void bigBedSummary(char *fileName, char *chrom, int start, int end, int dataPoints)
/* bigBedSummary - Extract summary information from a bigBed file.. */
{
/* Make up values array initialized to not-a-number. */
double nan0 = strtod("NaN", NULL);
double summaryValues[dataPoints];
int i;
for (i=0; i<dataPoints; ++i)
summaryValues[i] = nan0;
struct bbiFile *bbi = bigBedFileOpen(fileName);
if (bigBedSummaryArray(bbi, chrom, start, end, bbiSummaryTypeFromString(summaryType),
dataPoints, summaryValues))
{
for (i=0; i<dataPoints; ++i)
{
double val = summaryValues[i];
if (i != 0)
printf("\t");
if (isnan(val))
printf("n/a");
else
printf("%g", val);
}
printf("\n");
}
else
{
errAbort("no data in region %s:%d-%d in %s\n", chrom, start, end, fileName);
}
bbiFileClose(&bbi);
}
/* --- .Call ENTRY POINT --- */
SEXP BWGFile_summary(SEXP r_filename, SEXP r_chrom, SEXP r_ranges,
SEXP r_size, SEXP r_type, SEXP r_default_value)
{
pushRHandlers();
struct bbiFile * file = bigWigFileOpen((char *)CHAR(asChar(r_filename)));
enum bbiSummaryType type =
bbiSummaryTypeFromString((char *)CHAR(asChar(r_type)));
double default_value = asReal(r_default_value);
int *start = INTEGER(get_IRanges_start(r_ranges));
int *width = INTEGER(get_IRanges_width(r_ranges));
SEXP ans;
PROTECT(ans = allocVector(VECSXP, length(r_chrom)));
for (int i = 0; i < length(r_chrom); i++) {
int size = INTEGER(r_size)[i];
char *chrom = (char *)CHAR(STRING_ELT(r_chrom, i));
SEXP r_values = allocVector(REALSXP, size);
double *values = REAL(r_values);
for (int j = 0; j < size; j++)
values[j] = default_value;
SET_VECTOR_ELT(ans, i, r_values);
bool success = bigWigSummaryArray(file, chrom, start[i] - 1,
start[i] - 1 + width[i], type, size,
values);
if (!success)
warning("Failed to summarize range %d (%s:%d-%d)", i, chrom, start[i],
start[i] - 1 + width[i]);
}
bbiFileClose(&file);
popRHandlers();
UNPROTECT(1);
return ans;
}
enum bbiSummaryType I_bbiSummaryTypeFromString(const char *string)
{
char c_string[256];
strcpy(c_string, string);
return bbiSummaryTypeFromString(c_string);
}
