int bigWigOutRegion(char *table, struct sqlConnection *conn,
struct region *region, int maxOut,
enum wigOutputType wigOutType)
/* Write out bigWig for region, doing intersecting and filtering as need be. */
{
boolean isMerged = anySubtrackMerge(table, database);
int resultCount = 0;
char *wigFileName = bigWigFileName(table, conn);
if (wigFileName)
{
struct bbiFile *bwf = bigWigFileOpen(wigFileName);
if (bwf)
{
/* Easy case, just dump out data. */
if (!anyFilter() && !anyIntersection() && !isMerged && wigOutType == wigOutData)
resultCount = bigWigIntervalDump(bwf, region->chrom, region->start, region->end,
maxOut, stdout);
/* Pretty easy case, still do it ourselves. */
else if (!isMerged && wigOutType == wigOutData)
{
double ll, ul;
enum wigCompare cmp;
getWigFilter(database, curTable, &cmp, &ll, &ul);
struct lm *lm = lmInit(0);
struct bbiInterval *ivList, *iv;
ivList = intersectedFilteredBbiIntervalsOnRegion(conn, bwf, region, cmp, ll, ul, lm);
for (iv=ivList; iv != NULL && resultCount < maxOut; iv = iv->next, ++resultCount)
{
fprintf(stdout, "%s\t%d\t%d\t%g\n", region->chrom, iv->start, iv->end, iv->val);
}
lmCleanup(&lm);
}
/* Harder cases - resort to making a data vector and letting that machinery handle it. */
else
{
struct dataVector *dv = bigWigDataVector(table, conn, region);
resultCount = wigPrintDataVectorOut(dv, wigOutType, maxOut, NULL);
dataVectorFree(&dv);
}
}
bbiFileClose(&bwf);
}
freeMem(wigFileName);
return resultCount;
}
void bigWigToWig(char *inFile, char *outFile)
/* bigWigToWig - Convert bigWig to wig. This will keep more of the same structure of the
* original wig than bigWigToBedGraph does, but still will break up large stepped sections into
* smaller ones. */
{
struct bbiFile *bwf = bigWigFileOpen(inFile);
FILE *f = mustOpen(outFile, "w");
struct bbiChromInfo *chrom, *chromList = bbiChromList(bwf);
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
if (clChrom != NULL && !sameString(clChrom, chrom->name))
continue;
char *chromName = chrom->name;
int start = 0, end = chrom->size;
if (clStart > 0)
start = clStart;
if (clEnd > 0)
end = clEnd;
bigWigIntervalDump(bwf, chromName, start, end, 0, f);
}
bbiChromInfoFreeList(&chromList);
carefulClose(&f);
bbiFileClose(&bwf);
}