bio-bigwig 0.0.1 → 0.0.2

data/ext/bio/bigwig/libBigWig/bwStats.c

@@ -1,537 +0,0 @@
-#include "bigWig.h"
-#include "bwCommon.h"
-#include <errno.h>
-#include <stdlib.h>
-#include <zlib.h>
-#include <math.h>
-#include <string.h>
-
-//Returns -1 if there are no applicable levels, otherwise an integer indicating the most appropriate level.
-//Like Kent's library, this divides the desired bin size by 2 to minimize the effect of blocks overlapping multiple bins
-static int32_t determineZoomLevel(bigWigFile_t *fp, int basesPerBin) {
-    int32_t out = -1;
-    int64_t diff;
-    uint32_t bestDiff = -1;
-    uint16_t i;
-
-    basesPerBin/=2;
-    for(i=0; i<fp->hdr->nLevels; i++) {
-        diff = basesPerBin - (int64_t) fp->hdr->zoomHdrs->level[i];
-        if(diff >= 0 && diff < bestDiff) {
-            bestDiff = diff;
-            out = i;
-        }
-    }
-    return out;
-}
-
-/// @cond SKIP
-struct val_t {
-    uint32_t nBases;
-    float min, max, sum, sumsq;
-    double scalar;
-};
-
-struct vals_t {
-    uint32_t n;
-    struct val_t **vals;
-};
-/// @endcond
-
-void destroyVals_t(struct vals_t *v) {
-    uint32_t i;
-    if(!v) return;
-    for(i=0; i<v->n; i++) free(v->vals[i]);
-    if(v->vals) free(v->vals);
-    free(v);
-}
-
-//Determine the base-pair overlap between an interval and a block
-double getScalar(uint32_t i_start, uint32_t i_end, uint32_t b_start, uint32_t b_end) {
-    double rv = 0.0;
-    if(b_start <= i_start) {
-        if(b_end > i_start) rv = ((double)(b_end - i_start))/(b_end-b_start);
-    } else if(b_start < i_end) {
-        if(b_end < i_end) rv = ((double)(b_end - b_start))/(b_end-b_start);
-        else rv = ((double)(i_end - b_start))/(b_end-b_start);
-    }
-
-    return rv;
-}
-
-//Returns NULL on error
-static struct vals_t *getVals(bigWigFile_t *fp, bwOverlapBlock_t *o, int i, uint32_t tid, uint32_t start, uint32_t end) {
-    void *buf = NULL, *compBuf = NULL;
-    uLongf sz = fp->hdr->bufSize;
-    int compressed = 0, rv;
-    uint32_t *p, vtid, vstart, vend;
-    struct vals_t *vals = NULL;
-    struct val_t *v = NULL;
-
-    if(sz) {
-        compressed = 1;
-        buf = malloc(sz); 
-    }
-    sz = 0; //This is now the size of the compressed buffer
-
-    if(bwSetPos(fp, o->offset[i])) goto error;
-
-    vals = calloc(1,sizeof(struct vals_t));
-    if(!vals) goto error;
-
-    v = malloc(sizeof(struct val_t));
-    if(!v) goto error;
-
-    if(sz < o->size[i]) compBuf = malloc(o->size[i]);
-    if(!compBuf) goto error;
-
-    if(bwRead(compBuf, o->size[i], 1, fp) != 1) goto error;
-    if(compressed) {
-        sz = fp->hdr->bufSize;
-        rv = uncompress(buf, &sz, compBuf, o->size[i]);
-        if(rv != Z_OK) goto error;
-    } else {
-        buf = compBuf;
-        sz = o->size[i];
-    }
-
-    p = buf;
-    while(((uLongf) ((void*)p-buf)) < sz) {
-        vtid = p[0];
-        vstart = p[1];
-        vend = p[2];
-        v->nBases = p[3];
-        v->min = ((float*) p)[4];
-        v->max = ((float*) p)[5];
-        v->sum = ((float*) p)[6];
-        v->sumsq = ((float*) p)[7];
-        v->scalar = getScalar(start, end, vstart, vend);
-
-        if(tid == vtid) {
-            if((start <= vstart && end > vstart) || (start < vend && start >= vstart)) {
-                vals->vals = realloc(vals->vals, sizeof(struct val_t*)*(vals->n+1));
-                if(!vals->vals) goto error;
-                vals->vals[vals->n++] = v;
-                v = malloc(sizeof(struct val_t));
-                if(!v) goto error;
-            }
-            if(vstart > end) break;
-        } else if(vtid > tid) {
-            break;
-        }
-        p+=8;
-    }
-
-    free(v);
-    free(buf);
-    if(compressed) free(compBuf);
-    return vals;
-
-error:
-    if(buf) free(buf);
-    if(compBuf && compressed) free(compBuf);
-    if(v) free(v);
-    destroyVals_t(vals);
-    return NULL;
-}
-
-//On error, errno is set to ENOMEM and NaN is returned (though NaN can be returned normally)
-static double blockMean(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
-    uint32_t i, j;
-    double output = 0.0, coverage = 0.0;
-    struct vals_t *v = NULL;
-
-    if(!blocks->n) return strtod("NaN", NULL);
-
-    //Iterate over the blocks
-    for(i=0; i<blocks->n; i++) {
-        v = getVals(fp, blocks, i, tid, start, end);
-        if(!v) goto error;
-        for(j=0; j<v->n; j++) {
-            output += v->vals[j]->sum * v->vals[j]->scalar;
-            coverage += v->vals[j]->nBases * v->vals[j]->scalar;
-        }
-        destroyVals_t(v);
-    }
-
-
-    if(!coverage) return strtod("NaN", NULL);
-
-    return output/coverage;
-
-error:
-    if(v) free(v);
-    errno = ENOMEM;
-    return strtod("NaN", NULL);
-}
-
-static double intMean(bwOverlappingIntervals_t* ints, uint32_t start, uint32_t end) {
-    double sum = 0.0;
-    uint32_t nBases = 0, i, start_use, end_use;
-
-    if(!ints->l) return strtod("NaN", NULL);
-
-    for(i=0; i<ints->l; i++) {
-        start_use = ints->start[i];
-        end_use = ints->end[i];
-        if(ints->start[i] < start) start_use = start;
-        if(ints->end[i] > end) end_use = end;
-        nBases += end_use-start_use;
-        sum += (end_use-start_use)*((double) ints->value[i]);
-    }
-
-    return sum/nBases;
-}
-
-//Does UCSC compensate for partial block/range overlap?
-static double blockDev(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
-    uint32_t i, j;
-    double mean = 0.0, ssq = 0.0, coverage = 0.0, diff;
-    struct vals_t *v = NULL;
-
-    if(!blocks->n) return strtod("NaN", NULL);
-
-    //Iterate over the blocks
-    for(i=0; i<blocks->n; i++) {
-        v = getVals(fp, blocks, i, tid, start, end);
-        if(!v) goto error;
-        for(j=0; j<v->n; j++) {
-            coverage += v->vals[j]->nBases * v->vals[j]->scalar;
-            mean += v->vals[j]->sum * v->vals[j]->scalar;
-            ssq += v->vals[j]->sumsq * v->vals[j]->scalar;
-        }
-        destroyVals_t(v);
-        v = NULL;
-    }
-
-    if(coverage<=1.0) return strtod("NaN", NULL);
-    diff = ssq-mean*mean/coverage;
-    if(coverage > 1.0) diff /= coverage-1;
-    if(fabs(diff) > 1e-8) { //Ignore floating point differences
-        return sqrt(diff);
-    } else {
-        return 0.0;
-    }
-
-error:
-    if(v) destroyVals_t(v);
-    errno = ENOMEM;
-    return strtod("NaN", NULL);
-}
-
-//This uses compensated summation to account for finite precision math
-static double intDev(bwOverlappingIntervals_t* ints, uint32_t start, uint32_t end) {
-    double v1 = 0.0, mean, rv;
-    uint32_t nBases = 0, i, start_use, end_use;
-
-    if(!ints->l) return strtod("NaN", NULL);
-    mean = intMean(ints, start, end);
-
-    for(i=0; i<ints->l; i++) {
-        start_use = ints->start[i];
-        end_use = ints->end[i];
-        if(ints->start[i] < start) start_use = start;
-        if(ints->end[i] > end) end_use = end;
-        nBases += end_use-start_use;
-        v1 += (end_use-start_use) * pow(ints->value[i]-mean, 2.0); //running sum of squared difference
-    }
-
-    if(nBases>=2) rv = sqrt(v1/(nBases-1));
-    else if(nBases==1) rv = sqrt(v1);
-    else rv = strtod("NaN", NULL);
-
-    return rv;
-}
-
-static double blockMax(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
-    uint32_t i, j, isNA = 1;
-    double o = strtod("NaN", NULL);
-    struct vals_t *v = NULL;
-
-    if(!blocks->n) return o;
-
-    //Iterate the blocks
-    for(i=0; i<blocks->n; i++) {
-        v = getVals(fp, blocks, i, tid, start, end);
-        if(!v) goto error;
-        for(j=0; j<v->n; j++) {
-            if(isNA) {
-                o = v->vals[j]->max;
-                isNA = 0;
-            } else if(v->vals[j]->max > o) {
-                o = v->vals[j]->max;
-            }
-        }
-        destroyVals_t(v);
-    }
-
-    return o;
-
-error:
-    destroyVals_t(v);
-    errno = ENOMEM;
-    return strtod("NaN", NULL);
-}
-
-static double intMax(bwOverlappingIntervals_t* ints) {
-    uint32_t i;
-    double o;
-
-    if(ints->l < 1) return strtod("NaN", NULL);
-
-    o = ints->value[0];
-    for(i=1; i<ints->l; i++) {
-        if(ints->value[i] > o) o = ints->value[i];
-    }
-
-    return o;
-}
-
-static double blockMin(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
-    uint32_t i, j, isNA = 1;
-    double o = strtod("NaN", NULL);
-    struct vals_t *v = NULL;
-
-    if(!blocks->n) return o;
-
-    //Iterate the blocks
-    for(i=0; i<blocks->n; i++) {
-        v = getVals(fp, blocks, i, tid, start, end);
-        if(!v) goto error;
-        for(j=0; j<v->n; j++) {
-            if(isNA) {
-                o = v->vals[j]->min;
-                isNA = 0;
-            } else if(v->vals[j]->min < o) o = v->vals[j]->min;
-        }
-        destroyVals_t(v);
-    }
-
-    return o;
-
-error:
-    destroyVals_t(v);
-    errno = ENOMEM;
-    return strtod("NaN", NULL);
-}
-
-static double intMin(bwOverlappingIntervals_t* ints) {
-    uint32_t i;
-    double o;
-
-    if(ints->l < 1) return strtod("NaN", NULL);
-
-    o = ints->value[0];
-    for(i=1; i<ints->l; i++) {
-        if(ints->value[i] < o) o = ints->value[i];
-    }
-
-    return o;
-}
-
-//Does UCSC compensate for only partial block/interval overlap?
-static double blockCoverage(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
-    uint32_t i, j;
-    double o = 0.0;
-    struct vals_t *v = NULL;
-
-    if(!blocks->n) return strtod("NaN", NULL);
-
-    //Iterate over the blocks
-    for(i=0; i<blocks->n; i++) {
-        v = getVals(fp, blocks, i, tid, start, end);
-        if(!v) goto error;
-        for(j=0; j<v->n; j++) {
-            o+= v->vals[j]->nBases * v->vals[j]->scalar;
-        }
-        destroyVals_t(v);
-    }
-
-    if(o == 0.0) return strtod("NaN", NULL);
-    return o;
-
-error:
-    destroyVals_t(v);
-    errno = ENOMEM;
-    return strtod("NaN", NULL);
-}
-
-static double intCoverage(bwOverlappingIntervals_t* ints, uint32_t start, uint32_t end) {
-    uint32_t i, start_use, end_use;
-    double o = 0.0;
-
-    if(!ints->l) return strtod("NaN", NULL);
-
-    for(i=0; i<ints->l; i++) {
-        start_use = ints->start[i];
-        end_use = ints->end[i];
-        if(start_use < start) start_use = start;
-        if(end_use > end) end_use = end;
-        o += end_use - start_use;
-    }
-
-    return o/(end-start);
-}
-
-static double blockSum(bigWigFile_t *fp, bwOverlapBlock_t *blocks, uint32_t tid, uint32_t start, uint32_t end) {
-    uint32_t i, j, sizeUse;
-    double o = 0.0;
-    struct vals_t *v = NULL;
-
-    if(!blocks->n) return strtod("NaN", NULL);
-
-    //Iterate over the blocks
-    for(i=0; i<blocks->n; i++) {
-        v = getVals(fp, blocks, i, tid, start, end);
-        if(!v) goto error;
-        for(j=0; j<v->n; j++) {
-            //Multiply the block average by min(bases covered, block overlap with interval)
-            sizeUse = v->vals[j]->scalar;
-            if(sizeUse > v->vals[j]->nBases) sizeUse = v->vals[j]->nBases;
-            o+= (v->vals[j]->sum * sizeUse) / v->vals[j]->nBases;
-        }
-        destroyVals_t(v);
-    }
-
-    if(o == 0.0) return strtod("NaN", NULL);
-    return o;
-
-error:
-    destroyVals_t(v);
-    errno = ENOMEM;
-    return strtod("NaN", NULL);
-}
-
-static double intSum(bwOverlappingIntervals_t* ints, uint32_t start, uint32_t end) {
-    uint32_t i, start_use, end_use;
-    double o = 0.0;
-
-    if(!ints->l) return strtod("NaN", NULL);
-
-    for(i=0; i<ints->l; i++) {
-        start_use = ints->start[i];
-        end_use = ints->end[i];
-        if(start_use < start) start_use = start;
-        if(end_use > end) end_use = end;
-        o += (end_use - start_use) * ints->value[i];
-    }
-
-    return o;
-}
-
-//Returns NULL on error, otherwise a double* that needs to be free()d
-double *bwStatsFromZoom(bigWigFile_t *fp, int32_t level, uint32_t tid, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type) {
-    bwOverlapBlock_t *blocks = NULL;
-    double *output = NULL;
-    uint32_t pos = start, i, end2;
-
-    if(!fp->hdr->zoomHdrs->idx[level]) {
-        fp->hdr->zoomHdrs->idx[level] = bwReadIndex(fp, fp->hdr->zoomHdrs->indexOffset[level]);
-        if(!fp->hdr->zoomHdrs->idx[level]) return NULL;
-    }
-    errno = 0; //Sometimes libCurls sets and then doesn't unset errno on errors
-
-    output = malloc(sizeof(double)*nBins);
-    if(!output) return NULL;
-
-    for(i=0, pos=start; i<nBins; i++) {
-        end2 = start + ((double)(end-start)*(i+1))/((int) nBins);
-        blocks = walkRTreeNodes(fp, fp->hdr->zoomHdrs->idx[level]->root, tid, pos, end2);
-        if(!blocks) goto error;
-
-        switch(type) {
-        case 0:
-            //mean
-            output[i] = blockMean(fp, blocks, tid, pos, end2);
-            break;
-        case 1:
-            //stdev
-            output[i] = blockDev(fp, blocks, tid, pos, end2);
-            break;
-        case 2:
-            //max
-            output[i] = blockMax(fp, blocks, tid, pos, end2);
-            break;
-        case 3:
-            //min
-            output[i] = blockMin(fp, blocks, tid, pos, end2);
-            break;
-        case 4:
-            //cov
-            output[i] = blockCoverage(fp, blocks, tid, pos, end2)/(end2-pos);
-            break;
-        case 5:
-            //sum
-            output[i] = blockSum(fp, blocks, tid, pos, end2);
-            break;
-        default:
-            goto error;
-            break;
-        }
-        if(errno) goto error;
-        destroyBWOverlapBlock(blocks);
-        pos = end2;
-    }
-
-    return output;
-
-error:
-    fprintf(stderr, "got an error in bwStatsFromZoom in the range %"PRIu32"-%"PRIu32": %s\n", pos, end2, strerror(errno));
-    if(blocks) destroyBWOverlapBlock(blocks);
-    if(output) free(output);
-    return NULL;
-}
-
-double *bwStatsFromFull(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type) {
-    bwOverlappingIntervals_t *ints = NULL;
-    double *output = malloc(sizeof(double)*nBins);
-    uint32_t i, pos = start, end2;
-    if(!output) return NULL;
-
-    for(i=0; i<nBins; i++) {
-        end2 = start + ((double)(end-start)*(i+1))/((int) nBins);
-        ints = bwGetOverlappingIntervals(fp, chrom, pos, end2);
-
-        if(!ints) {
-            output[i] = strtod("NaN", NULL);
-            continue;
-        }
-
-        switch(type) {
-        default :
-        case 0:
-            output[i] = intMean(ints, pos, end2);
-            break;
-        case 1:
-            output[i] = intDev(ints, pos, end2);
-            break;
-        case 2:
-            output[i] = intMax(ints);
-            break;
-        case 3:
-            output[i] = intMin(ints);
-            break;
-        case 4:
-            output[i] = intCoverage(ints, pos, end2);
-            break;
-        case 5:
-            output[i] = intSum(ints, pos, end2);
-            break;
-        }
-        bwDestroyOverlappingIntervals(ints);
-        pos = end2;
-    }
-
-    return output;
-}
-
-//Returns a list of floats of length nBins that must be free()d
-//On error, NULL is returned
-double *bwStats(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type) {
-    int32_t level = determineZoomLevel(fp, ((double)(end-start))/((int) nBins));
-    uint32_t tid = bwGetTid(fp, chrom);
-    if(tid == (uint32_t) -1) return NULL;
-
-    if(level == -1) return bwStatsFromFull(fp, chrom, start, end, nBins, type);
-    return bwStatsFromZoom(fp, level, tid, start, end, nBins, type);
-}