRead.c +427 -0
- data/ext/bio/bigwig/libBigWig/bwStats.c +537 -0
- data/ext/bio/bigwig/libBigWig/bwValues.c +803 -0
- data/ext/bio/bigwig/libBigWig/bwValues.h +77 -0
- data/ext/bio/bigwig/libBigWig/bwWrite.c +1333 -0
- data/ext/bio/bigwig/libBigWig/io.c +296 -0
- data/ext/bio/bigwig/libBigWig/test/exampleWrite.c +76 -0
- data/ext/bio/bigwig/libBigWig/test/testBigBed.c +132 -0
- data/ext/bio/bigwig/libBigWig/test/testIterator.c +67 -0
- data/ext/bio/bigwig/libBigWig/test/testLocal.c +223 -0
- data/ext/bio/bigwig/libBigWig/test/testRemote.c +203 -0
- data/ext/bio/bigwig/libBigWig/test/testRemoteManyContigs.c +46 -0
- data/ext/bio/bigwig/libBigWig/test/testWrite.c +68 -0
- data/lib/bio/bigwig/version.rb +7 -0
- data/lib/bio/bigwig.rb +47 -0
- metadata +69 -0
@@ -0,0 +1,537 @@
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#include "bigWig.h"
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#include "bwCommon.h"
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#include <errno.h>
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#include <stdlib.h>
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#include <zlib.h>
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#include <math.h>
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#include <string.h>
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9
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//Returns -1 if there are no applicable levels, otherwise an integer indicating the most appropriate level.
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//Like Kent's library, this divides the desired bin size by 2 to minimize the effect of blocks overlapping multiple bins
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static int32_t determineZoomLevel(bigWigFile_t *fp, int basesPerBin) {
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int32_t out = -1;
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int64_t diff;
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uint32_t bestDiff = -1;
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uint16_t i;
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basesPerBin/=2;
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for(i=0; i<fp->hdr->nLevels; i++) {
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diff = basesPerBin - (int64_t) fp->hdr->zoomHdrs->level[i];
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if(diff >= 0 && diff < bestDiff) {
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bestDiff = diff;
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out = i;
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}
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}
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return out;
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}
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/// @cond SKIP
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struct val_t {
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uint32_t nBases;
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float min, max, sum, sumsq;
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double scalar;
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};
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struct vals_t {
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uint32_t n;
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struct val_t **vals;
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};
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/// @endcond
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void destroyVals_t(struct vals_t *v) {
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uint32_t i;
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if(!v) return;
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for(i=0; i<v->n; i++) free(v->vals[i]);
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if(v->vals) free(v->vals);
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free(v);
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}
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//Determine the base-pair overlap between an interval and a block
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double getScalar(uint32_t i_start, uint32_t i_end, uint32_t b_start, uint32_t b_end) {
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double rv = 0.0;
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if(b_start <= i_start) {
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if(b_end > i_start) rv = ((double)(b_end - i_start))/(b_end-b_start);
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} else if(b_start < i_end) {
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if(b_end < i_end) rv = ((double)(b_end - b_start))/(b_end-b_start);
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else rv = ((double)(i_end - b_start))/(b_end-b_start);
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}
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return rv;
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}
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//Returns NULL on error
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static struct vals_t *getVals(bigWigFile_t *fp, bwOverlapBlock_t *o, int i, uint32_t tid, uint32_t start, uint32_t end) {
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void *buf = NULL, *compBuf = NULL;
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uLongf sz = fp->hdr->bufSize;
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int compressed = 0, rv;
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uint32_t *p, vtid, vstart, vend;
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struct vals_t *vals = NULL;
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struct val_t *v = NULL;
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if(sz) {
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compressed = 1;
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buf = malloc(sz);
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}
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sz = 0; //This is now the size of the compressed buffer
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if(bwSetPos(fp, o->offset[i])) goto error;
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vals = calloc(1,sizeof(struct vals_t));
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if(!vals) goto error;
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v = malloc(sizeof(struct val_t));
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if(!v) goto error;
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if(sz < o->size[i]) compBuf = malloc(o->size[i]);
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if(!compBuf) goto error;
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if(bwRead(compBuf, o->size[i], 1, fp) != 1) goto error;
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if(compressed) {
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sz = fp->hdr->bufSize;
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rv = uncompress(buf, &sz, compBuf, o->size[i]);
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if(rv != Z_OK) goto error;
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} else {
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buf = compBuf;
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sz = o->size[i];
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}
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p = buf;
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while(((uLongf) ((void*)p-buf)) < sz) {
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vtid = p[0];
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vstart = p[1];
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vend = p[2];
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v->nBases = p[3];
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v->min = ((float*) p)[4];
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v->max = ((float*) p)[5];
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v->sum = ((float*) p)[6];
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v->sumsq = ((float*) p)[7];
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v->scalar = getScalar(start, end, vstart, vend);
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if(tid == vtid) {
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if((start <= vstart && end > vstart) || (start < vend && start >= vstart)) {
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vals->vals = realloc(vals->vals, sizeof(struct val_t*)*(vals->n+1));
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if(!vals->vals) goto error;
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vals->vals[vals->n++] = v;
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v = malloc(sizeof(struct val_t));
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if(!v) goto error;
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}
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if(vstart > end) break;
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} else if(vtid > tid) {
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break;
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}
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p+=8;
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}
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free(v);
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free(buf);
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if(compressed) free(compBuf);
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return vals;
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error:
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if(buf) free(buf);
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if(compBuf && compressed) free(compBuf);
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if(v) free(v);
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destroyVals_t(vals);
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return NULL;
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}
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//On error, errno is set to ENOMEM and NaN is returned (though NaN can be returned normally)
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static double blockMean(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
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uint32_t i, j;
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double output = 0.0, coverage = 0.0;
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struct vals_t *v = NULL;
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if(!blocks->n) return strtod("NaN", NULL);
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//Iterate over the blocks
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for(i=0; i<blocks->n; i++) {
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v = getVals(fp, blocks, i, tid, start, end);
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if(!v) goto error;
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for(j=0; j<v->n; j++) {
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output += v->vals[j]->sum * v->vals[j]->scalar;
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coverage += v->vals[j]->nBases * v->vals[j]->scalar;
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}
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destroyVals_t(v);
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}
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if(!coverage) return strtod("NaN", NULL);
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return output/coverage;
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error:
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if(v) free(v);
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errno = ENOMEM;
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return strtod("NaN", NULL);
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}
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static double intMean(bwOverlappingIntervals_t* ints, uint32_t start, uint32_t end) {
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double sum = 0.0;
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uint32_t nBases = 0, i, start_use, end_use;
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if(!ints->l) return strtod("NaN", NULL);
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for(i=0; i<ints->l; i++) {
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start_use = ints->start[i];
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end_use = ints->end[i];
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if(ints->start[i] < start) start_use = start;
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if(ints->end[i] > end) end_use = end;
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nBases += end_use-start_use;
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sum += (end_use-start_use)*((double) ints->value[i]);
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}
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return sum/nBases;
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}
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//Does UCSC compensate for partial block/range overlap?
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static double blockDev(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
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uint32_t i, j;
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double mean = 0.0, ssq = 0.0, coverage = 0.0, diff;
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struct vals_t *v = NULL;
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if(!blocks->n) return strtod("NaN", NULL);
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//Iterate over the blocks
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195
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for(i=0; i<blocks->n; i++) {
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v = getVals(fp, blocks, i, tid, start, end);
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if(!v) goto error;
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for(j=0; j<v->n; j++) {
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coverage += v->vals[j]->nBases * v->vals[j]->scalar;
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mean += v->vals[j]->sum * v->vals[j]->scalar;
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201
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ssq += v->vals[j]->sumsq * v->vals[j]->scalar;
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202
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}
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203
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destroyVals_t(v);
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v = NULL;
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}
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if(coverage<=1.0) return strtod("NaN", NULL);
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diff = ssq-mean*mean/coverage;
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209
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if(coverage > 1.0) diff /= coverage-1;
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210
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if(fabs(diff) > 1e-8) { //Ignore floating point differences
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211
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return sqrt(diff);
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} else {
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213
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return 0.0;
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214
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}
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215
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error:
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217
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if(v) destroyVals_t(v);
|
218
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errno = ENOMEM;
|
219
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return strtod("NaN", NULL);
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220
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}
|
221
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+
|
222
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//This uses compensated summation to account for finite precision math
|
223
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static double intDev(bwOverlappingIntervals_t* ints, uint32_t start, uint32_t end) {
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224
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double v1 = 0.0, mean, rv;
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225
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uint32_t nBases = 0, i, start_use, end_use;
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226
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+
|
227
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if(!ints->l) return strtod("NaN", NULL);
|
228
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mean = intMean(ints, start, end);
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229
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|
230
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for(i=0; i<ints->l; i++) {
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231
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start_use = ints->start[i];
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232
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end_use = ints->end[i];
|
233
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if(ints->start[i] < start) start_use = start;
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234
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if(ints->end[i] > end) end_use = end;
|
235
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+
nBases += end_use-start_use;
|
236
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+
v1 += (end_use-start_use) * pow(ints->value[i]-mean, 2.0); //running sum of squared difference
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237
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+
}
|
238
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+
|
239
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+
if(nBases>=2) rv = sqrt(v1/(nBases-1));
|
240
|
+
else if(nBases==1) rv = sqrt(v1);
|
241
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+
else rv = strtod("NaN", NULL);
|
242
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+
|
243
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return rv;
|
244
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+
}
|
245
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+
|
246
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static double blockMax(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
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247
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uint32_t i, j, isNA = 1;
|
248
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+
double o = strtod("NaN", NULL);
|
249
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struct vals_t *v = NULL;
|
250
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+
|
251
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if(!blocks->n) return o;
|
252
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+
|
253
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+
//Iterate the blocks
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254
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+
for(i=0; i<blocks->n; i++) {
|
255
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+
v = getVals(fp, blocks, i, tid, start, end);
|
256
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+
if(!v) goto error;
|
257
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+
for(j=0; j<v->n; j++) {
|
258
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if(isNA) {
|
259
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o = v->vals[j]->max;
|
260
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isNA = 0;
|
261
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+
} else if(v->vals[j]->max > o) {
|
262
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o = v->vals[j]->max;
|
263
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}
|
264
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+
}
|
265
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destroyVals_t(v);
|
266
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}
|
267
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+
|
268
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return o;
|
269
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+
|
270
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error:
|
271
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destroyVals_t(v);
|
272
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errno = ENOMEM;
|
273
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+
return strtod("NaN", NULL);
|
274
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+
}
|
275
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+
|
276
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+
static double intMax(bwOverlappingIntervals_t* ints) {
|
277
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uint32_t i;
|
278
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double o;
|
279
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+
|
280
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if(ints->l < 1) return strtod("NaN", NULL);
|
281
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+
|
282
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o = ints->value[0];
|
283
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for(i=1; i<ints->l; i++) {
|
284
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if(ints->value[i] > o) o = ints->value[i];
|
285
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+
}
|
286
|
+
|
287
|
+
return o;
|
288
|
+
}
|
289
|
+
|
290
|
+
static double blockMin(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
|
291
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+
uint32_t i, j, isNA = 1;
|
292
|
+
double o = strtod("NaN", NULL);
|
293
|
+
struct vals_t *v = NULL;
|
294
|
+
|
295
|
+
if(!blocks->n) return o;
|
296
|
+
|
297
|
+
//Iterate the blocks
|
298
|
+
for(i=0; i<blocks->n; i++) {
|
299
|
+
v = getVals(fp, blocks, i, tid, start, end);
|
300
|
+
if(!v) goto error;
|
301
|
+
for(j=0; j<v->n; j++) {
|
302
|
+
if(isNA) {
|
303
|
+
o = v->vals[j]->min;
|
304
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+
isNA = 0;
|
305
|
+
} else if(v->vals[j]->min < o) o = v->vals[j]->min;
|
306
|
+
}
|
307
|
+
destroyVals_t(v);
|
308
|
+
}
|
309
|
+
|
310
|
+
return o;
|
311
|
+
|
312
|
+
error:
|
313
|
+
destroyVals_t(v);
|
314
|
+
errno = ENOMEM;
|
315
|
+
return strtod("NaN", NULL);
|
316
|
+
}
|
317
|
+
|
318
|
+
static double intMin(bwOverlappingIntervals_t* ints) {
|
319
|
+
uint32_t i;
|
320
|
+
double o;
|
321
|
+
|
322
|
+
if(ints->l < 1) return strtod("NaN", NULL);
|
323
|
+
|
324
|
+
o = ints->value[0];
|
325
|
+
for(i=1; i<ints->l; i++) {
|
326
|
+
if(ints->value[i] < o) o = ints->value[i];
|
327
|
+
}
|
328
|
+
|
329
|
+
return o;
|
330
|
+
}
|
331
|
+
|
332
|
+
//Does UCSC compensate for only partial block/interval overlap?
|
333
|
+
static double blockCoverage(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
|
334
|
+
uint32_t i, j;
|
335
|
+
double o = 0.0;
|
336
|
+
struct vals_t *v = NULL;
|
337
|
+
|
338
|
+
if(!blocks->n) return strtod("NaN", NULL);
|
339
|
+
|
340
|
+
//Iterate over the blocks
|
341
|
+
for(i=0; i<blocks->n; i++) {
|
342
|
+
v = getVals(fp, blocks, i, tid, start, end);
|
343
|
+
if(!v) goto error;
|
344
|
+
for(j=0; j<v->n; j++) {
|
345
|
+
o+= v->vals[j]->nBases * v->vals[j]->scalar;
|
346
|
+
}
|
347
|
+
destroyVals_t(v);
|
348
|
+
}
|
349
|
+
|
350
|
+
if(o == 0.0) return strtod("NaN", NULL);
|
351
|
+
return o;
|
352
|
+
|
353
|
+
error:
|
354
|
+
destroyVals_t(v);
|
355
|
+
errno = ENOMEM;
|
356
|
+
return strtod("NaN", NULL);
|
357
|
+
}
|
358
|
+
|
359
|
+
static double intCoverage(bwOverlappingIntervals_t* ints, uint32_t start, uint32_t end) {
|
360
|
+
uint32_t i, start_use, end_use;
|
361
|
+
double o = 0.0;
|
362
|
+
|
363
|
+
if(!ints->l) return strtod("NaN", NULL);
|
364
|
+
|
365
|
+
for(i=0; i<ints->l; i++) {
|
366
|
+
start_use = ints->start[i];
|
367
|
+
end_use = ints->end[i];
|
368
|
+
if(start_use < start) start_use = start;
|
369
|
+
if(end_use > end) end_use = end;
|
370
|
+
o += end_use - start_use;
|
371
|
+
}
|
372
|
+
|
373
|
+
return o/(end-start);
|
374
|
+
}
|
375
|
+
|
376
|
+
static double blockSum(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
|
377
|
+
uint32_t i, j, sizeUse;
|
378
|
+
double o = 0.0;
|
379
|
+
struct vals_t *v = NULL;
|
380
|
+
|
381
|
+
if(!blocks->n) return strtod("NaN", NULL);
|
382
|
+
|
383
|
+
//Iterate over the blocks
|
384
|
+
for(i=0; i<blocks->n; i++) {
|
385
|
+
v = getVals(fp, blocks, i, tid, start, end);
|
386
|
+
if(!v) goto error;
|
387
|
+
for(j=0; j<v->n; j++) {
|
388
|
+
//Multiply the block average by min(bases covered, block overlap with interval)
|
389
|
+
sizeUse = v->vals[j]->scalar;
|
390
|
+
if(sizeUse > v->vals[j]->nBases) sizeUse = v->vals[j]->nBases;
|
391
|
+
o+= (v->vals[j]->sum * sizeUse) / v->vals[j]->nBases;
|
392
|
+
}
|
393
|
+
destroyVals_t(v);
|
394
|
+
}
|
395
|
+
|
396
|
+
if(o == 0.0) return strtod("NaN", NULL);
|
397
|
+
return o;
|
398
|
+
|
399
|
+
error:
|
400
|
+
destroyVals_t(v);
|
401
|
+
errno = ENOMEM;
|
402
|
+
return strtod("NaN", NULL);
|
403
|
+
}
|
404
|
+
|
405
|
+
static double intSum(bwOverlappingIntervals_t* ints, uint32_t start, uint32_t end) {
|
406
|
+
uint32_t i, start_use, end_use;
|
407
|
+
double o = 0.0;
|
408
|
+
|
409
|
+
if(!ints->l) return strtod("NaN", NULL);
|
410
|
+
|
411
|
+
for(i=0; i<ints->l; i++) {
|
412
|
+
start_use = ints->start[i];
|
413
|
+
end_use = ints->end[i];
|
414
|
+
if(start_use < start) start_use = start;
|
415
|
+
if(end_use > end) end_use = end;
|
416
|
+
o += (end_use - start_use) * ints->value[i];
|
417
|
+
}
|
418
|
+
|
419
|
+
return o;
|
420
|
+
}
|
421
|
+
|
422
|
+
//Returns NULL on error, otherwise a double* that needs to be free()d
|
423
|
+
double *bwStatsFromZoom(bigWigFile_t *fp, int32_t level, uint32_t tid, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type) {
|
424
|
+
bwOverlapBlock_t *blocks = NULL;
|
425
|
+
double *output = NULL;
|
426
|
+
uint32_t pos = start, i, end2;
|
427
|
+
|
428
|
+
if(!fp->hdr->zoomHdrs->idx[level]) {
|
429
|
+
fp->hdr->zoomHdrs->idx[level] = bwReadIndex(fp, fp->hdr->zoomHdrs->indexOffset[level]);
|
430
|
+
if(!fp->hdr->zoomHdrs->idx[level]) return NULL;
|
431
|
+
}
|
432
|
+
errno = 0; //Sometimes libCurls sets and then doesn't unset errno on errors
|
433
|
+
|
434
|
+
output = malloc(sizeof(double)*nBins);
|
435
|
+
if(!output) return NULL;
|
436
|
+
|
437
|
+
for(i=0, pos=start; i<nBins; i++) {
|
438
|
+
end2 = start + ((double)(end-start)*(i+1))/((int) nBins);
|
439
|
+
blocks = walkRTreeNodes(fp, fp->hdr->zoomHdrs->idx[level]->root, tid, pos, end2);
|
440
|
+
if(!blocks) goto error;
|
441
|
+
|
442
|
+
switch(type) {
|
443
|
+
case 0:
|
444
|
+
//mean
|
445
|
+
output[i] = blockMean(fp, blocks, tid, pos, end2);
|
446
|
+
break;
|
447
|
+
case 1:
|
448
|
+
//stdev
|
449
|
+
output[i] = blockDev(fp, blocks, tid, pos, end2);
|
450
|
+
break;
|
451
|
+
case 2:
|
452
|
+
//max
|
453
|
+
output[i] = blockMax(fp, blocks, tid, pos, end2);
|
454
|
+
break;
|
455
|
+
case 3:
|
456
|
+
//min
|
457
|
+
output[i] = blockMin(fp, blocks, tid, pos, end2);
|
458
|
+
break;
|
459
|
+
case 4:
|
460
|
+
//cov
|
461
|
+
output[i] = blockCoverage(fp, blocks, tid, pos, end2)/(end2-pos);
|
462
|
+
break;
|
463
|
+
case 5:
|
464
|
+
//sum
|
465
|
+
output[i] = blockSum(fp, blocks, tid, pos, end2);
|
466
|
+
break;
|
467
|
+
default:
|
468
|
+
goto error;
|
469
|
+
break;
|
470
|
+
}
|
471
|
+
if(errno) goto error;
|
472
|
+
destroyBWOverlapBlock(blocks);
|
473
|
+
pos = end2;
|
474
|
+
}
|
475
|
+
|
476
|
+
return output;
|
477
|
+
|
478
|
+
error:
|
479
|
+
fprintf(stderr, "got an error in bwStatsFromZoom in the range %"PRIu32"-%"PRIu32": %s\n", pos, end2, strerror(errno));
|
480
|
+
if(blocks) destroyBWOverlapBlock(blocks);
|
481
|
+
if(output) free(output);
|
482
|
+
return NULL;
|
483
|
+
}
|
484
|
+
|
485
|
+
double *bwStatsFromFull(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type) {
|
486
|
+
bwOverlappingIntervals_t *ints = NULL;
|
487
|
+
double *output = malloc(sizeof(double)*nBins);
|
488
|
+
uint32_t i, pos = start, end2;
|
489
|
+
if(!output) return NULL;
|
490
|
+
|
491
|
+
for(i=0; i<nBins; i++) {
|
492
|
+
end2 = start + ((double)(end-start)*(i+1))/((int) nBins);
|
493
|
+
ints = bwGetOverlappingIntervals(fp, chrom, pos, end2);
|
494
|
+
|
495
|
+
if(!ints) {
|
496
|
+
output[i] = strtod("NaN", NULL);
|
497
|
+
continue;
|
498
|
+
}
|
499
|
+
|
500
|
+
switch(type) {
|
501
|
+
default :
|
502
|
+
case 0:
|
503
|
+
output[i] = intMean(ints, pos, end2);
|
504
|
+
break;
|
505
|
+
case 1:
|
506
|
+
output[i] = intDev(ints, pos, end2);
|
507
|
+
break;
|
508
|
+
case 2:
|
509
|
+
output[i] = intMax(ints);
|
510
|
+
break;
|
511
|
+
case 3:
|
512
|
+
output[i] = intMin(ints);
|
513
|
+
break;
|
514
|
+
case 4:
|
515
|
+
output[i] = intCoverage(ints, pos, end2);
|
516
|
+
break;
|
517
|
+
case 5:
|
518
|
+
output[i] = intSum(ints, pos, end2);
|
519
|
+
break;
|
520
|
+
}
|
521
|
+
bwDestroyOverlappingIntervals(ints);
|
522
|
+
pos = end2;
|
523
|
+
}
|
524
|
+
|
525
|
+
return output;
|
526
|
+
}
|
527
|
+
|
528
|
+
//Returns a list of floats of length nBins that must be free()d
|
529
|
+
//On error, NULL is returned
|
530
|
+
double *bwStats(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type) {
|
531
|
+
int32_t level = determineZoomLevel(fp, ((double)(end-start))/((int) nBins));
|
532
|
+
uint32_t tid = bwGetTid(fp, chrom);
|
533
|
+
if(tid == (uint32_t) -1) return NULL;
|
534
|
+
|
535
|
+
if(level == -1) return bwStatsFromFull(fp, chrom, start, end, nBins, type);
|
536
|
+
return bwStatsFromZoom(fp, level, tid, start, end, nBins, type);
|
537
|
+
}
|