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 +1,803 @@
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1
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#include "bigWig.h"
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2
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#include "bwCommon.h"
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3
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#include <stdlib.h>
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4
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#include <math.h>
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5
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#include <string.h>
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6
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#include <zlib.h>
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7
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+
#include <errno.h>
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8
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+
|
9
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+
static uint32_t roundup(uint32_t v) {
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10
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v--;
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11
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v |= v >> 1;
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v |= v >> 2;
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v |= v >> 4;
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v |= v >> 8;
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v |= v >> 16;
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v++;
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return v;
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}
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19
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20
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//Returns the root node on success and NULL on error
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static bwRTree_t *readRTreeIdx(bigWigFile_t *fp, uint64_t offset) {
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uint32_t magic;
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bwRTree_t *node;
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25
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if(!offset) {
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26
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if(bwSetPos(fp, fp->hdr->indexOffset)) return NULL;
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27
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} else {
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28
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if(bwSetPos(fp, offset)) return NULL;
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29
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}
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30
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if(bwRead(&magic, sizeof(uint32_t), 1, fp) != 1) return NULL;
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if(magic != IDX_MAGIC) {
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33
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fprintf(stderr, "[readRTreeIdx] Mismatch in the magic number!\n");
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return NULL;
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35
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}
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36
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37
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node = calloc(1, sizeof(bwRTree_t));
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if(!node) return NULL;
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39
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40
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if(bwRead(&(node->blockSize), sizeof(uint32_t), 1, fp) != 1) goto error;
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41
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if(bwRead(&(node->nItems), sizeof(uint64_t), 1, fp) != 1) goto error;
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42
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if(bwRead(&(node->chrIdxStart), sizeof(uint32_t), 1, fp) != 1) goto error;
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if(bwRead(&(node->baseStart), sizeof(uint32_t), 1, fp) != 1) goto error;
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if(bwRead(&(node->chrIdxEnd), sizeof(uint32_t), 1, fp) != 1) goto error;
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if(bwRead(&(node->baseEnd), sizeof(uint32_t), 1, fp) != 1) goto error;
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46
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if(bwRead(&(node->idxSize), sizeof(uint64_t), 1, fp) != 1) goto error;
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47
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if(bwRead(&(node->nItemsPerSlot), sizeof(uint32_t), 1, fp) != 1) goto error;
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//Padding
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if(bwRead(&(node->blockSize), sizeof(uint32_t), 1, fp) != 1) goto error;
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node->rootOffset = bwTell(fp);
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//For remote files, libCurl sometimes sets errno to 115 and doesn't clear it
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errno = 0;
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return node;
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error:
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free(node);
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return NULL;
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}
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//Returns a bwRTreeNode_t on success and NULL on an error
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//For the root node, set offset to 0
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static bwRTreeNode_t *bwGetRTreeNode(bigWigFile_t *fp, uint64_t offset) {
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bwRTreeNode_t *node = NULL;
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uint8_t padding;
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uint16_t i;
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if(offset) {
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if(bwSetPos(fp, offset)) return NULL;
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} else {
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//seek
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if(bwSetPos(fp, fp->idx->rootOffset)) return NULL;
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}
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node = calloc(1, sizeof(bwRTreeNode_t));
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if(!node) return NULL;
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if(bwRead(&(node->isLeaf), sizeof(uint8_t), 1, fp) != 1) goto error;
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if(bwRead(&padding, sizeof(uint8_t), 1, fp) != 1) goto error;
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if(bwRead(&(node->nChildren), sizeof(uint16_t), 1, fp) != 1) goto error;
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node->chrIdxStart = malloc(sizeof(uint32_t)*(node->nChildren));
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if(!node->chrIdxStart) goto error;
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node->baseStart = malloc(sizeof(uint32_t)*(node->nChildren));
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if(!node->baseStart) goto error;
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node->chrIdxEnd = malloc(sizeof(uint32_t)*(node->nChildren));
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if(!node->chrIdxEnd) goto error;
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node->baseEnd = malloc(sizeof(uint32_t)*(node->nChildren));
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if(!node->baseEnd) goto error;
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node->dataOffset = malloc(sizeof(uint64_t)*(node->nChildren));
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if(!node->dataOffset) goto error;
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92
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if(node->isLeaf) {
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93
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node->x.size = malloc(node->nChildren * sizeof(uint64_t));
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if(!node->x.size) goto error;
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} else {
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node->x.child = calloc(node->nChildren, sizeof(struct bwRTreeNode_t *));
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if(!node->x.child) goto error;
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}
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99
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for(i=0; i<node->nChildren; i++) {
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100
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if(bwRead(&(node->chrIdxStart[i]), sizeof(uint32_t), 1, fp) != 1) goto error;
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101
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if(bwRead(&(node->baseStart[i]), sizeof(uint32_t), 1, fp) != 1) goto error;
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102
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if(bwRead(&(node->chrIdxEnd[i]), sizeof(uint32_t), 1, fp) != 1) goto error;
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103
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if(bwRead(&(node->baseEnd[i]), sizeof(uint32_t), 1, fp) != 1) goto error;
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104
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if(bwRead(&(node->dataOffset[i]), sizeof(uint64_t), 1, fp) != 1) goto error;
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105
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if(node->isLeaf) {
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if(bwRead(&(node->x.size[i]), sizeof(uint64_t), 1, fp) != 1) goto error;
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}
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}
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110
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return node;
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111
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error:
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113
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if(node->chrIdxStart) free(node->chrIdxStart);
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114
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if(node->baseStart) free(node->baseStart);
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115
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if(node->chrIdxEnd) free(node->chrIdxEnd);
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116
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if(node->baseEnd) free(node->baseEnd);
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117
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if(node->dataOffset) free(node->dataOffset);
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118
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if(node->isLeaf && node->x.size) free(node->x.size);
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else if((!node->isLeaf) && node->x.child) free(node->x.child);
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free(node);
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return NULL;
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}
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124
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void destroyBWOverlapBlock(bwOverlapBlock_t *b) {
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if(!b) return;
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if(b->size) free(b->size);
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127
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if(b->offset) free(b->offset);
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128
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free(b);
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}
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//Returns a bwOverlapBlock_t * object or NULL on error.
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132
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static bwOverlapBlock_t *overlapsLeaf(bwRTreeNode_t *node, uint32_t tid, uint32_t start, uint32_t end) {
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133
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uint16_t i, idx = 0;
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bwOverlapBlock_t *o = calloc(1, sizeof(bwOverlapBlock_t));
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if(!o) return NULL;
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137
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for(i=0; i<node->nChildren; i++) {
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138
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if(tid < node->chrIdxStart[i]) break;
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139
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if(tid > node->chrIdxEnd[i]) continue;
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140
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141
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/*
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142
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The individual blocks can theoretically span multiple contigs.
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143
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So if we treat the first/last contig in the range as special
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but anything in the middle is a guaranteed match
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145
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*/
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146
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if(node->chrIdxStart[i] != node->chrIdxEnd[i]) {
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147
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if(tid == node->chrIdxStart[i]) {
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148
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if(node->baseStart[i] >= end) break;
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149
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} else if(tid == node->chrIdxEnd[i]) {
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if(node->baseEnd[i] <= start) continue;
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}
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152
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} else {
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153
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if(node->baseStart[i] >= end || node->baseEnd[i] <= start) continue;
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154
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}
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155
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o->n++;
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156
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}
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157
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158
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if(o->n) {
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159
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o->offset = malloc(sizeof(uint64_t) * (o->n));
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160
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if(!o->offset) goto error;
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161
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o->size = malloc(sizeof(uint64_t) * (o->n));
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162
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if(!o->size) goto error;
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163
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+
|
164
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for(i=0; i<node->nChildren; i++) {
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165
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if(tid < node->chrIdxStart[i]) break;
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if(tid < node->chrIdxStart[i] || tid > node->chrIdxEnd[i]) continue;
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167
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+
if(node->chrIdxStart[i] != node->chrIdxEnd[i]) {
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168
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if(tid == node->chrIdxStart[i]) {
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169
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if(node->baseStart[i] >= end) continue;
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170
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+
} else if(tid == node->chrIdxEnd[i]) {
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171
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if(node->baseEnd[i] <= start) continue;
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172
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}
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173
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} else {
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174
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if(node->baseStart[i] >= end || node->baseEnd[i] <= start) continue;
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175
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}
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176
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o->offset[idx] = node->dataOffset[i];
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177
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o->size[idx++] = node->x.size[i];
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178
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if(idx >= o->n) break;
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179
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}
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180
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+
}
|
181
|
+
|
182
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+
if(idx != o->n) { //This should never happen
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183
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+
fprintf(stderr, "[overlapsLeaf] Mismatch between number of overlaps calculated and found!\n");
|
184
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+
goto error;
|
185
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+
}
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186
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+
|
187
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+
return o;
|
188
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+
|
189
|
+
error:
|
190
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+
if(o) destroyBWOverlapBlock(o);
|
191
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return NULL;
|
192
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+
}
|
193
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+
|
194
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+
//This will free l2 unless there's an error!
|
195
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+
//Returns NULL on error, otherwise the merged lists
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196
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static bwOverlapBlock_t *mergeOverlapBlocks(bwOverlapBlock_t *b1, bwOverlapBlock_t *b2) {
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197
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uint64_t i,j;
|
198
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+
if(!b2) return b1;
|
199
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+
if(!b2->n) {
|
200
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+
destroyBWOverlapBlock(b2);
|
201
|
+
return b1;
|
202
|
+
}
|
203
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+
if(!b1->n) {
|
204
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+
destroyBWOverlapBlock(b1);
|
205
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+
return b2;
|
206
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+
}
|
207
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+
j = b1->n;
|
208
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b1->n += b2->n;
|
209
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b1->offset = realloc(b1->offset, sizeof(uint64_t) * (b1->n+b2->n));
|
210
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+
if(!b1->offset) goto error;
|
211
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+
b1->size = realloc(b1->size, sizeof(uint64_t) * (b1->n+b2->n));
|
212
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+
if(!b1->size) goto error;
|
213
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+
|
214
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+
for(i=0; i<b2->n; i++) {
|
215
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+
b1->offset[j+i] = b2->offset[i];
|
216
|
+
b1->size[j+i] = b2->size[i];
|
217
|
+
}
|
218
|
+
destroyBWOverlapBlock(b2);
|
219
|
+
return b1;
|
220
|
+
|
221
|
+
error:
|
222
|
+
destroyBWOverlapBlock(b1);
|
223
|
+
return NULL;
|
224
|
+
}
|
225
|
+
|
226
|
+
//Returns NULL and sets nOverlaps to >0 on error, otherwise nOverlaps is the number of file offsets returned
|
227
|
+
//The output needs to be free()d if not NULL (likewise with *sizes)
|
228
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+
static bwOverlapBlock_t *overlapsNonLeaf(bigWigFile_t *fp, bwRTreeNode_t *node, uint32_t tid, uint32_t start, uint32_t end) {
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229
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+
uint16_t i;
|
230
|
+
bwOverlapBlock_t *nodeBlocks, *output = calloc(1, sizeof(bwOverlapBlock_t));
|
231
|
+
if(!output) return NULL;
|
232
|
+
|
233
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+
for(i=0; i<node->nChildren; i++) {
|
234
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+
if(tid < node->chrIdxStart[i]) break;
|
235
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+
if(tid < node->chrIdxStart[i] || tid > node->chrIdxEnd[i]) continue;
|
236
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+
if(node->chrIdxStart[i] != node->chrIdxEnd[i]) { //child spans contigs
|
237
|
+
if(tid == node->chrIdxStart[i]) {
|
238
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+
if(node->baseStart[i] >= end) continue;
|
239
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+
} else if(tid == node->chrIdxEnd[i]) {
|
240
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+
if(node->baseEnd[i] <= start) continue;
|
241
|
+
}
|
242
|
+
} else {
|
243
|
+
if(end <= node->baseStart[i] || start >= node->baseEnd[i]) continue;
|
244
|
+
}
|
245
|
+
|
246
|
+
//We have an overlap!
|
247
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+
if(!node->x.child[i])
|
248
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+
node->x.child[i] = bwGetRTreeNode(fp, node->dataOffset[i]);
|
249
|
+
if(!node->x.child[i]) goto error;
|
250
|
+
|
251
|
+
if(node->x.child[i]->isLeaf) { //leaf
|
252
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+
nodeBlocks = overlapsLeaf(node->x.child[i], tid, start, end);
|
253
|
+
} else { //non-leaf
|
254
|
+
nodeBlocks = overlapsNonLeaf(fp, node->x.child[i], tid, start, end);
|
255
|
+
}
|
256
|
+
|
257
|
+
//The output is processed the same regardless of leaf/non-leaf
|
258
|
+
if(!nodeBlocks) goto error;
|
259
|
+
else {
|
260
|
+
output = mergeOverlapBlocks(output, nodeBlocks);
|
261
|
+
if(!output) {
|
262
|
+
destroyBWOverlapBlock(nodeBlocks);
|
263
|
+
goto error;
|
264
|
+
}
|
265
|
+
}
|
266
|
+
}
|
267
|
+
|
268
|
+
return output;
|
269
|
+
|
270
|
+
error:
|
271
|
+
destroyBWOverlapBlock(output);
|
272
|
+
return NULL;
|
273
|
+
}
|
274
|
+
|
275
|
+
//Returns NULL and sets nOverlaps to >0 on error, otherwise nOverlaps is the number of file offsets returned
|
276
|
+
//The output must be free()d
|
277
|
+
bwOverlapBlock_t *walkRTreeNodes(bigWigFile_t *bw, bwRTreeNode_t *root, uint32_t tid, uint32_t start, uint32_t end) {
|
278
|
+
if(root->isLeaf) return overlapsLeaf(root, tid, start, end);
|
279
|
+
return overlapsNonLeaf(bw, root, tid, start, end);
|
280
|
+
}
|
281
|
+
|
282
|
+
//In reality, a hash or some sort of tree structure is probably faster...
|
283
|
+
//Return -1 (AKA 0xFFFFFFFF...) on "not there", so we can hold (2^32)-1 items.
|
284
|
+
uint32_t bwGetTid(bigWigFile_t *fp, char *chrom) {
|
285
|
+
uint32_t i;
|
286
|
+
if(!chrom) return -1;
|
287
|
+
for(i=0; i<fp->cl->nKeys; i++) {
|
288
|
+
if(strcmp(chrom, fp->cl->chrom[i]) == 0) return i;
|
289
|
+
}
|
290
|
+
return -1;
|
291
|
+
}
|
292
|
+
|
293
|
+
static bwOverlapBlock_t *bwGetOverlappingBlocks(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end) {
|
294
|
+
uint32_t tid = bwGetTid(fp, chrom);
|
295
|
+
|
296
|
+
if(tid == (uint32_t) -1) {
|
297
|
+
fprintf(stderr, "[bwGetOverlappingBlocks] Non-existent contig: %s\n", chrom);
|
298
|
+
return NULL;
|
299
|
+
}
|
300
|
+
|
301
|
+
//Get the info if needed
|
302
|
+
if(!fp->idx) {
|
303
|
+
fp->idx = readRTreeIdx(fp, fp->hdr->indexOffset);
|
304
|
+
if(!fp->idx) {
|
305
|
+
return NULL;
|
306
|
+
}
|
307
|
+
}
|
308
|
+
|
309
|
+
if(!fp->idx->root) fp->idx->root = bwGetRTreeNode(fp, 0);
|
310
|
+
if(!fp->idx->root) return NULL;
|
311
|
+
|
312
|
+
return walkRTreeNodes(fp, fp->idx->root, tid, start, end);
|
313
|
+
}
|
314
|
+
|
315
|
+
void bwFillDataHdr(bwDataHeader_t *hdr, void *b) {
|
316
|
+
hdr->tid = ((uint32_t*)b)[0];
|
317
|
+
hdr->start = ((uint32_t*)b)[1];
|
318
|
+
hdr->end = ((uint32_t*)b)[2];
|
319
|
+
hdr->step = ((uint32_t*)b)[3];
|
320
|
+
hdr->span = ((uint32_t*)b)[4];
|
321
|
+
hdr->type = ((uint8_t*)b)[20];
|
322
|
+
hdr->nItems = ((uint16_t*)b)[11];
|
323
|
+
}
|
324
|
+
|
325
|
+
void bwDestroyOverlappingIntervals(bwOverlappingIntervals_t *o) {
|
326
|
+
if(!o) return;
|
327
|
+
if(o->start) free(o->start);
|
328
|
+
if(o->end) free(o->end);
|
329
|
+
if(o->value) free(o->value);
|
330
|
+
free(o);
|
331
|
+
}
|
332
|
+
|
333
|
+
void bbDestroyOverlappingEntries(bbOverlappingEntries_t *o) {
|
334
|
+
uint32_t i;
|
335
|
+
if(!o) return;
|
336
|
+
if(o->start) free(o->start);
|
337
|
+
if(o->end) free(o->end);
|
338
|
+
if(o->str) {
|
339
|
+
for(i=0; i<o->l; i++) {
|
340
|
+
if(o->str[i]) free(o->str[i]);
|
341
|
+
}
|
342
|
+
free(o->str);
|
343
|
+
}
|
344
|
+
free(o);
|
345
|
+
}
|
346
|
+
|
347
|
+
//Returns NULL on error, in which case o has been free()d
|
348
|
+
static bwOverlappingIntervals_t *pushIntervals(bwOverlappingIntervals_t *o, uint32_t start, uint32_t end, float value) {
|
349
|
+
if(o->l+1 >= o->m) {
|
350
|
+
o->m = roundup(o->l+1);
|
351
|
+
o->start = realloc(o->start, o->m * sizeof(uint32_t));
|
352
|
+
if(!o->start) goto error;
|
353
|
+
o->end = realloc(o->end, o->m * sizeof(uint32_t));
|
354
|
+
if(!o->end) goto error;
|
355
|
+
o->value = realloc(o->value, o->m * sizeof(float));
|
356
|
+
if(!o->value) goto error;
|
357
|
+
}
|
358
|
+
o->start[o->l] = start;
|
359
|
+
o->end[o->l] = end;
|
360
|
+
o->value[o->l++] = value;
|
361
|
+
return o;
|
362
|
+
|
363
|
+
error:
|
364
|
+
bwDestroyOverlappingIntervals(o);
|
365
|
+
return NULL;
|
366
|
+
}
|
367
|
+
|
368
|
+
static bbOverlappingEntries_t *pushBBIntervals(bbOverlappingEntries_t *o, uint32_t start, uint32_t end, char *str, int withString) {
|
369
|
+
if(o->l+1 >= o->m) {
|
370
|
+
o->m = roundup(o->l+1);
|
371
|
+
o->start = realloc(o->start, o->m * sizeof(uint32_t));
|
372
|
+
if(!o->start) goto error;
|
373
|
+
o->end = realloc(o->end, o->m * sizeof(uint32_t));
|
374
|
+
if(!o->end) goto error;
|
375
|
+
if(withString) {
|
376
|
+
o->str = realloc(o->str, o->m * sizeof(char**));
|
377
|
+
if(!o->str) goto error;
|
378
|
+
}
|
379
|
+
}
|
380
|
+
o->start[o->l] = start;
|
381
|
+
o->end[o->l] = end;
|
382
|
+
if(withString) o->str[o->l] = strdup(str);
|
383
|
+
o->l++;
|
384
|
+
return o;
|
385
|
+
|
386
|
+
error:
|
387
|
+
bbDestroyOverlappingEntries(o);
|
388
|
+
return NULL;
|
389
|
+
}
|
390
|
+
|
391
|
+
//Returns NULL on error
|
392
|
+
bwOverlappingIntervals_t *bwGetOverlappingIntervalsCore(bigWigFile_t *fp, bwOverlapBlock_t *o, uint32_t tid, uint32_t ostart, uint32_t oend) {
|
393
|
+
uint64_t i;
|
394
|
+
uint16_t j;
|
395
|
+
int compressed = 0, rv;
|
396
|
+
uLongf sz = fp->hdr->bufSize, tmp;
|
397
|
+
void *buf = NULL, *compBuf = NULL;
|
398
|
+
uint32_t start = 0, end , *p;
|
399
|
+
float value;
|
400
|
+
bwDataHeader_t hdr;
|
401
|
+
bwOverlappingIntervals_t *output = calloc(1, sizeof(bwOverlappingIntervals_t));
|
402
|
+
|
403
|
+
if(!output) goto error;
|
404
|
+
|
405
|
+
if(!o) return output;
|
406
|
+
if(!o->n) return output;
|
407
|
+
|
408
|
+
if(sz) {
|
409
|
+
compressed = 1;
|
410
|
+
buf = malloc(sz);
|
411
|
+
}
|
412
|
+
sz = 0; //This is now the size of the compressed buffer
|
413
|
+
|
414
|
+
for(i=0; i<o->n; i++) {
|
415
|
+
if(bwSetPos(fp, o->offset[i])) goto error;
|
416
|
+
|
417
|
+
if(sz < o->size[i]) {
|
418
|
+
compBuf = realloc(compBuf, o->size[i]);
|
419
|
+
sz = o->size[i];
|
420
|
+
}
|
421
|
+
if(!compBuf) goto error;
|
422
|
+
|
423
|
+
if(bwRead(compBuf, o->size[i], 1, fp) != 1) goto error;
|
424
|
+
if(compressed) {
|
425
|
+
tmp = fp->hdr->bufSize; //This gets over-written by uncompress
|
426
|
+
rv = uncompress(buf, (uLongf *) &tmp, compBuf, o->size[i]);
|
427
|
+
if(rv != Z_OK) goto error;
|
428
|
+
} else {
|
429
|
+
buf = compBuf;
|
430
|
+
}
|
431
|
+
|
432
|
+
//TODO: ensure that tmp is large enough!
|
433
|
+
bwFillDataHdr(&hdr, buf);
|
434
|
+
|
435
|
+
p = ((uint32_t*) buf);
|
436
|
+
p += 6;
|
437
|
+
if(hdr.tid != tid) continue;
|
438
|
+
|
439
|
+
if(hdr.type == 3) start = hdr.start - hdr.step;
|
440
|
+
|
441
|
+
//FIXME: We should ensure that sz is large enough to hold nItems of the given type
|
442
|
+
for(j=0; j<hdr.nItems; j++) {
|
443
|
+
switch(hdr.type) {
|
444
|
+
case 1:
|
445
|
+
start = *p;
|
446
|
+
p++;
|
447
|
+
end = *p;
|
448
|
+
p++;
|
449
|
+
value = *((float *)p);
|
450
|
+
p++;
|
451
|
+
break;
|
452
|
+
case 2:
|
453
|
+
start = *p;
|
454
|
+
p++;
|
455
|
+
end = start + hdr.span;
|
456
|
+
value = *((float *)p);
|
457
|
+
p++;
|
458
|
+
break;
|
459
|
+
case 3:
|
460
|
+
start += hdr.step;
|
461
|
+
end = start+hdr.span;
|
462
|
+
value = *((float *)p);
|
463
|
+
p++;
|
464
|
+
break;
|
465
|
+
default :
|
466
|
+
goto error;
|
467
|
+
break;
|
468
|
+
}
|
469
|
+
|
470
|
+
if(end <= ostart || start >= oend) continue;
|
471
|
+
//Push the overlap
|
472
|
+
if(!pushIntervals(output, start, end, value)) goto error;
|
473
|
+
}
|
474
|
+
}
|
475
|
+
|
476
|
+
if(compressed && buf) free(buf);
|
477
|
+
if(compBuf) free(compBuf);
|
478
|
+
return output;
|
479
|
+
|
480
|
+
error:
|
481
|
+
fprintf(stderr, "[bwGetOverlappingIntervalsCore] Got an error\n");
|
482
|
+
if(output) bwDestroyOverlappingIntervals(output);
|
483
|
+
if(compressed && buf) free(buf);
|
484
|
+
if(compBuf) free(compBuf);
|
485
|
+
return NULL;
|
486
|
+
}
|
487
|
+
|
488
|
+
bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapBlock_t *o, uint32_t tid, uint32_t ostart, uint32_t oend, int withString) {
|
489
|
+
uint64_t i;
|
490
|
+
int compressed = 0, rv, slen;
|
491
|
+
uLongf sz = fp->hdr->bufSize, tmp = 0;
|
492
|
+
void *buf = NULL, *bufEnd = NULL, *compBuf = NULL;
|
493
|
+
uint32_t entryTid = 0, start = 0, end;
|
494
|
+
char *str;
|
495
|
+
bbOverlappingEntries_t *output = calloc(1, sizeof(bbOverlappingEntries_t));
|
496
|
+
|
497
|
+
if(!output) goto error;
|
498
|
+
|
499
|
+
if(!o) return output;
|
500
|
+
if(!o->n) return output;
|
501
|
+
|
502
|
+
if(sz) {
|
503
|
+
compressed = 1;
|
504
|
+
buf = malloc(sz);
|
505
|
+
}
|
506
|
+
sz = 0; //This is now the size of the compressed buffer
|
507
|
+
|
508
|
+
for(i=0; i<o->n; i++) {
|
509
|
+
if(bwSetPos(fp, o->offset[i])) goto error;
|
510
|
+
|
511
|
+
if(sz < o->size[i]) {
|
512
|
+
compBuf = realloc(compBuf, o->size[i]);
|
513
|
+
sz = o->size[i];
|
514
|
+
}
|
515
|
+
if(!compBuf) goto error;
|
516
|
+
|
517
|
+
if(bwRead(compBuf, o->size[i], 1, fp) != 1) goto error;
|
518
|
+
if(compressed) {
|
519
|
+
tmp = fp->hdr->bufSize; //This gets over-written by uncompress
|
520
|
+
rv = uncompress(buf, (uLongf *) &tmp, compBuf, o->size[i]);
|
521
|
+
if(rv != Z_OK) goto error;
|
522
|
+
} else {
|
523
|
+
buf = compBuf;
|
524
|
+
tmp = o->size[i]; //TODO: Is this correct? Do non-gzipped bigBeds exist?
|
525
|
+
}
|
526
|
+
|
527
|
+
bufEnd = buf + tmp;
|
528
|
+
while(buf < bufEnd) {
|
529
|
+
entryTid = ((uint32_t*)buf)[0];
|
530
|
+
start = ((uint32_t*)buf)[1];
|
531
|
+
end = ((uint32_t*)buf)[2];
|
532
|
+
buf += 12;
|
533
|
+
str = (char*)buf;
|
534
|
+
slen = strlen(str) + 1;
|
535
|
+
buf += slen;
|
536
|
+
|
537
|
+
if(entryTid < tid) continue;
|
538
|
+
if(entryTid > tid) break;
|
539
|
+
if(end <= ostart) continue;
|
540
|
+
if(start >= oend) break;
|
541
|
+
|
542
|
+
//Push the overlap
|
543
|
+
if(!pushBBIntervals(output, start, end, str, withString)) goto error;
|
544
|
+
}
|
545
|
+
|
546
|
+
buf = bufEnd - tmp; //reset the buffer pointer
|
547
|
+
}
|
548
|
+
|
549
|
+
if(compressed && buf) free(buf);
|
550
|
+
if(compBuf) free(compBuf);
|
551
|
+
return output;
|
552
|
+
|
553
|
+
error:
|
554
|
+
fprintf(stderr, "[bbGetOverlappingEntriesCore] Got an error\n");
|
555
|
+
buf = bufEnd - tmp;
|
556
|
+
if(output) bbDestroyOverlappingEntries(output);
|
557
|
+
if(compressed && buf) free(buf);
|
558
|
+
if(compBuf) free(compBuf);
|
559
|
+
return NULL;
|
560
|
+
}
|
561
|
+
|
562
|
+
//Returns NULL on error OR no intervals, which is a bad design...
|
563
|
+
bwOverlappingIntervals_t *bwGetOverlappingIntervals(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end) {
|
564
|
+
bwOverlappingIntervals_t *output;
|
565
|
+
uint32_t tid = bwGetTid(fp, chrom);
|
566
|
+
if(tid == (uint32_t) -1) return NULL;
|
567
|
+
bwOverlapBlock_t *blocks = bwGetOverlappingBlocks(fp, chrom, start, end);
|
568
|
+
if(!blocks) return NULL;
|
569
|
+
output = bwGetOverlappingIntervalsCore(fp, blocks, tid, start, end);
|
570
|
+
destroyBWOverlapBlock(blocks);
|
571
|
+
return output;
|
572
|
+
}
|
573
|
+
|
574
|
+
//Like above, but for bigBed files
|
575
|
+
bbOverlappingEntries_t *bbGetOverlappingEntries(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString) {
|
576
|
+
bbOverlappingEntries_t *output;
|
577
|
+
uint32_t tid = bwGetTid(fp, chrom);
|
578
|
+
if(tid == (uint32_t) -1) return NULL;
|
579
|
+
bwOverlapBlock_t *blocks = bwGetOverlappingBlocks(fp, chrom, start, end);
|
580
|
+
if(!blocks) return NULL;
|
581
|
+
output = bbGetOverlappingEntriesCore(fp, blocks, tid, start, end, withString);
|
582
|
+
destroyBWOverlapBlock(blocks);
|
583
|
+
return output;
|
584
|
+
}
|
585
|
+
|
586
|
+
//Returns NULL on error
|
587
|
+
bwOverlapIterator_t *bwOverlappingIntervalsIterator(bigWigFile_t *bw, char *chrom, uint32_t start, uint32_t end, uint32_t blocksPerIteration) {
|
588
|
+
bwOverlapIterator_t *output = NULL;
|
589
|
+
uint64_t n;
|
590
|
+
uint32_t tid = bwGetTid(bw, chrom);
|
591
|
+
if(tid == (uint32_t) -1) return output;
|
592
|
+
output = calloc(1, sizeof(bwOverlapIterator_t));
|
593
|
+
if(!output) return output;
|
594
|
+
bwOverlapBlock_t *blocks = bwGetOverlappingBlocks(bw, chrom, start, end);
|
595
|
+
|
596
|
+
output->bw = bw;
|
597
|
+
output->tid = tid;
|
598
|
+
output->start = start;
|
599
|
+
output->end = end;
|
600
|
+
output->blocks = blocks;
|
601
|
+
output->blocksPerIteration = blocksPerIteration;
|
602
|
+
|
603
|
+
if(blocks) {
|
604
|
+
n = blocks->n;
|
605
|
+
if(n>blocksPerIteration) blocks->n = blocksPerIteration;
|
606
|
+
output->intervals = bwGetOverlappingIntervalsCore(bw, blocks,tid, start, end);
|
607
|
+
blocks->n = n;
|
608
|
+
output->offset = blocksPerIteration;
|
609
|
+
}
|
610
|
+
output->data = output->intervals;
|
611
|
+
return output;
|
612
|
+
}
|
613
|
+
|
614
|
+
//Returns NULL on error
|
615
|
+
bwOverlapIterator_t *bbOverlappingEntriesIterator(bigWigFile_t *bw, char *chrom, uint32_t start, uint32_t end, int withString, uint32_t blocksPerIteration) {
|
616
|
+
bwOverlapIterator_t *output = NULL;
|
617
|
+
uint64_t n;
|
618
|
+
uint32_t tid = bwGetTid(bw, chrom);
|
619
|
+
if(tid == (uint32_t) -1) return output;
|
620
|
+
output = calloc(1, sizeof(bwOverlapIterator_t));
|
621
|
+
if(!output) return output;
|
622
|
+
bwOverlapBlock_t *blocks = bwGetOverlappingBlocks(bw, chrom, start, end);
|
623
|
+
|
624
|
+
output->bw = bw;
|
625
|
+
output->tid = tid;
|
626
|
+
output->start = start;
|
627
|
+
output->end = end;
|
628
|
+
output->blocks = blocks;
|
629
|
+
output->blocksPerIteration = blocksPerIteration;
|
630
|
+
output->withString = withString;
|
631
|
+
|
632
|
+
if(blocks) {
|
633
|
+
n = blocks->n;
|
634
|
+
if(n>blocksPerIteration) blocks->n = blocksPerIteration;
|
635
|
+
output->entries = bbGetOverlappingEntriesCore(bw, blocks,tid, start, end, withString);
|
636
|
+
blocks->n = n;
|
637
|
+
output->offset = blocksPerIteration;
|
638
|
+
}
|
639
|
+
output->data = output->entries;
|
640
|
+
return output;
|
641
|
+
}
|
642
|
+
|
643
|
+
void bwIteratorDestroy(bwOverlapIterator_t *iter) {
|
644
|
+
if(!iter) return;
|
645
|
+
if(iter->blocks) destroyBWOverlapBlock((bwOverlapBlock_t*) iter->blocks);
|
646
|
+
if(iter->intervals) bwDestroyOverlappingIntervals(iter->intervals);
|
647
|
+
if(iter->entries) bbDestroyOverlappingEntries(iter->entries);
|
648
|
+
free(iter);
|
649
|
+
}
|
650
|
+
|
651
|
+
//On error, points to NULL and destroys the input
|
652
|
+
bwOverlapIterator_t *bwIteratorNext(bwOverlapIterator_t *iter) {
|
653
|
+
uint64_t n, *offset, *size;
|
654
|
+
bwOverlapBlock_t *blocks = iter->blocks;
|
655
|
+
|
656
|
+
if(iter->intervals) {
|
657
|
+
bwDestroyOverlappingIntervals(iter->intervals);
|
658
|
+
iter->intervals = NULL;
|
659
|
+
}
|
660
|
+
if(iter->entries) {
|
661
|
+
bbDestroyOverlappingEntries(iter->entries);
|
662
|
+
iter->entries = NULL;
|
663
|
+
}
|
664
|
+
iter->data = NULL;
|
665
|
+
|
666
|
+
if(iter->offset < blocks->n) {
|
667
|
+
//store the previous values
|
668
|
+
n = blocks->n;
|
669
|
+
offset = blocks->offset;
|
670
|
+
size = blocks->size;
|
671
|
+
|
672
|
+
//Move the start of the blocks
|
673
|
+
blocks->offset += iter->offset;
|
674
|
+
blocks->size += iter->offset;
|
675
|
+
if(iter->offset + iter->blocksPerIteration > n) {
|
676
|
+
blocks->n = blocks->n - iter->offset;
|
677
|
+
} else {
|
678
|
+
blocks->n = iter->blocksPerIteration;
|
679
|
+
}
|
680
|
+
|
681
|
+
//Get the intervals or entries, as appropriate
|
682
|
+
if(iter->bw->type == 0) {
|
683
|
+
//bigWig
|
684
|
+
iter->intervals = bwGetOverlappingIntervalsCore(iter->bw, blocks, iter->tid, iter->start, iter->end);
|
685
|
+
iter->data = iter->intervals;
|
686
|
+
} else {
|
687
|
+
//bigBed
|
688
|
+
iter->entries = bbGetOverlappingEntriesCore(iter->bw, blocks, iter->tid, iter->start, iter->end, iter->withString);
|
689
|
+
iter->data = iter->entries;
|
690
|
+
}
|
691
|
+
iter->offset += iter->blocksPerIteration;
|
692
|
+
|
693
|
+
//reset the values in iter->blocks
|
694
|
+
blocks->n = n;
|
695
|
+
blocks->offset = offset;
|
696
|
+
blocks->size = size;
|
697
|
+
|
698
|
+
//Check for error
|
699
|
+
if(!iter->intervals && !iter->entries) goto error;
|
700
|
+
}
|
701
|
+
|
702
|
+
return iter;
|
703
|
+
|
704
|
+
error:
|
705
|
+
bwIteratorDestroy(iter);
|
706
|
+
return NULL;
|
707
|
+
}
|
708
|
+
|
709
|
+
//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).
|
710
|
+
//The ->end member is NULL
|
711
|
+
//If includeNA is not 0 then ->start is also NULL, since it's implied
|
712
|
+
//Note that bwDestroyOverlappingIntervals() will work in either case
|
713
|
+
bwOverlappingIntervals_t *bwGetValues(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int includeNA) {
|
714
|
+
uint32_t i, j, n;
|
715
|
+
bwOverlappingIntervals_t *output = NULL;
|
716
|
+
bwOverlappingIntervals_t *intermediate = bwGetOverlappingIntervals(fp, chrom, start, end);
|
717
|
+
if(!intermediate) return NULL;
|
718
|
+
|
719
|
+
output = calloc(1, sizeof(bwOverlappingIntervals_t));
|
720
|
+
if(!output) goto error;
|
721
|
+
if(includeNA) {
|
722
|
+
output->l = end-start;
|
723
|
+
output->value = malloc(output->l*sizeof(float));
|
724
|
+
if(!output->value) goto error;
|
725
|
+
for(i=0; i<output->l; i++) output->value[i] = NAN;
|
726
|
+
for(i=0; i<intermediate->l; i++) {
|
727
|
+
for(j=intermediate->start[i]; j<intermediate->end[i]; j++) {
|
728
|
+
if(j < start || j >= end) continue;
|
729
|
+
output->value[j-start] = intermediate->value[i];
|
730
|
+
}
|
731
|
+
}
|
732
|
+
} else {
|
733
|
+
n = 0;
|
734
|
+
for(i=0; i<intermediate->l; i++) {
|
735
|
+
if(intermediate->start[i] < start) intermediate->start[i] = start;
|
736
|
+
if(intermediate->end[i] > end) intermediate->end[i] = end;
|
737
|
+
n += intermediate->end[i]-intermediate->start[i];
|
738
|
+
}
|
739
|
+
output->l = n;
|
740
|
+
output->start = malloc(sizeof(uint32_t)*n);
|
741
|
+
if(!output->start) goto error;
|
742
|
+
output->value = malloc(sizeof(float)*n);
|
743
|
+
if(!output->value) goto error;
|
744
|
+
n = 0; //this is now the index
|
745
|
+
for(i=0; i<intermediate->l; i++) {
|
746
|
+
for(j=intermediate->start[i]; j<intermediate->end[i]; j++) {
|
747
|
+
if(j < start || j >= end) continue;
|
748
|
+
output->start[n] = j;
|
749
|
+
output->value[n++] = intermediate->value[i];
|
750
|
+
}
|
751
|
+
}
|
752
|
+
}
|
753
|
+
|
754
|
+
bwDestroyOverlappingIntervals(intermediate);
|
755
|
+
return output;
|
756
|
+
|
757
|
+
error:
|
758
|
+
if(intermediate) bwDestroyOverlappingIntervals(intermediate);
|
759
|
+
if(output) bwDestroyOverlappingIntervals(output);
|
760
|
+
return NULL;
|
761
|
+
}
|
762
|
+
|
763
|
+
void bwDestroyIndexNode(bwRTreeNode_t *node) {
|
764
|
+
uint16_t i;
|
765
|
+
|
766
|
+
if(!node) return;
|
767
|
+
|
768
|
+
free(node->chrIdxStart);
|
769
|
+
free(node->baseStart);
|
770
|
+
free(node->chrIdxEnd);
|
771
|
+
free(node->baseEnd);
|
772
|
+
free(node->dataOffset);
|
773
|
+
if(!node->isLeaf) {
|
774
|
+
for(i=0; i<node->nChildren; i++) {
|
775
|
+
bwDestroyIndexNode(node->x.child[i]);
|
776
|
+
}
|
777
|
+
free(node->x.child);
|
778
|
+
} else {
|
779
|
+
free(node->x.size);
|
780
|
+
}
|
781
|
+
free(node);
|
782
|
+
}
|
783
|
+
|
784
|
+
void bwDestroyIndex(bwRTree_t *idx) {
|
785
|
+
bwDestroyIndexNode(idx->root);
|
786
|
+
free(idx);
|
787
|
+
}
|
788
|
+
|
789
|
+
//Returns a pointer to the requested index (@offset, unless it's 0, in which case the index for the values is returned
|
790
|
+
//Returns NULL on error
|
791
|
+
bwRTree_t *bwReadIndex(bigWigFile_t *fp, uint64_t offset) {
|
792
|
+
bwRTree_t *idx = readRTreeIdx(fp, offset);
|
793
|
+
if(!idx) return NULL;
|
794
|
+
|
795
|
+
//Read in the root node
|
796
|
+
idx->root = bwGetRTreeNode(fp, idx->rootOffset);
|
797
|
+
|
798
|
+
if(!idx->root) {
|
799
|
+
bwDestroyIndex(idx);
|
800
|
+
return NULL;
|
801
|
+
}
|
802
|
+
return idx;
|
803
|
+
}
|