Go to the documentation of this file.
56 #define LIBBIGWIG_VERSION 0.4.4
62 #define LIBBIGWIG_CURL 0
66 #define LIBBIGWIG_CURL 1
72 #define BIGWIG_MAGIC 0x888FFC26
76 #define BIGBED_MAGIC 0x8789F2EB
80 #define CIRTREE_MAGIC 0x78ca8c91
84 #define IDX_MAGIC 0x2468ace0
88 #define DEFAULT_nCHILDREN 64
92 #define DEFAULT_BLOCKSIZE 32768
162 typedef struct bwLL bwLL;
167 typedef struct bwZoomBuffer_t bwZoomBuffer_t;
168 struct bwZoomBuffer_t {
171 struct bwZoomBuffer_t *next;
261 int bwInit(
size_t bufSize);
276 int bwIsBigWig(
char *fname, CURLcode (*callBack)(CURL*));
285 int bbIsBigBed(
char *fname, CURLcode (*callBack)(CURL*));
double minVal
Definition: bigWig.h:144
A node within an R-tree holding the index for data.
Definition: bwValues.h:17
double maxVal
Definition: bigWig.h:145
double * bwStatsFromFull(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type)
Determines per-interval bigWig statistics Can determine mean/min/max/coverage/standard deviation of v...
Definition: bwStats.c:485
bwOverlappingIntervals_t * bwGetValues(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int includeNA)
Return all per-base bigWig values in a given interval. Given an interval (e.g., chr1:0-100),...
Definition: bwValues.c:712
bwRTree_t * idx
Definition: bigWig.h:208
uint64_t summaryOffset
Definition: bigWig.h:138
int bwAppendIntervalSpanSteps(bigWigFile_t *fp, float *values, uint32_t n)
Append to a previous block of fixed-step entries. If you previously used bwAddIntervalSpanSteps(),...
Definition: bwWrite.c:552
bwRTree_t ** idx
Definition: bigWig.h:121
bwZoomBuffer_t ** lastZoomBuffer
Definition: bigWig.h:195
uint32_t tid
Definition: bigWig.h:242
uint32_t end
Definition: bigWig.h:186
uint64_t nBlocks
Definition: bigWig.h:180
void * blocks
Definition: bigWig.h:248
void * compressP
Definition: bigWig.h:198
bwOverlapIterator_t * bbOverlappingEntriesIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString, uint32_t blocksPerIteration)
Creates an iterator over entries in a bigBed file Iterators can be traversed with bwIteratorNext() an...
Definition: bwValues.c:614
uint16_t fieldCount
Definition: bigWig.h:135
bwLL * currentIndexNode
Definition: bigWig.h:193
char ** str
Definition: bigWig.h:233
bwOverlappingIntervals_t * intervals
Definition: bigWig.h:249
Holds interval:str associations.
Definition: bigWig.h:228
bwZoomHdr_t * zoomHdrs
Definition: bigWig.h:141
bwOverlappingIntervals_t * bwGetOverlappingIntervals(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end)
Return bigWig entries overlapping an interval. Find all bigWig entries overlapping a range and return...
Definition: bwValues.c:562
bbOverlappingEntries_t * entries
Definition: bigWig.h:250
uint32_t m
Definition: bigWig.h:230
int bwIsBigWig(char *fname, CURLcode(*callBack)(CURL *))
Determine if a file is a bigWig file. This function will quickly check either local or remote files t...
Definition: bwRead.c:302
A structure to hold iterations One of intervals and entries should be used to access records from big...
Definition: bigWig.h:240
Definition: bwValues.h:36
bwOverlapIterator_t * bwIteratorNext(bwOverlapIterator_t *iter)
Traverses to the entries/intervals in the next group of blocks.
Definition: bwValues.c:651
uint32_t l
Definition: bigWig.h:229
uint32_t tid
Definition: bigWig.h:184
chromList_t * bwCreateChromList(char **chroms, uint32_t *lengths, int64_t n)
Take a list of chromosome names and lengths and return a pointer to a chromList_t This MUST be run be...
Definition: bwWrite.c:22
double sumData
Definition: bigWig.h:146
uint32_t start
Definition: bigWig.h:185
uint16_t nLevels
Definition: bigWig.h:131
int bwInit(size_t bufSize)
Initializes curl and global variables. This MUST be called before other functions (at least if you wa...
Definition: bwRead.c:38
uint64_t nBasesCovered
Definition: bigWig.h:143
Holds the chromosomes and their lengths.
Definition: bigWig.h:154
uint8_t ltype
Definition: bigWig.h:189
int bwAppendIntervalSpans(bigWigFile_t *fp, uint32_t *start, float *values, uint32_t n)
Append to a previous block of variable-step entries. If you previously used bwAddIntervalSpans(),...
Definition: bwWrite.c:495
uint32_t * end
Definition: bigWig.h:232
uint32_t l
Definition: bigWig.h:190
void bbDestroyOverlappingEntries(bbOverlappingEntries_t *o)
Frees space allocated by bbGetOverlappingEntries
Definition: bwValues.c:332
void * data
Definition: bigWig.h:251
uint64_t dataOffset
Definition: bigWig.h:133
int bbIsBigBed(char *fname, CURLcode(*callBack)(CURL *))
Determine is a file is a bigBed file. This function will quickly check either local or remote files t...
Definition: bwRead.c:332
bigWigFile_t * bw
Definition: bigWig.h:241
uint32_t step
Definition: bigWig.h:188
int bwAddIntervals(bigWigFile_t *fp, char **chrom, uint32_t *start, uint32_t *end, float *values, uint32_t n)
Write a new block of bedGraph-like intervals to a bigWig file Adds entries of the form: chromosome st...
Definition: bwWrite.c:374
This is only needed for writing bigWig files (and won't be created otherwise) This should be removed ...
Definition: bigWig.h:179
bwZoomBuffer_t ** firstZoomBuffer
Definition: bigWig.h:194
Holds interval:value associations.
Definition: bigWig.h:217
uint32_t blockSize
Definition: bigWig.h:181
int bwAppendIntervals(bigWigFile_t *fp, uint32_t *start, uint32_t *end, float *values, uint32_t n)
Append bedGraph-like intervals to a previous block of bedGraph-like intervals in a bigWig file....
Definition: bwWrite.c:434
void * p
Definition: bigWig.h:191
uint32_t bufSize
Definition: bigWig.h:139
float * value
Definition: bigWig.h:222
uint64_t nEntries
Definition: bigWig.h:182
bigWigFile_t * bwOpen(char *fname, CURLcode(*callBack)(CURL *), const char *mode)
Opens a local or remote bigWig file. This will open a local or remote bigWig file....
Definition: bwRead.c:345
void bwCleanup(void)
The counterpart to bwInit, this cleans up curl.
Definition: bwRead.c:52
uint16_t version
Definition: bigWig.h:130
double sumSquared
Definition: bigWig.h:147
uint64_t * indexOffset
Definition: bigWig.h:120
URL_t * URL
Definition: bigWig.h:205
uint32_t * len
Definition: bigWig.h:157
chromList_t * cl
Definition: bigWig.h:207
bigWigHdr_t * hdr
Definition: bigWig.h:206
uint64_t * nNodes
Definition: bigWig.h:196
uint64_t runningWidthSum
Definition: bigWig.h:183
void bwClose(bigWigFile_t *fp)
Closes a bigWigFile_t and frees up allocated memory This closes both bigWig and bigBed files.
Definition: bwRead.c:289
uint64_t ctOffset
Definition: bigWig.h:132
bigWigFile_t * bbOpen(char *fname, CURLcode(*callBack)(CURL *))
Opens a local or remote bigBed file. This will open a local or remote bigBed file....
Definition: bwRead.c:397
uint64_t sqlOffset
Definition: bigWig.h:137
int64_t nKeys
Definition: bigWig.h:155
uint32_t bwGetTid(bigWigFile_t *fp, char *chrom)
Converts between chromosome name and ID.
Definition: bwValues.c:283
BigWig files have multiple "zoom" levels, each of which has its own header. This hold those headers.
Definition: bigWig.h:116
int bwWriteHdr(bigWigFile_t *bw)
Write a the header to a bigWig file. You must have already opened the output file,...
Definition: bwWrite.c:187
uint64_t indexOffset
Definition: bigWig.h:134
bwOverlapIterator_t * bwOverlappingIntervalsIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t blocksPerIteration)
Creates an iterator over intervals in a bigWig file Iterators can be traversed with bwIteratorNext() ...
Definition: bwValues.c:586
uint32_t * end
Definition: bigWig.h:221
bwWriteBuffer_t * writeBuffer
Definition: bigWig.h:209
The header section of a bigWig file.
Definition: bigWig.h:129
This structure holds the file pointers and buffers needed for raw access to local and remote files.
Definition: bigWigIO.h:32
bwLL * firstIndexNode
Definition: bigWig.h:192
int withString
Definition: bigWig.h:247
uint32_t m
Definition: bigWig.h:219
uint16_t definedFieldCount
Definition: bigWig.h:136
uint32_t l
Definition: bigWig.h:218
int isWrite
Definition: bigWig.h:210
uint32_t * level
Definition: bigWig.h:117
uint32_t * start
Definition: bigWig.h:220
uint32_t end
Definition: bigWig.h:244
uint32_t blocksPerIteration
Definition: bigWig.h:246
int bwAddIntervalSpanSteps(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t span, uint32_t step, float *values, uint32_t n)
Add a new block of fixed-step entries to a bigWig file Adds entries for the form value to the file....
Definition: bwWrite.c:520
uint32_t * start
Definition: bigWig.h:231
char * bbGetSQL(bigWigFile_t *fp)
Returns a string containing the SQL entry (or NULL). The "auto SQL" field contains the names and valu...
Definition: bwRead.c:315
int bwAddIntervalSpans(bigWigFile_t *fp, char *chrom, uint32_t *start, uint32_t span, float *values, uint32_t n)
Add a new block of variable-step entries to a bigWig file Adds entries for the form chromosome start ...
Definition: bwWrite.c:462
int bwCreateHdr(bigWigFile_t *fp, int32_t maxZooms)
Create a largely empty bigWig header Every bigWig file has a header, this creates the template for on...
Definition: bwWrite.c:56
bbOverlappingEntries_t * bbGetOverlappingEntries(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString)
Return bigBed entries overlapping an interval. Find all bigBed entries overlapping a range and return...
Definition: bwValues.c:574
void bwIteratorDestroy(bwOverlapIterator_t *iter)
Destroys a bwOverlapIterator_t.
Definition: bwValues.c:642
uint32_t start
Definition: bigWig.h:243
int type
Definition: bigWig.h:211
A structure that holds everything needed to access a bigWig file.
Definition: bigWig.h:204
uint64_t * dataOffset
Definition: bigWig.h:119
uLongf compressPsz
Definition: bigWig.h:197
uint64_t extensionOffset
Definition: bigWig.h:140
char ** chrom
Definition: bigWig.h:156
double * bwStats(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type)
Determines per-interval bigWig statistics Can determine mean/min/max/coverage/standard deviation of v...
Definition: bwStats.c:530
uint64_t offset
Definition: bigWig.h:245
uint32_t span
Definition: bigWig.h:187
void bwDestroyOverlappingIntervals(bwOverlappingIntervals_t *o)
Frees space allocated by bwGetOverlappingIntervals
Definition: bwValues.c:324
bwStatsType
Definition: bigWig.h:97