bigWig.h

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#ifndef LIBBIGWIG_H
#define LIBBIGWIG_H
 
#include "bigWigIO.h"
#include "bwValues.h"
#include <inttypes.h>
#include <zlib.h>
 
#ifdef __cplusplus
extern "C" {
#endif
 
#define LIBBIGWIG_VERSION 0.4.5
 
#ifdef NOCURL
#define LIBBIGWIG_CURL 0
#ifndef CURLTYPE_DEFINED
#define CURLTYPE_DEFINED
typedef int CURLcode;
typedef void CURL;
#endif
#else
#define LIBBIGWIG_CURL 1
#endif
 
#define BIGWIG_MAGIC 0x888FFC26
 
#define BIGBED_MAGIC 0x8789F2EB
 
#define CIRTREE_MAGIC 0x78ca8c91
 
#define IDX_MAGIC 0x2468ace0
 
#define DEFAULT_nCHILDREN 64
 
#define DEFAULT_BLOCKSIZE 32768
 
enum bwStatsType {
    doesNotExist = -1, 
    mean = 0, 
    average = 0, 
    stdev = 1, 
    dev = 1, 
    max = 2, 
    min = 3, 
    cov = 4, 
    coverage = 4, 
    sum = 5 
};
 
//Should hide this from end users
typedef struct {
    uint32_t *level; 
    //There's 4 bytes of padding between these
    uint64_t *dataOffset; 
    uint64_t *indexOffset; 
    bwRTree_t **idx; 
} bwZoomHdr_t;
 
typedef struct {
    uint16_t version; 
    uint16_t nLevels; 
    uint64_t ctOffset; 
    uint64_t dataOffset; 
    uint64_t indexOffset; 
    uint16_t fieldCount; 
    uint16_t definedFieldCount; 
    uint64_t sqlOffset; 
    uint64_t summaryOffset; 
    uint32_t bufSize; 
    uint64_t extensionOffset; 
    bwZoomHdr_t *zoomHdrs; 
    //total Summary
    uint64_t nBasesCovered; 
    double minVal; 
    double maxVal; 
    double sumData; 
    double sumSquared; 
} bigWigHdr_t;
 
//Should probably replace this with a hash
typedef struct {
    int64_t nKeys; 
    char **chrom; 
    uint32_t *len; 
} chromList_t;
 
//TODO remove from bigWig.h
typedef struct bwLL bwLL;
struct bwLL {
    bwRTreeNode_t *node;
    struct bwLL *next;
};
typedef struct bwZoomBuffer_t bwZoomBuffer_t;
struct bwZoomBuffer_t { //each individual entry takes 32 bytes
    void *p;
    uint32_t l, m;
    struct bwZoomBuffer_t *next;
};
 
typedef struct {
    uint64_t nBlocks; 
    uint32_t blockSize; 
    uint64_t nEntries; 
    uint64_t runningWidthSum; 
    uint32_t tid; 
    uint32_t start; 
    uint32_t end; 
    uint32_t span; 
    uint32_t step; 
    uint8_t ltype; 
    uint32_t l; 
    void *p; 
    bwLL *firstIndexNode; 
    bwLL *currentIndexNode; 
    bwZoomBuffer_t **firstZoomBuffer; 
    bwZoomBuffer_t **lastZoomBuffer; 
    uint64_t *nNodes; 
    uLongf compressPsz; 
    void *compressP; 
} bwWriteBuffer_t;
 
typedef struct {
    URL_t *URL; 
    bigWigHdr_t *hdr; 
    chromList_t *cl; 
    bwRTree_t *idx; 
    bwWriteBuffer_t *writeBuffer; 
    int isWrite; 
    int type; 
} bigWigFile_t;
 
typedef struct {
    uint32_t l; 
    uint32_t m; 
    uint32_t *start; 
    uint32_t *end; 
    float *value; 
} bwOverlappingIntervals_t;
 
typedef struct {
    uint32_t l; 
    uint32_t m; 
    uint32_t *start; 
    uint32_t *end; 
    char **str; 
} bbOverlappingEntries_t;
 
typedef struct {
    bigWigFile_t *bw; 
    uint32_t tid; 
    uint32_t start; 
    uint32_t end; 
    uint64_t offset; 
    uint32_t blocksPerIteration; 
    int withString; 
    void *blocks; 
    bwOverlappingIntervals_t *intervals; 
    bbOverlappingEntries_t *entries; 
    void *data; 
} bwOverlapIterator_t;
 
int bwInit(size_t bufSize);
 
void bwCleanup(void);
 
int bwIsBigWig(char *fname, CURLcode (*callBack)(CURL*));
 
int bbIsBigBed(char *fname, CURLcode (*callBack)(CURL*));
 
bigWigFile_t *bwOpen(char *fname, CURLcode (*callBack)(CURL*), const char* mode);
 
bigWigFile_t *bbOpen(char *fname, CURLcode (*callBack)(CURL*));
 
char *bbGetSQL(bigWigFile_t *fp);
 
void bwClose(bigWigFile_t *fp);
 
/*******************************************************************************
*
* The following are in bwStats.c
*
*******************************************************************************/
 
uint32_t bwGetTid(bigWigFile_t *fp, char *chrom);
 
void bwDestroyOverlappingIntervals(bwOverlappingIntervals_t *o);
 
void bbDestroyOverlappingEntries(bbOverlappingEntries_t *o);
 
bwOverlappingIntervals_t *bwGetOverlappingIntervals(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end);
 
bbOverlappingEntries_t *bbGetOverlappingEntries(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString);
 
bwOverlapIterator_t *bwOverlappingIntervalsIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t blocksPerIteration);
 
bwOverlapIterator_t *bbOverlappingEntriesIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString, uint32_t blocksPerIteration);
 
bwOverlapIterator_t *bwIteratorNext(bwOverlapIterator_t *iter);
 
void bwIteratorDestroy(bwOverlapIterator_t *iter);
 
bwOverlappingIntervals_t *bwGetValues(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int includeNA);
 
double *bwStats(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type);
 
double *bwStatsFromFull(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type);
 
//Writer functions
 
int bwCreateHdr(bigWigFile_t *fp, int32_t maxZooms);
 
chromList_t *bwCreateChromList(char **chroms, uint32_t *lengths, int64_t n);
 
int bwWriteHdr(bigWigFile_t *bw);
 
int bwAddIntervals(bigWigFile_t *fp, char **chrom, uint32_t *start, uint32_t *end, float *values, uint32_t n);
 
int bwAppendIntervals(bigWigFile_t *fp, uint32_t *start, uint32_t *end, float *values, uint32_t n);
 
int bwAddIntervalSpans(bigWigFile_t *fp, char *chrom, uint32_t *start, uint32_t span, float *values, uint32_t n);
 
int bwAppendIntervalSpans(bigWigFile_t *fp, uint32_t *start, float *values, uint32_t n);
 
int bwAddIntervalSpanSteps(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t span, uint32_t step, float *values, uint32_t n);
 
int bwAppendIntervalSpanSteps(bigWigFile_t *fp, float *values, uint32_t n);
 
#ifdef __cplusplus
}
#endif
 
#endif // LIBBIGWIG_H