60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b jcasper Fri Jun 11 15:17:21 2021 -0700 Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593 diff --git src/hg/inc/cStraw.h src/hg/inc/cStraw.h new file mode 100644 index 0000000..7a7a576 --- /dev/null +++ src/hg/inc/cStraw.h @@ -0,0 +1,34 @@ +/* cStraw - a wrapper header file for making C++ functions associated with retrieving + * data from .hic files available to C libraries. The underlying functions come + * from the Straw library by the Aiden Lab at the Broad Institute (see + * kent/src/hg/lib/straw/). +*/ +#ifndef CSTRAW_H +#define CSTRAW_H + +typedef struct Straw Straw; + +Straw *cStrawOpen (char *fname); +/* Return a pointer to a Straw object for further operations (i.e. reads) */ + +Straw *cStrawClose (Straw **hicFile); +/* Close out a Straw record, freeing the object */ + +char* cStraw (Straw *hicFile, char *norm, int binsize, char *chr1loc, char *chr2loc, char *unit, int **xActual, int **yActual, double **counts, int *numRecords); +/* Wrapper function to retrieve a data chunk from a .hic file, for use by C libraries. + * norm is one of NONE/VC/VC_SQRT/KR. + * binsize is one of the supported bin sizes as determined by cStrawHeader. + * chr1loc and chr2loc are the two positions to retrieve interaction data for, specified as chr:start-end. + * unit is one of BP/FRAG. + * Values are returned in newly allocated arrays in xActual, yActual, and counts, with the number of + * returned records in numRecords. + * The function returns NULL unless an error was encountered, in which case the return value points + * to a character string explaining the error. */ + +char* cStrawHeader (Straw *hicFile, char **genome, char ***chromNames, int **chromSizes, int *nChroms, char ***bpResolutions, int *nBpRes, char ***fragResolutions, int *nFragRes, char ***attributes, int *nAttributes); +/* Wrapper function to retrieve header fields from a .hic file, for use by C libraries. + * This retrieves the assembly name, list of chromosome names, list of available binsize resolutions, + * and list of available fragment resolutions in the specific .hic file. + * The function returns NULL unless an error was encountered, in which case the return value points + * to a character string explaining the error. */ +#endif