bio-bigwig 0.0.1

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

@@ -0,0 +1,803 @@
+#include "bigWig.h"
+#include "bwCommon.h"
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <zlib.h>
+#include <errno.h>
+
+static uint32_t roundup(uint32_t v) {
+    v--;
+    v |= v >> 1;
+    v |= v >> 2;
+    v |= v >> 4;
+    v |= v >> 8;
+    v |= v >> 16;
+    v++;
+    return v;
+}
+
+//Returns the root node on success and NULL on error
+static bwRTree_t *readRTreeIdx(bigWigFile_t *fp, uint64_t offset) {
+    uint32_t magic;
+    bwRTree_t *node;
+
+    if(!offset) {
+        if(bwSetPos(fp, fp->hdr->indexOffset)) return NULL;
+    } else {
+        if(bwSetPos(fp, offset)) return NULL;
+    }
+
+    if(bwRead(&magic, sizeof(uint32_t), 1, fp) != 1) return NULL;
+    if(magic != IDX_MAGIC) {
+        fprintf(stderr, "[readRTreeIdx] Mismatch in the magic number!\n");
+        return NULL;
+    }
+
+    node = calloc(1, sizeof(bwRTree_t));
+    if(!node) return NULL;
+
+    if(bwRead(&(node->blockSize), sizeof(uint32_t), 1, fp) != 1) goto error;
+    if(bwRead(&(node->nItems), sizeof(uint64_t), 1, fp) != 1) goto error;
+    if(bwRead(&(node->chrIdxStart), sizeof(uint32_t), 1, fp) != 1) goto error;
+    if(bwRead(&(node->baseStart), sizeof(uint32_t), 1, fp) != 1) goto error;
+    if(bwRead(&(node->chrIdxEnd), sizeof(uint32_t), 1, fp) != 1) goto error;
+    if(bwRead(&(node->baseEnd), sizeof(uint32_t), 1, fp) != 1) goto error;
+    if(bwRead(&(node->idxSize), sizeof(uint64_t), 1, fp) != 1) goto error;
+    if(bwRead(&(node->nItemsPerSlot), sizeof(uint32_t), 1, fp) != 1) goto error;
+    //Padding
+    if(bwRead(&(node->blockSize), sizeof(uint32_t), 1, fp) != 1) goto error;
+    node->rootOffset = bwTell(fp);
+
+    //For remote files, libCurl sometimes sets errno to 115 and doesn't clear it
+    errno = 0;
+
+    return node;
+
+error:
+    free(node);
+    return NULL;
+}
+
+//Returns a bwRTreeNode_t on success and NULL on an error
+//For the root node, set offset to 0
+static bwRTreeNode_t *bwGetRTreeNode(bigWigFile_t *fp, uint64_t offset) {
+    bwRTreeNode_t *node = NULL;
+    uint8_t padding;
+    uint16_t i;
+    if(offset) {
+        if(bwSetPos(fp, offset)) return NULL;
+    } else {
+        //seek
+        if(bwSetPos(fp, fp->idx->rootOffset)) return NULL;
+    }
+
+    node = calloc(1, sizeof(bwRTreeNode_t));
+    if(!node) return NULL;
+
+    if(bwRead(&(node->isLeaf), sizeof(uint8_t), 1, fp) != 1) goto error;
+    if(bwRead(&padding, sizeof(uint8_t), 1, fp) != 1) goto error;
+    if(bwRead(&(node->nChildren), sizeof(uint16_t), 1, fp) != 1) goto error;
+
+    node->chrIdxStart = malloc(sizeof(uint32_t)*(node->nChildren));
+    if(!node->chrIdxStart) goto error;
+    node->baseStart = malloc(sizeof(uint32_t)*(node->nChildren));
+    if(!node->baseStart) goto error;
+    node->chrIdxEnd = malloc(sizeof(uint32_t)*(node->nChildren));
+    if(!node->chrIdxEnd) goto error;
+    node->baseEnd = malloc(sizeof(uint32_t)*(node->nChildren));
+    if(!node->baseEnd) goto error;
+    node->dataOffset = malloc(sizeof(uint64_t)*(node->nChildren));
+    if(!node->dataOffset) goto error;
+    if(node->isLeaf) {
+        node->x.size = malloc(node->nChildren * sizeof(uint64_t));
+        if(!node->x.size) goto error;
+    } else {
+        node->x.child = calloc(node->nChildren, sizeof(struct bwRTreeNode_t *));
+        if(!node->x.child) goto error;
+    }
+    for(i=0; i<node->nChildren; i++) {
+        if(bwRead(&(node->chrIdxStart[i]), sizeof(uint32_t), 1, fp) != 1) goto error;
+        if(bwRead(&(node->baseStart[i]), sizeof(uint32_t), 1, fp) != 1) goto error;
+        if(bwRead(&(node->chrIdxEnd[i]), sizeof(uint32_t), 1, fp) != 1) goto error;
+        if(bwRead(&(node->baseEnd[i]), sizeof(uint32_t), 1, fp) != 1) goto error;
+        if(bwRead(&(node->dataOffset[i]), sizeof(uint64_t), 1, fp) != 1) goto error;
+        if(node->isLeaf) {
+            if(bwRead(&(node->x.size[i]), sizeof(uint64_t), 1, fp) != 1) goto error;
+        }
+    }
+
+    return node;
+
+error:
+    if(node->chrIdxStart) free(node->chrIdxStart);
+    if(node->baseStart) free(node->baseStart);
+    if(node->chrIdxEnd) free(node->chrIdxEnd);
+    if(node->baseEnd) free(node->baseEnd);
+    if(node->dataOffset) free(node->dataOffset);
+    if(node->isLeaf && node->x.size) free(node->x.size);
+    else if((!node->isLeaf) && node->x.child) free(node->x.child);
+    free(node);
+    return NULL;
+}
+
+void destroyBWOverlapBlock(bwOverlapBlock_t *b) {
+    if(!b) return;
+    if(b->size) free(b->size);
+    if(b->offset) free(b->offset);
+    free(b);
+}
+
+//Returns a bwOverlapBlock_t * object or NULL on error.
+static bwOverlapBlock_t *overlapsLeaf(bwRTreeNode_t *node, uint32_t tid, uint32_t start, uint32_t end) {
+    uint16_t i, idx = 0;
+    bwOverlapBlock_t *o = calloc(1, sizeof(bwOverlapBlock_t));
+    if(!o) return NULL;
+
+    for(i=0; i<node->nChildren; i++) {
+        if(tid < node->chrIdxStart[i]) break;
+        if(tid > node->chrIdxEnd[i]) continue;
+
+        /*
+          The individual blocks can theoretically span multiple contigs.
+          So if we treat the first/last contig in the range as special 
+          but anything in the middle is a guaranteed match
+        */
+        if(node->chrIdxStart[i] != node->chrIdxEnd[i]) {
+            if(tid == node->chrIdxStart[i]) {
+                if(node->baseStart[i] >= end) break;
+            } else if(tid == node->chrIdxEnd[i]) {
+                if(node->baseEnd[i] <= start) continue;
+            }
+        } else {
+            if(node->baseStart[i] >= end || node->baseEnd[i] <= start) continue;
+        }
+        o->n++;
+    }
+
+    if(o->n) {
+        o->offset = malloc(sizeof(uint64_t) * (o->n));
+        if(!o->offset) goto error;
+        o->size = malloc(sizeof(uint64_t) * (o->n));
+        if(!o->size) goto error;
+
+        for(i=0; i<node->nChildren; i++) {
+            if(tid < node->chrIdxStart[i]) break;
+            if(tid < node->chrIdxStart[i] || tid > node->chrIdxEnd[i]) continue;
+            if(node->chrIdxStart[i] != node->chrIdxEnd[i]) {
+                if(tid == node->chrIdxStart[i]) {
+                    if(node->baseStart[i] >= end) continue;
+                } else if(tid == node->chrIdxEnd[i]) {
+                    if(node->baseEnd[i] <= start) continue;
+                }
+            } else {
+                if(node->baseStart[i] >= end || node->baseEnd[i] <= start) continue;
+            }
+            o->offset[idx] = node->dataOffset[i];
+            o->size[idx++] = node->x.size[i];
+            if(idx >= o->n) break;
+        }
+    }
+
+    if(idx != o->n) { //This should never happen
+        fprintf(stderr, "[overlapsLeaf] Mismatch between number of overlaps calculated and found!\n");
+        goto error;
+    }
+
+    return o;
+
+error:
+    if(o) destroyBWOverlapBlock(o);
+    return NULL;
+}
+
+//This will free l2 unless there's an error!
+//Returns NULL on error, otherwise the merged lists
+static bwOverlapBlock_t *mergeOverlapBlocks(bwOverlapBlock_t *b1, bwOverlapBlock_t *b2) {
+    uint64_t i,j;
+    if(!b2) return b1;
+    if(!b2->n) {
+        destroyBWOverlapBlock(b2);
+        return b1;
+    }
+    if(!b1->n) {
+        destroyBWOverlapBlock(b1);
+        return b2;
+    }
+    j = b1->n;
+    b1->n += b2->n;
+    b1->offset = realloc(b1->offset, sizeof(uint64_t) * (b1->n+b2->n));
+    if(!b1->offset) goto error;
+    b1->size = realloc(b1->size, sizeof(uint64_t) * (b1->n+b2->n));
+    if(!b1->size) goto error;
+
+    for(i=0; i<b2->n; i++) {
+        b1->offset[j+i] = b2->offset[i];
+        b1->size[j+i] = b2->size[i];
+    }
+    destroyBWOverlapBlock(b2);
+    return b1;
+
+error:
+    destroyBWOverlapBlock(b1);
+    return NULL;
+}
+
+//Returns NULL and sets nOverlaps to >0 on error, otherwise nOverlaps is the number of file offsets returned
+//The output needs to be free()d if not NULL (likewise with *sizes)
+static bwOverlapBlock_t *overlapsNonLeaf(bigWigFile_t *fp, bwRTreeNode_t *node, uint32_t tid, uint32_t start, uint32_t end) {
+    uint16_t i;
+    bwOverlapBlock_t *nodeBlocks, *output = calloc(1, sizeof(bwOverlapBlock_t));
+    if(!output) return NULL;
+
+    for(i=0; i<node->nChildren; i++) {
+        if(tid < node->chrIdxStart[i]) break;
+        if(tid < node->chrIdxStart[i] || tid > node->chrIdxEnd[i]) continue;
+        if(node->chrIdxStart[i] != node->chrIdxEnd[i]) { //child spans contigs
+            if(tid == node->chrIdxStart[i]) {
+                if(node->baseStart[i] >= end) continue;
+            } else if(tid == node->chrIdxEnd[i]) {
+                if(node->baseEnd[i] <= start) continue;
+            }
+        } else {
+            if(end <= node->baseStart[i] || start >= node->baseEnd[i]) continue;
+        }
+
+        //We have an overlap!
+        if(!node->x.child[i])
+          node->x.child[i] = bwGetRTreeNode(fp, node->dataOffset[i]);
+        if(!node->x.child[i]) goto error;
+
+        if(node->x.child[i]->isLeaf) { //leaf
+            nodeBlocks = overlapsLeaf(node->x.child[i], tid, start, end);
+        } else { //non-leaf
+            nodeBlocks = overlapsNonLeaf(fp, node->x.child[i], tid, start, end);
+        }
+
+        //The output is processed the same regardless of leaf/non-leaf
+        if(!nodeBlocks) goto error;
+        else {
+            output = mergeOverlapBlocks(output, nodeBlocks);
+            if(!output) {
+                destroyBWOverlapBlock(nodeBlocks);
+                goto error;
+            }
+        }
+    }
+
+    return output;
+
+error:
+    destroyBWOverlapBlock(output);
+    return NULL;
+}
+
+//Returns NULL and sets nOverlaps to >0 on error, otherwise nOverlaps is the number of file offsets returned
+//The output must be free()d
+bwOverlapBlock_t *walkRTreeNodes(bigWigFile_t *bw, bwRTreeNode_t *root, uint32_t tid, uint32_t start, uint32_t end) {
+    if(root->isLeaf) return overlapsLeaf(root, tid, start, end);
+    return overlapsNonLeaf(bw, root, tid, start, end);
+}
+
+//In reality, a hash or some sort of tree structure is probably faster...
+//Return -1 (AKA 0xFFFFFFFF...) on "not there", so we can hold (2^32)-1 items.
+uint32_t bwGetTid(bigWigFile_t *fp, char *chrom) {
+    uint32_t i;
+    if(!chrom) return -1;
+    for(i=0; i<fp->cl->nKeys; i++) {
+        if(strcmp(chrom, fp->cl->chrom[i]) == 0) return i;
+    }
+    return -1;
+}
+
+static bwOverlapBlock_t *bwGetOverlappingBlocks(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end) {
+    uint32_t tid = bwGetTid(fp, chrom);
+
+    if(tid == (uint32_t) -1) {
+        fprintf(stderr, "[bwGetOverlappingBlocks] Non-existent contig: %s\n", chrom);
+        return NULL;
+    }
+
+    //Get the info if needed
+    if(!fp->idx) {
+        fp->idx = readRTreeIdx(fp, fp->hdr->indexOffset);
+        if(!fp->idx) {
+            return NULL;
+        }
+    }
+
+    if(!fp->idx->root) fp->idx->root = bwGetRTreeNode(fp, 0);
+    if(!fp->idx->root) return NULL;
+
+    return walkRTreeNodes(fp, fp->idx->root, tid, start, end);
+}
+
+void bwFillDataHdr(bwDataHeader_t *hdr, void *b) {
+    hdr->tid = ((uint32_t*)b)[0];
+    hdr->start = ((uint32_t*)b)[1];
+    hdr->end = ((uint32_t*)b)[2];
+    hdr->step = ((uint32_t*)b)[3];
+    hdr->span = ((uint32_t*)b)[4];
+    hdr->type = ((uint8_t*)b)[20];
+    hdr->nItems = ((uint16_t*)b)[11];
+}
+
+void bwDestroyOverlappingIntervals(bwOverlappingIntervals_t *o) {
+    if(!o) return;
+    if(o->start) free(o->start);
+    if(o->end) free(o->end);
+    if(o->value) free(o->value);
+    free(o);
+}
+
+void bbDestroyOverlappingEntries(bbOverlappingEntries_t *o) {
+    uint32_t i;
+    if(!o) return;
+    if(o->start) free(o->start);
+    if(o->end) free(o->end);
+    if(o->str) {
+        for(i=0; i<o->l; i++) {
+            if(o->str[i]) free(o->str[i]);
+        }
+        free(o->str);
+    }
+    free(o);
+}
+
+//Returns NULL on error, in which case o has been free()d
+static bwOverlappingIntervals_t *pushIntervals(bwOverlappingIntervals_t *o, uint32_t start, uint32_t end, float value) {
+    if(o->l+1 >= o->m) {
+        o->m = roundup(o->l+1);
+        o->start = realloc(o->start, o->m * sizeof(uint32_t));
+        if(!o->start) goto error;
+        o->end = realloc(o->end, o->m * sizeof(uint32_t));
+        if(!o->end) goto error;
+        o->value = realloc(o->value, o->m * sizeof(float));
+        if(!o->value) goto error;
+    }
+    o->start[o->l] = start;
+    o->end[o->l] = end;
+    o->value[o->l++] = value;
+    return o;
+
+error:
+    bwDestroyOverlappingIntervals(o);
+    return NULL;
+}
+
+static bbOverlappingEntries_t *pushBBIntervals(bbOverlappingEntries_t *o, uint32_t start, uint32_t end, char *str, int withString) {
+    if(o->l+1 >= o->m) {
+        o->m = roundup(o->l+1);
+        o->start = realloc(o->start, o->m * sizeof(uint32_t));
+        if(!o->start) goto error;
+        o->end = realloc(o->end, o->m * sizeof(uint32_t));
+        if(!o->end) goto error;
+        if(withString) {
+            o->str = realloc(o->str, o->m * sizeof(char**));
+            if(!o->str) goto error;
+        }
+    }
+    o->start[o->l] = start;
+    o->end[o->l] = end;
+    if(withString) o->str[o->l] = strdup(str);
+    o->l++;
+    return o;
+
+error:
+    bbDestroyOverlappingEntries(o);
+    return NULL;
+}
+
+//Returns NULL on error
+bwOverlappingIntervals_t *bwGetOverlappingIntervalsCore(bigWigFile_t *fp, bwOverlapBlock_t *o, uint32_t tid, uint32_t ostart, uint32_t oend) {
+    uint64_t i;
+    uint16_t j;
+    int compressed = 0, rv;
+    uLongf sz = fp->hdr->bufSize, tmp;
+    void *buf = NULL, *compBuf = NULL;
+    uint32_t start = 0, end , *p;
+    float value;
+    bwDataHeader_t hdr;
+    bwOverlappingIntervals_t *output = calloc(1, sizeof(bwOverlappingIntervals_t));
+
+    if(!output) goto error;
+
+    if(!o) return output;
+    if(!o->n) return output;
+
+    if(sz) {
+        compressed = 1;
+        buf = malloc(sz);
+    }
+    sz = 0; //This is now the size of the compressed buffer
+
+    for(i=0; i<o->n; i++) {
+        if(bwSetPos(fp, o->offset[i])) goto error;
+
+        if(sz < o->size[i]) {
+            compBuf = realloc(compBuf, o->size[i]);
+            sz = o->size[i];
+        }
+        if(!compBuf) goto error;
+
+        if(bwRead(compBuf, o->size[i], 1, fp) != 1) goto error;
+        if(compressed) {
+            tmp = fp->hdr->bufSize; //This gets over-written by uncompress
+            rv = uncompress(buf, (uLongf *) &tmp, compBuf, o->size[i]);
+            if(rv != Z_OK) goto error;
+        } else {
+            buf = compBuf;
+        }
+
+        //TODO: ensure that tmp is large enough!
+        bwFillDataHdr(&hdr, buf);
+
+        p = ((uint32_t*) buf);
+        p += 6;
+        if(hdr.tid != tid) continue;
+
+        if(hdr.type == 3) start = hdr.start - hdr.step;
+        
+        //FIXME: We should ensure that sz is large enough to hold nItems of the given type
+        for(j=0; j<hdr.nItems; j++) {
+            switch(hdr.type) {
+            case 1:
+                start = *p;
+                p++;
+                end = *p;
+                p++;
+                value = *((float *)p);
+                p++;
+                break;
+            case 2:
+                start = *p;
+                p++;
+                end = start + hdr.span;
+                value = *((float *)p);
+                p++;
+                break;
+            case 3:
+                start += hdr.step;
+                end = start+hdr.span;
+                value = *((float *)p);
+                p++;
+                break;
+            default :
+                goto error;
+                break;
+            }
+
+            if(end <= ostart || start >= oend) continue;
+            //Push the overlap
+            if(!pushIntervals(output, start, end, value)) goto error;
+        }
+    }
+
+    if(compressed && buf) free(buf);
+    if(compBuf) free(compBuf);
+    return output;
+
+error:
+    fprintf(stderr, "[bwGetOverlappingIntervalsCore] Got an error\n");
+    if(output) bwDestroyOverlappingIntervals(output);
+    if(compressed && buf) free(buf);
+    if(compBuf) free(compBuf);
+    return NULL;
+}
+
+bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapBlock_t *o, uint32_t tid, uint32_t ostart, uint32_t oend, int withString) {
+    uint64_t i;
+    int compressed = 0, rv, slen;
+    uLongf sz = fp->hdr->bufSize, tmp = 0;
+    void *buf = NULL, *bufEnd = NULL, *compBuf = NULL;
+    uint32_t entryTid = 0, start = 0, end;
+    char *str;
+    bbOverlappingEntries_t *output = calloc(1, sizeof(bbOverlappingEntries_t));
+
+    if(!output) goto error;
+
+    if(!o) return output;
+    if(!o->n) return output;
+
+    if(sz) {
+        compressed = 1;
+        buf = malloc(sz);
+    }
+    sz = 0; //This is now the size of the compressed buffer
+
+    for(i=0; i<o->n; i++) {
+        if(bwSetPos(fp, o->offset[i])) goto error;
+
+        if(sz < o->size[i]) {
+            compBuf = realloc(compBuf, o->size[i]);
+            sz = o->size[i];
+        }
+        if(!compBuf) goto error;
+
+        if(bwRead(compBuf, o->size[i], 1, fp) != 1) goto error;
+        if(compressed) {
+            tmp = fp->hdr->bufSize; //This gets over-written by uncompress
+            rv = uncompress(buf, (uLongf *) &tmp, compBuf, o->size[i]);
+            if(rv != Z_OK) goto error;
+        } else {
+            buf = compBuf;
+            tmp = o->size[i]; //TODO: Is this correct? Do non-gzipped bigBeds exist?
+        }
+
+        bufEnd = buf + tmp;
+        while(buf < bufEnd) {
+            entryTid = ((uint32_t*)buf)[0];
+            start = ((uint32_t*)buf)[1];
+            end = ((uint32_t*)buf)[2];
+            buf += 12;
+            str = (char*)buf;
+            slen = strlen(str) + 1;
+            buf += slen;
+
+            if(entryTid < tid) continue;
+            if(entryTid > tid) break;
+            if(end <= ostart) continue;
+            if(start >= oend) break;
+
+            //Push the overlap
+            if(!pushBBIntervals(output, start, end, str, withString)) goto error;
+        }
+
+        buf = bufEnd - tmp; //reset the buffer pointer
+    }
+
+    if(compressed && buf) free(buf);
+    if(compBuf) free(compBuf);
+    return output;
+
+error:
+    fprintf(stderr, "[bbGetOverlappingEntriesCore] Got an error\n");
+    buf = bufEnd - tmp;
+    if(output) bbDestroyOverlappingEntries(output);
+    if(compressed && buf) free(buf);
+    if(compBuf) free(compBuf);
+    return NULL;
+}
+
+//Returns NULL on error OR no intervals, which is a bad design...
+bwOverlappingIntervals_t *bwGetOverlappingIntervals(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end) {
+    bwOverlappingIntervals_t *output;
+    uint32_t tid = bwGetTid(fp, chrom);
+    if(tid == (uint32_t) -1) return NULL;
+    bwOverlapBlock_t *blocks = bwGetOverlappingBlocks(fp, chrom, start, end);
+    if(!blocks) return NULL;
+    output = bwGetOverlappingIntervalsCore(fp, blocks, tid, start, end);
+    destroyBWOverlapBlock(blocks);
+    return output;
+}
+
+//Like above, but for bigBed files
+bbOverlappingEntries_t *bbGetOverlappingEntries(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString) {
+    bbOverlappingEntries_t *output;
+    uint32_t tid = bwGetTid(fp, chrom);
+    if(tid == (uint32_t) -1) return NULL;
+    bwOverlapBlock_t *blocks = bwGetOverlappingBlocks(fp, chrom, start, end);
+    if(!blocks) return NULL;
+    output = bbGetOverlappingEntriesCore(fp, blocks, tid, start, end, withString);
+    destroyBWOverlapBlock(blocks);
+    return output;
+}
+
+//Returns NULL on error
+bwOverlapIterator_t *bwOverlappingIntervalsIterator(bigWigFile_t *bw, char *chrom, uint32_t start, uint32_t end, uint32_t blocksPerIteration) {
+    bwOverlapIterator_t *output = NULL;
+    uint64_t n;
+    uint32_t tid = bwGetTid(bw, chrom);
+    if(tid == (uint32_t) -1) return output;
+    output = calloc(1, sizeof(bwOverlapIterator_t));
+    if(!output) return output;
+    bwOverlapBlock_t *blocks = bwGetOverlappingBlocks(bw, chrom, start, end);
+
+    output->bw = bw;
+    output->tid = tid;
+    output->start = start;
+    output->end = end;
+    output->blocks = blocks;
+    output->blocksPerIteration = blocksPerIteration;
+
+    if(blocks) {
+        n = blocks->n;
+        if(n>blocksPerIteration) blocks->n = blocksPerIteration;
+        output->intervals = bwGetOverlappingIntervalsCore(bw, blocks,tid, start, end);
+        blocks->n = n;
+        output->offset = blocksPerIteration;
+    }
+    output->data = output->intervals;
+    return output;
+}
+
+//Returns NULL on error
+bwOverlapIterator_t *bbOverlappingEntriesIterator(bigWigFile_t *bw, char *chrom, uint32_t start, uint32_t end, int withString, uint32_t blocksPerIteration) {
+    bwOverlapIterator_t *output = NULL;
+    uint64_t n;
+    uint32_t tid = bwGetTid(bw, chrom);
+    if(tid == (uint32_t) -1) return output;
+    output = calloc(1, sizeof(bwOverlapIterator_t));
+    if(!output) return output;
+    bwOverlapBlock_t *blocks = bwGetOverlappingBlocks(bw, chrom, start, end);
+
+    output->bw = bw;
+    output->tid = tid;
+    output->start = start;
+    output->end = end;
+    output->blocks = blocks;
+    output->blocksPerIteration = blocksPerIteration;
+    output->withString = withString;
+
+    if(blocks) {
+        n = blocks->n;
+        if(n>blocksPerIteration) blocks->n = blocksPerIteration;
+        output->entries = bbGetOverlappingEntriesCore(bw, blocks,tid, start, end, withString);
+        blocks->n = n;
+        output->offset = blocksPerIteration;
+    }
+    output->data = output->entries;
+    return output;
+}
+
+void bwIteratorDestroy(bwOverlapIterator_t *iter) {
+    if(!iter) return;
+    if(iter->blocks) destroyBWOverlapBlock((bwOverlapBlock_t*) iter->blocks);
+    if(iter->intervals) bwDestroyOverlappingIntervals(iter->intervals);
+    if(iter->entries) bbDestroyOverlappingEntries(iter->entries);
+    free(iter);
+}
+
+//On error, points to NULL and destroys the input
+bwOverlapIterator_t *bwIteratorNext(bwOverlapIterator_t *iter) {
+    uint64_t n, *offset, *size;
+    bwOverlapBlock_t *blocks = iter->blocks;
+
+    if(iter->intervals) {
+        bwDestroyOverlappingIntervals(iter->intervals);
+        iter->intervals = NULL;
+    }
+    if(iter->entries) {
+        bbDestroyOverlappingEntries(iter->entries);
+        iter->entries = NULL;
+    }
+    iter->data = NULL;
+
+    if(iter->offset < blocks->n) {
+        //store the previous values
+        n = blocks->n;
+        offset = blocks->offset;
+        size = blocks->size;
+
+        //Move the start of the blocks
+        blocks->offset += iter->offset;
+        blocks->size += iter->offset;
+        if(iter->offset + iter->blocksPerIteration > n) {
+            blocks->n = blocks->n - iter->offset;
+        } else {
+            blocks->n = iter->blocksPerIteration;
+        }
+
+        //Get the intervals or entries, as appropriate
+        if(iter->bw->type == 0) {
+            //bigWig
+            iter->intervals = bwGetOverlappingIntervalsCore(iter->bw, blocks, iter->tid, iter->start, iter->end);
+            iter->data = iter->intervals;
+        } else {
+            //bigBed
+            iter->entries = bbGetOverlappingEntriesCore(iter->bw, blocks, iter->tid, iter->start, iter->end, iter->withString);
+            iter->data = iter->entries;
+        }
+        iter->offset += iter->blocksPerIteration;
+
+        //reset the values in iter->blocks
+        blocks->n = n;
+        blocks->offset = offset;
+        blocks->size = size;
+
+        //Check for error
+        if(!iter->intervals && !iter->entries) goto error;
+    }
+
+    return iter;
+
+error:
+    bwIteratorDestroy(iter);
+    return NULL;
+}
+
+//This is like bwGetOverlappingIntervals, except it returns 1 base windows. If includeNA is not 0, then a value will be returned for every position in the range (defaulting to NAN).
+//The ->end member is NULL
+//If includeNA is not 0 then ->start is also NULL, since it's implied
+//Note that bwDestroyOverlappingIntervals() will work in either case
+bwOverlappingIntervals_t *bwGetValues(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int includeNA) {
+    uint32_t i, j, n;
+    bwOverlappingIntervals_t *output = NULL;
+    bwOverlappingIntervals_t *intermediate = bwGetOverlappingIntervals(fp, chrom, start, end);
+    if(!intermediate) return NULL;
+
+    output = calloc(1, sizeof(bwOverlappingIntervals_t));
+    if(!output) goto error;
+    if(includeNA) {
+        output->l = end-start;
+        output->value = malloc(output->l*sizeof(float));
+        if(!output->value) goto error;
+        for(i=0; i<output->l; i++) output->value[i] = NAN;
+        for(i=0; i<intermediate->l; i++) {
+            for(j=intermediate->start[i]; j<intermediate->end[i]; j++) {
+                if(j < start || j >= end) continue;
+                output->value[j-start] = intermediate->value[i];
+            }
+        }
+    } else {
+        n = 0;
+        for(i=0; i<intermediate->l; i++) {
+            if(intermediate->start[i] < start) intermediate->start[i] = start;
+            if(intermediate->end[i] > end) intermediate->end[i] = end;
+            n += intermediate->end[i]-intermediate->start[i];
+        }
+        output->l = n;
+        output->start = malloc(sizeof(uint32_t)*n);
+        if(!output->start) goto error;
+        output->value = malloc(sizeof(float)*n);
+        if(!output->value) goto error;
+        n = 0; //this is now the index
+        for(i=0; i<intermediate->l; i++) {
+            for(j=intermediate->start[i]; j<intermediate->end[i]; j++) {
+                if(j < start || j >= end) continue;
+                output->start[n] = j;
+                output->value[n++] = intermediate->value[i];
+            }
+        }
+    }
+
+    bwDestroyOverlappingIntervals(intermediate);
+    return output;
+
+error:
+    if(intermediate) bwDestroyOverlappingIntervals(intermediate);
+    if(output) bwDestroyOverlappingIntervals(output);
+    return NULL;
+}
+
+void bwDestroyIndexNode(bwRTreeNode_t *node) {
+    uint16_t i;
+
+    if(!node) return;
+
+    free(node->chrIdxStart);
+    free(node->baseStart);
+    free(node->chrIdxEnd);
+    free(node->baseEnd);
+    free(node->dataOffset);
+    if(!node->isLeaf) {
+        for(i=0; i<node->nChildren; i++) {
+            bwDestroyIndexNode(node->x.child[i]);
+        }
+        free(node->x.child);
+    } else {
+        free(node->x.size);
+    }
+    free(node);
+}
+
+void bwDestroyIndex(bwRTree_t *idx) {
+    bwDestroyIndexNode(idx->root);
+    free(idx);
+}
+
+//Returns a pointer to the requested index (@offset, unless it's 0, in which case the index for the values is returned
+//Returns NULL on error
+bwRTree_t *bwReadIndex(bigWigFile_t *fp, uint64_t offset) {
+    bwRTree_t *idx = readRTreeIdx(fp, offset);
+    if(!idx) return NULL;
+
+    //Read in the root node
+    idx->root = bwGetRTreeNode(fp, idx->rootOffset);
+
+    if(!idx->root) {
+        bwDestroyIndex(idx);
+        return NULL;
+    }
+    return idx;
+}