#include "bigWigIO.h"
#include "bwValues.h"
#include <inttypes.h>
#include <zlib.h>

Data Structures
struct	bwZoomHdr_t
	BigWig files have multiple "zoom" levels, each of which has its own header. This hold those headers. More...

struct	bigWigHdr_t
	The header section of a bigWig file. More...

struct	chromList_t
	Holds the chromosomes and their lengths. More...

struct	bwWriteBuffer_t
	This is only needed for writing bigWig files (and won't be created otherwise) This should be removed from bigWig.h. More...

struct	bigWigFile_t
	A structure that holds everything needed to access a bigWig file. More...

struct	bwOverlappingIntervals_t
	Holds interval:value associations. More...

struct	bbOverlappingEntries_t
	Holds interval:str associations. More...

struct	bwOverlapIterator_t
	A structure to hold iterations One of intervals and entries should be used to access records from bigWig or bigBed files, respectively. More...

Macros
#define	LIBBIGWIG_VERSION 0.4.5

#define	LIBBIGWIG_CURL 1

#define	BIGWIG_MAGIC 0x888FFC26

#define	BIGBED_MAGIC 0x8789F2EB

#define	CIRTREE_MAGIC 0x78ca8c91

#define	IDX_MAGIC 0x2468ace0

#define	DEFAULT_nCHILDREN 64

#define	DEFAULT_BLOCKSIZE 32768

Enumerations
enum	bwStatsType { doesNotExist = -1, mean = 0, average = 0, stdev = 1, dev = 1, max = 2, min = 3, cov = 4, coverage = 4, sum = 5 }

Functions
int	bwInit (size_t bufSize)
	Initializes curl and global variables. This MUST be called before other functions (at least if you want to connect to remote files). For remote file, curl must be initialized and regions of a file read into an internal buffer. If the buffer is too small then an excessive number of connections will be made. If the buffer is too large than more data than required is fetched. 128KiB is likely sufficient for most needs. More...

void	bwCleanup (void)
	The counterpart to bwInit, this cleans up curl. More...

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 to determine if they appear to be valid bigWig files. This can be determined by reading the first 4 bytes of the file. More...

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 to determine if they appear to be valid bigWig files. This can be determined by reading the first 4 bytes of the file. More...

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. Writing of local bigWig files is also supported. More...

bigWigFile_t *	bbOpen (char fname, CURLcode(callBack)(CURL *))
	Opens a local or remote bigBed file. This will open a local or remote bigBed file. Note that this file format can only be read and NOT written! More...

char *	bbGetSQL (bigWigFile_t *fp)
	Returns a string containing the SQL entry (or NULL). The "auto SQL" field contains the names and value types of the entries in each bigBed entry. If you need to parse a particular value out of each entry, then you'll need to first parse this. More...

void	bwClose (bigWigFile_t *fp)
	Closes a bigWigFile_t and frees up allocated memory This closes both bigWig and bigBed files. More...

uint32_t	bwGetTid (bigWigFile_t fp, char chrom)
	Converts between chromosome name and ID. More...

void	bwDestroyOverlappingIntervals (bwOverlappingIntervals_t *o)
	Frees space allocated by `bwGetOverlappingIntervals` More...

void	bbDestroyOverlappingEntries (bbOverlappingEntries_t *o)
	Frees space allocated by `bbGetOverlappingEntries` More...

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 returns them, including their associated values. More...

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 returns them. More...

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()` and destroyed with `bwIteratorDestroy()`. Intervals are in the `intervals` member and `data` can be used to determine when to end iteration. More...

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()` and destroyed with `bwIteratorDestroy()`. Entries are in the `entries` member and `data` can be used to determine when to end iteration. More...

bwOverlapIterator_t *	bwIteratorNext (bwOverlapIterator_t *iter)
	Traverses to the entries/intervals in the next group of blocks. More...

void	bwIteratorDestroy (bwOverlapIterator_t *iter)
	Destroys a bwOverlapIterator_t. More...

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), return the value at each position in a bigWig file. Positions without associated values are suppressed by default, but may be returned if `includeNA` is not 0. More...

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 values in one or more intervals in a bigWig file. You can optionally give it an interval and ask for values from X number of sub-intervals. More...

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 values in one or more intervals in a bigWig file. You can optionally give it an interval and ask for values from X number of sub-intervals. The difference with bwStats is that zoom levels are never used. More...

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 one. It also takes care of space allocation in the output write buffer. More...

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 before `bwWriteHdr()`. Note that the input is NOT free()d! More...

int	bwWriteHdr (bigWigFile_t *bw)
	Write a the header to a bigWig file. You must have already opened the output file, created a header and a chromosome list. More...

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 start end value to the file. These will always be added in a new block, so you may have previously used a different storage type. More...

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. If you have previously used bwAddIntervals() then this will append additional entries into the previous block (or start a new one if needed). More...

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 value to the file. Each block of such entries has an associated "span", so each value describes the region chromosome:start-(start+span) More...

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()`, this will continue appending more values to the block(s) it created. More...

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. Each block of such entries has an associated "span", "step", chromosome and start position. See the wiggle format for more details. More...

int	bwAppendIntervalSpanSteps (bigWigFile_t fp, float values, uint32_t n)
	Append to a previous block of fixed-step entries. If you previously used `bwAddIntervalSpanSteps()`, this will continue appending more values to the block(s) it created. More...

Detailed Description

These are the functions and structured that should be used by external users. While I don't particularly recommend dealing with some of the structures (e.g., a bigWigHdr_t), they're described here in case you need them.

BTW, this library doesn't switch endianness as appropriate, since I kind of assume that there's only one type produced these days.

Macro Definition Documentation

◆ BIGBED_MAGIC

#define BIGBED_MAGIC 0x8789F2EB

The magic number of a bigBed file.

◆ BIGWIG_MAGIC

#define BIGWIG_MAGIC 0x888FFC26

The magic number of a bigWig file.

◆ CIRTREE_MAGIC

#define CIRTREE_MAGIC 0x78ca8c91

The magic number of a "cirTree" block in a file.

◆ DEFAULT_BLOCKSIZE

#define DEFAULT_BLOCKSIZE 32768

The default decompression buffer size in bytes. This is used to determin

◆ DEFAULT_nCHILDREN

#define DEFAULT_nCHILDREN 64

The default number of children per block.

◆ IDX_MAGIC

#define IDX_MAGIC 0x2468ace0

The magic number of an index block in a file.

◆ LIBBIGWIG_CURL

#define LIBBIGWIG_CURL 1

If 1, then this library was compiled with remote file support.

◆ LIBBIGWIG_VERSION

#define LIBBIGWIG_VERSION 0.4.5

The library version number

Enumeration Type Documentation

◆ bwStatsType

enum bwStatsType

An enum that dictates the type of statistic to fetch for a given interval

Enumerator
doesNotExist	This does nothing
mean	The mean value
average	The mean value
stdev	The standard deviation of the values
dev	The standard deviation of the values
max	The maximum value
min	The minimum value
cov	The number of bases covered
coverage	The number of bases covered
sum	The sum of per-base values

Function Documentation

◆ bbDestroyOverlappingEntries()

void bbDestroyOverlappingEntries ( bbOverlappingEntries_t * o )

Frees space allocated by bbGetOverlappingEntries

Parameters

o	A valid `bbOverlappingEntries_t` pointer.

See also: bbGetOverlappingEntries

◆ bbGetOverlappingEntries()

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 returns them.

Parameters

fp	A valid bigWigFile_t pointer. This MUST be for a bigBed file!
chrom	A valid chromosome name.
start	The start position of the interval. This is 0-based half open, so 0 is the first base.
end	The end position of the interval. Again, this is 0-based half open, so 100 will include the 100th base...which is at position 99.
withString	If not 0, return the string associated with each entry in the output. If 0, there are no associated strings returned. This is useful if the only information needed are the locations of the entries, which require significantly less memory.

Returns: NULL on error or no overlapping values, otherwise a bbOverlappingEntries_t * holding the intervals and (optionally) the associated string.

See also: bbOverlappingEntries_t; bbDestroyOverlappingEntries

◆ bbGetSQL()

char* bbGetSQL ( bigWigFile_t * fp )

Returns a string containing the SQL entry (or NULL). The "auto SQL" field contains the names and value types of the entries in each bigBed entry. If you need to parse a particular value out of each entry, then you'll need to first parse this.

Parameters

fp	The file pointer to a valid bigWigFile_t

Returns: A char *, which you MUST free!

◆ bbIsBigBed()

int bbIsBigBed	(	char *	fname,
		CURLcode()(CURL )	callBack
	)

Determine is a file is a bigBed file. This function will quickly check either local or remote files to determine if they appear to be valid bigWig files. This can be determined by reading the first 4 bytes of the file.

Parameters

fname	The file name or URL (http, https, and ftp are supported)
callBack	An optional user-supplied function. This is applied to remote connections so users can specify things like proxy and password information. See `test/testRemote` for an example.

Returns: 1 if the file appears to be bigWig, otherwise 0.

◆ bbOpen()

bigWigFile_t* bbOpen	(	char *	fname,
		CURLcode()(CURL )	callBack
	)

Opens a local or remote bigBed file. This will open a local or remote bigBed file. Note that this file format can only be read and NOT written!

Parameters

fname	The file name or URL (http, https, and ftp are supported)
callBack	An optional user-supplied function. This is applied to remote connections so users can specify things like proxy and password information. See `test/testRemote` for an example.

Returns: A bigWigFile_t * on success and NULL on error.

◆ bbOverlappingEntriesIterator()

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() and destroyed with bwIteratorDestroy(). Entries are in the entries member and data can be used to determine when to end iteration.

Parameters

fp	A valid bigWigFile_t pointer. This MUST be for a bigBed file!
chrom	A valid chromosome name.
start	The start position of the interval. This is 0-based half open, so 0 is the first base.
end	The end position of the interval. Again, this is 0-based half open, so 100 will include the 100th base...which is at position 99.
withString	Whether the returned entries should include their associated strings.
blocksPerIteration	The number of blocks (internal groupings of entries in bigBed files) to return per iteration.

Returns: NULL on error, otherwise a bwOverlapIterator_t pointer

See also: bbGetOverlappingEntries; bwOverlapIterator_t; bwIteratorNext; bwIteratorDestroy

◆ bwAddIntervals()

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 start end value to the file. These will always be added in a new block, so you may have previously used a different storage type.

In general it's more efficient to use the bwAppend* functions, but then you MUST know that the previously written block is of the same type. In other words, you can only use bwAppendIntervals() after bwAddIntervals() or a previous bwAppendIntervals().

Parameters

fp	The output file pointer.
chrom	A list of chromosomes, of length `n`.
start	A list of start positions of length`n`.
end	A list of end positions of length`n`.
values	A list of values of length`n`.
n	The length of the aforementioned lists.

Returns: 0 on success and another value on error.

See also: bwAppendIntervals

◆ bwAddIntervalSpans()

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 value to the file. Each block of such entries has an associated "span", so each value describes the region chromosome:start-(start+span)

This will always start a new block of values.

Parameters

fp	The output file pointer.
chrom	A list of chromosomes, of length `n`.
start	A list of start positions of length`n`.
span	The span of each entry (the must all be the same).
values	A list of values of length`n`.
n	The length of the aforementioned lists.

Returns: 0 on success and another value on error.

See also: bwAppendIntervalSpans

◆ bwAddIntervalSpanSteps()

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. Each block of such entries has an associated "span", "step", chromosome and start position. See the wiggle format for more details.

This will always start a new block of values.

Parameters

fp	The output file pointer.
chrom	The chromosome that the entries describe.
start	The starting position of the block of entries.
span	The span of each entry (i.e., the number of bases it describes).
step	The step between entry start positions.
values	A list of values of length`n`.
n	The length of the aforementioned lists.

Returns: 0 on success and another value on error.

See also: bwAddIntervalSpanSteps

◆ bwAppendIntervals()

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. If you have previously used bwAddIntervals() then this will append additional entries into the previous block (or start a new one if needed).

Parameters

fp	The output file pointer.
start	A list of start positions of length`n`.
end	A list of end positions of length`n`.
values	A list of values of length`n`.
n	The length of the aforementioned lists.

Returns: 0 on success and another value on error.

Warning: Do NOT use this after bwAddIntervalSpanSteps(), bwAppendIntervalSpanSteps(), bwAddIntervalSpanSteps(), or bwAppendIntervalSpanSteps().

See also: bwAddIntervals

◆ bwAppendIntervalSpans()

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(), this will continue appending more values to the block(s) it created.

Parameters

fp	The output file pointer.
start	A list of start positions of length`n`.
values	A list of values of length`n`.
n	The length of the aforementioned lists.

Returns: 0 on success and another value on error.

Warning: Do NOT use this after bwAddIntervals(), bwAppendIntervals(), bwAddIntervalSpanSteps() or bwAppendIntervalSpanSteps()

See also: bwAddIntervalSpans

◆ bwAppendIntervalSpanSteps()

int bwAppendIntervalSpanSteps	(	bigWigFile_t *	fp,
		float *	values,
		uint32_t	n
	)

Append to a previous block of fixed-step entries. If you previously used bwAddIntervalSpanSteps(), this will continue appending more values to the block(s) it created.

Parameters

fp	The output file pointer.
values	A list of values of length`n`.
n	The length of the aforementioned lists.

Returns: 0 on success and another value on error.

Warning: Do NOT use this after bwAddIntervals(), bwAppendIntervals(), bwAddIntervalSpans() or bwAppendIntervalSpans()

See also: bwAddIntervalSpanSteps

◆ bwCleanup()

void bwCleanup ( void )

The counterpart to bwInit, this cleans up curl.

See also: bwInit

◆ bwClose()

void bwClose ( bigWigFile_t * fp )

Closes a bigWigFile_t and frees up allocated memory This closes both bigWig and bigBed files.

Parameters

fp	The file pointer.

◆ bwCreateChromList()

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 before bwWriteHdr(). Note that the input is NOT free()d!

Parameters

chroms	A list of chromosomes.
lengths	The length of each chromosome.
n	The number of chromosomes (thus, the length of `chroms` and `lengths`)

Returns: A pointer to a chromList_t or NULL on error.

◆ bwCreateHdr()

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 one. It also takes care of space allocation in the output write buffer.

Parameters

fp	The bigWigFile_t* that you want to write to.
maxZooms	The maximum number of zoom levels. If you specify 0 then there will be no zoom levels. A value <0 or > 65535 will result in a maximum of 10.

Returns: 0 on success.

◆ bwDestroyOverlappingIntervals()

void bwDestroyOverlappingIntervals ( bwOverlappingIntervals_t * o )

Frees space allocated by bwGetOverlappingIntervals

Parameters

o	A valid `bwOverlappingIntervals_t` pointer.

See also: bwGetOverlappingIntervals

◆ bwGetOverlappingIntervals()

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 returns them, including their associated values.

Parameters

fp	A valid bigWigFile_t pointer. This MUST be for a bigWig file!
chrom	A valid chromosome name.
start	The start position of the interval. This is 0-based half open, so 0 is the first base.
end	The end position of the interval. Again, this is 0-based half open, so 100 will include the 100th base...which is at position 99.

Returns: NULL on error or no overlapping values, otherwise a bwOverlappingIntervals_t * holding the values and intervals.

See also: bwOverlappingIntervals_t; bwDestroyOverlappingIntervals; bwGetValues

◆ bwGetTid()

uint32_t bwGetTid	(	bigWigFile_t *	fp,
		char *	chrom
	)

Converts between chromosome name and ID.

Parameters

fp	A valid bigWigFile_t pointer
chrom	A chromosome name

Returns: An ID, -1 will be returned on error (note that this is an unsigned value, so that's ~4 billion. bigWig/bigBed files can't store that many chromosomes anyway.

◆ bwGetValues()

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), return the value at each position in a bigWig file. Positions without associated values are suppressed by default, but may be returned if includeNA is not 0.

Parameters

fp	A valid bigWigFile_t pointer.
chrom	A valid chromosome name.
start	The start position of the interval. This is 0-based half open, so 0 is the first base.
end	The end position of the interval. Again, this is 0-based half open, so 100 will include the 100th base...which is at position 99.
includeNA	If not 0, report NA values as well (as NA).

Returns: NULL on error or no overlapping values, otherwise a bwOverlappingIntervals_t * holding the values and positions.

See also: bwOverlappingIntervals_t; bwDestroyOverlappingIntervals; bwGetOverlappingIntervals

◆ bwInit()

int bwInit ( size_t bufSize )

Initializes curl and global variables. This MUST be called before other functions (at least if you want to connect to remote files). For remote file, curl must be initialized and regions of a file read into an internal buffer. If the buffer is too small then an excessive number of connections will be made. If the buffer is too large than more data than required is fetched. 128KiB is likely sufficient for most needs.

Parameters

bufSize The internal buffer size used for remote connection.

See also: bwCleanup

Returns: 0 on success and 1 on error.

◆ bwIsBigWig()

int bwIsBigWig	(	char *	fname,
		CURLcode()(CURL )	callBack
	)

Determine if a file is a bigWig file. This function will quickly check either local or remote files to determine if they appear to be valid bigWig files. This can be determined by reading the first 4 bytes of the file.

Parameters

fname	The file name or URL (http, https, and ftp are supported)
callBack	An optional user-supplied function. This is applied to remote connections so users can specify things like proxy and password information. See `test/testRemote` for an example.

Returns: 1 if the file appears to be bigWig, otherwise 0.

◆ bwIteratorDestroy()

void bwIteratorDestroy ( bwOverlapIterator_t * iter )

Destroys a bwOverlapIterator_t.

Parameters

iter	The bwOverlapIterator_t that should be destroyed

◆ bwIteratorNext()

bwOverlapIterator_t* bwIteratorNext ( bwOverlapIterator_t * iter )

Traverses to the entries/intervals in the next group of blocks.

Parameters

iter	A bwOverlapIterator_t pointer that is updated (or destroyed on error)

Returns: NULL on error, otherwise a bwOverlapIterator_t pointer with the intervals or entries from the next set of blocks.

See also: bwOverlapIterator_t; bwIteratorDestroy

◆ bwOpen()

bigWigFile_t* bwOpen	(	char *	fname,
		CURLcode()(CURL )	callBack,
		const char *	mode
	)

Opens a local or remote bigWig file. This will open a local or remote bigWig file. Writing of local bigWig files is also supported.

Parameters

fname	The file name or URL (http, https, and ftp are supported)
callBack	An optional user-supplied function. This is applied to remote connections so users can specify things like proxy and password information. See `test/testRemote` for an example.
mode	The mode, by default "r". Both local and remote files can be read, but only local files can be written. For files being written the callback function is ignored. If and only if the mode contains "w" will the file be opened for writing (in all other cases the file will be opened for reading.

Returns: A bigWigFile_t * on success and NULL on error.

◆ bwOverlappingIntervalsIterator()

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() and destroyed with bwIteratorDestroy(). Intervals are in the intervals member and data can be used to determine when to end iteration.

Parameters

fp	A valid bigWigFile_t pointer. This MUST be for a bigWig file!
chrom	A valid chromosome name.
start	The start position of the interval. This is 0-based half open, so 0 is the first base.
end	The end position of the interval. Again, this is 0-based half open, so 100 will include the 100th base...which is at position 99.
blocksPerIteration	The number of blocks (internal groupings of intervals in bigWig files) to return per iteration.

Returns: NULL on error, otherwise a bwOverlapIterator_t pointer

See also: bwOverlapIterator_t; bwIteratorNext; bwIteratorDestroy

◆ bwStats()

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 values in one or more intervals in a bigWig file. You can optionally give it an interval and ask for values from X number of sub-intervals.

Parameters

fp	The file from which to extract statistics.
chrom	A valid chromosome name.
start	The start position of the interval. This is 0-based half open, so 0 is the first base.
end	The end position of the interval. Again, this is 0-based half open, so 100 will include the 100th base...which is at position 99.
nBins	The number of bins within the interval to calculate statistics for.
type	The type of statistic.

See also: bwStatsType

Returns: A pointer to an array of double precission floating point values. Note that bigWig files only hold 32-bit values, so this is done to help prevent overflows.

◆ bwStatsFromFull()

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 values in one or more intervals in a bigWig file. You can optionally give it an interval and ask for values from X number of sub-intervals. The difference with bwStats is that zoom levels are never used.

Parameters

fp	The file from which to extract statistics.
chrom	A valid chromosome name.
start	The start position of the interval. This is 0-based half open, so 0 is the first base.
end	The end position of the interval. Again, this is 0-based half open, so 100 will include the 100th base...which is at position 99.
nBins	The number of bins within the interval to calculate statistics for.
type	The type of statistic.

See also: bwStatsType

Returns: A pointer to an array of double precission floating point values. Note that bigWig files only hold 32-bit values, so this is done to help prevent overflows.

◆ bwWriteHdr()

int bwWriteHdr ( bigWigFile_t * bw )

Write a the header to a bigWig file. You must have already opened the output file, created a header and a chromosome list.

Parameters

bw	The output bigWigFile_t pointer.

See also: bwCreateHdr; bwCreateChromList

Data Structures

Macros

Enumerations

Functions

Detailed Description

Macro Definition Documentation

◆ BIGBED_MAGIC

◆ BIGWIG_MAGIC

◆ CIRTREE_MAGIC

◆ DEFAULT_BLOCKSIZE

◆ DEFAULT_nCHILDREN

◆ IDX_MAGIC

◆ LIBBIGWIG_CURL

◆ LIBBIGWIG_VERSION

Enumeration Type Documentation

◆ bwStatsType

Function Documentation

◆ bbDestroyOverlappingEntries()

◆ bbGetOverlappingEntries()

◆ bbGetSQL()

◆ bbIsBigBed()

◆ bbOpen()

◆ bbOverlappingEntriesIterator()

◆ bwAddIntervals()

◆ bwAddIntervalSpans()

◆ bwAddIntervalSpanSteps()

◆ bwAppendIntervals()

◆ bwAppendIntervalSpans()

◆ bwAppendIntervalSpanSteps()

◆ bwCleanup()

◆ bwClose()

◆ bwCreateChromList()

◆ bwCreateHdr()

◆ bwDestroyOverlappingIntervals()

◆ bwGetOverlappingIntervals()

◆ bwGetTid()

◆ bwGetValues()

◆ bwInit()

◆ bwIsBigWig()

◆ bwIteratorDestroy()

◆ bwIteratorNext()

◆ bwOpen()

◆ bwOverlappingIntervalsIterator()

◆ bwStats()

◆ bwStatsFromFull()

◆ bwWriteHdr()