static struct chromSize *getChroms(char *db)
/* get list of chroms to use in tests */
{
struct slName *specs = optionMultiVal("chrom", NULL);
if (specs == NULL)
return getLongestChrom(db);
else if (slNameInList(specs, "all"))
return getAllChroms(db);
else
return getChromsFromSpecs(db, specs);
}
void bigWigMerge(int inCount, char *inFiles[], char *outFile)
/* bigWigMerge - Merge together multiple bigWigs into a single one.. */
{
/* Make a list of open bigWig files. */
struct bbiFile *inFile, *inFileList = NULL;
int i;
for (i=0; i<inCount; ++i)
{
if (clInList)
{
addWigsInFile(inFiles[i], &inFileList);
}
else
{
inFile = bigWigFileOpen(inFiles[i]);
slAddTail(&inFileList, inFile);
}
}
FILE *f = mustOpen(outFile, "w");
struct bbiChromInfo *chrom, *chromList = getAllChroms(inFileList);
verbose(1, "Got %d chromosomes from %d bigWigs\nProcessing",
slCount(chromList), slCount(inFileList));
double *mergeBuf = NULL;
int mergeBufSize = 0;
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
struct lm *lm = lmInit(0);
/* Make sure merge buffer is big enough. */
int chromSize = chrom->size;
verboseDot();
verbose(2, "Processing %s (%d bases)\n", chrom->name, chromSize);
if (chromSize > mergeBufSize)
{
mergeBufSize = chromSize;
freeMem(mergeBuf);
mergeBuf = needHugeMem(mergeBufSize * sizeof(double));
}
int i;
for (i=0; i<chromSize; ++i)
mergeBuf[i] = 0.0;
/* Loop through each input file grabbing data and merging it in. */
for (inFile = inFileList; inFile != NULL; inFile = inFile->next)
{
struct bbiInterval *ivList = bigWigIntervalQuery(inFile, chrom->name, 0, chromSize, lm);
verbose(3, "Got %d intervals in %s\n", slCount(ivList), inFile->fileName);
struct bbiInterval *iv;
for (iv = ivList; iv != NULL; iv = iv->next)
{
double val = iv->val;
if (val > clClip)
val = clClip;
int end = iv->end;
for (i=iv->start; i < end; ++i)
mergeBuf[i] += val;
}
}
/* Output each range of same values as a bedGraph item */
int sameCount;
for (i=0; i<chromSize; i += sameCount)
{
sameCount = doublesTheSame(mergeBuf+i, chromSize-i);
double val = mergeBuf[i] + clAdjust;
if (val > clThreshold)
fprintf(f, "%s\t%d\t%d\t%g\n", chrom->name, i, i + sameCount, val);
}
lmCleanup(&lm);
}
verbose(1, "\n");
carefulClose(&f);
}
