A C library for reading/parsing local and remote BigWig files. While Kent's source code is free to use for these purposes, it's really inappropriate as library code since it has the unfortunate habit of calling exit()
whenever there's an error. If that's then used inside of something like python then the python interpreter gets killed. This library is aimed at resolving these sorts of issues and should also use more standard things like curl and has a friendlier license to boot.
Documentation is automatically generated by doxygen and can be found under docs/html
or online here.
#Example
The only functions and structures that end users need to care about are in "bigWig.h". Below is a commented example. You can see the files under test/
for further examples.
#include "bigWig.h" int main(int argc, char *argv[]) { bigWigFile_t *fp = NULL; bwOverlappingIntervals_t *intervals = NULL; double *stats = NULL; if(argc != 2) { fprintf(stderr, "Usage: %s {file.bw|URL://path/file.bw}\n", argv[0]); return 1; } //Initialize enough space to hold 128KiB (1<<17) of data at a time if(bwInit(1<<17) != 0) { fprintf(stderr, "Received an error in bwInit\n"); return 1; } //Open the local/remote file fp = bwOpen(argv[1], NULL); if(!fp) { fprintf(stderr, "An error occured while opening %s\n", argv[1]); return 1; } //Get values in a range (0-based, half open) without NAs intervals = bwGetValues(fp, "chr1", 10000000, 10000100, 0); bwDestroyOverlappingIntervals(intervals); //Free allocated memory //Get values in a range (0-based, half open) with NAs intervals = bwGetValues(fp, "chr1", 10000000, 10000100, 1); bwDestroyOverlappingIntervals(intervals); //Free allocated memory //Get the full intervals that overlap intervals = bwGetOverlappingIntervals(fp, "chr1", 10000000, 10000100); bwDestroyOverlappingIntervals(intervals); //Get an example statistic - standard deviation //We want ~4 bins in the range stats = bwStats(fp, "chr1", 10000000, 10000100, 4, dev); if(stats) { printf("chr1:10000000-10000100 std. dev.: %f %f %f %f\n", stats[0], stats[1], stats[2], stats[3]); free(stats); } bwClose(fp); bwCleanup(); return 0; }
#A note on statistics
The results of min
, max
, and mean
should be the same as those from BigWigSummary
. std
and coverage
, however, may differ due to Kent's tools producing incorrect results (at least for coverage
, though the same appears to be the case for std
).
#To do