boolean bigBedSummaryArray(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
enum bbiSummaryType summaryType, int summarySize, double *summaryValues)
/* Fill in summaryValues with data from indicated chromosome range in bigBed file.
* Be sure to initialize summaryValues to a default value, which will not be touched
* for regions without data in file. (Generally you want the default value to either
* be 0.0 or nan("") depending on the application.) Returns FALSE if no data
* at that position. */
{
return bbiSummaryArray(bbi, chrom, start, end, bigBedCoverageIntervals,
summaryType, summarySize, summaryValues);
}
boolean bigWigSummaryArray(char *fileName, char *chrom, bits32 start, bits32 end,
enum bbiSummaryType summaryType, int summarySize, double *summaryValues)
/* Fill in summaryValues with data from indicated chromosome range in bigWig file.
* Be sure to initialize summaryValues to a default value, which will not be touched
* for regions without data in file. (Generally you want the default value to either
* be 0.0 or nan("") depending on the application.) Returns FALSE if no data
* at that position. */
{
struct bbiFile *bwf = bigWigFileOpen(fileName);
boolean ret = bbiSummaryArray(bwf, chrom, start, end, bigWigIntervalQuery,
summaryType, summarySize, summaryValues);
bbiFileClose(&bwf);
return ret;
}
int main(int argc, char *argv[])
{
/*
1. urlpath bigwig
2. chrom
3. start
4. stop
5. spnum
6. outfile
7. summeth
*/
if(argc!=8)
{
fputs("bwquery: wrong arg\n", stderr);
return 1;
}
char *tail=NULL;
unsigned int start=strtol(argv[3],&tail,10);
if(tail[0]!='\0' || start<0)
{
fprintf(stderr, "bwquery: wrong start (%s)\n", argv[3]);
return 1;
}
unsigned int stop=strtol(argv[4],&tail,10);
if(tail[0]!='\0' || stop<=start)
{
fprintf(stderr, "bwquery: wrong stop (%s)\n", argv[4]);
return 1;
}
unsigned int spnum=strtol(argv[5],&tail,10);
if(tail[0]!='\0' || spnum<=0)
{
fprintf(stderr, "bwquery: wrong spnum (%s)\n", argv[5]);
return 1;
}
unsigned int summeth=strtol(argv[7],&tail,10);
if(tail[0]!='\0' || summeth<1)
{
fprintf(stderr, "bwquery: wrong summeth (%s)\n", argv[7]);
return 1;
}
double *data=malloc(sizeof(double)*spnum);
if(data==NULL)
{
fputs("bwquery: out of mem\n", stderr);
return 1;
}
int i;
for(i=0; i<spnum; i++) data[i]=0;
struct bbiFile *bwf = bigWigFileOpen(argv[1]);
if(bwf==NULL)
{
fprintf(stderr, "bwquery: no access to %s\n", argv[1]);
return 1;
}
bbiSummaryArray(bwf, argv[2], start, stop, (BbiFetchIntervals)bigWigIntervalQuery,
summeth==1?bbiSumMean:
summeth==2?bbiSumMax:bbiSumMin,
spnum, &data[0]);
bbiFileClose(&bwf);
FILE *fout=fopen(argv[6],"w");
if(fout==NULL)
{
fputs("bwquery: failed to open output file\n", stderr);
return 1;
}
for(i=0; i<spnum; i++)
fprintf(fout, "%f\n", data[i]);
fclose(fout);
return 0;
}
