/* --- .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;
}
void bigCoverageIntoTree(struct trackDb *tdb, struct bbiFile *bbi,
char *chrom, int chromSize, struct rbTree *rt, boolean isBigBed)
/* Find biggest gap in given chromosome in bigWig or bigBed */
{
int sampleSize = 10000;
int sampleCount = chromSize/sampleSize;
if (sampleCount > 1)
{
int evenEnd = sampleCount * sampleSize;
double *summaryVals;
AllocArray(summaryVals, sampleCount);
boolean ok;
if (isBigBed)
ok = bigBedSummaryArray(bbi, chrom, 0, evenEnd, bbiSumCoverage, sampleCount, summaryVals);
else
ok = bigWigSummaryArray(bbi, chrom, 0, evenEnd, bbiSumCoverage, sampleCount, summaryVals);
if (ok)
{
int s=0, e, i;
for (i=0; i<sampleCount; ++i)
{
e = s + sampleSize;
if (summaryVals[i] > 0.0)
rangeTreeAdd(rt, s, e);
s = e;
}
}
}
}
boolean I_bigWigSummaryArray(struct bbiFile *bwf, const char *chrom, bits32 start, bits32 end,
enum bbiSummaryType summaryType, int summarySize, double *summaryValues)
{
char c_chrom[256];
strcpy(c_chrom, chrom);
return bigWigSummaryArray(bwf, c_chrom, start, end, summaryType, summarySize, summaryValues);
}
double bigWigSingleSummary(struct bbiFile *bwf, char *chrom, int start, int end,
enum bbiSummaryType summaryType, double defaultVal)
/* Return the summarized single value for a range. */
{
double arrayOfOne = defaultVal;
bigWigSummaryArray(bwf, chrom, start, end, summaryType, 1, &arrayOfOne);
return arrayOfOne;
}