void bwtool_find_thresh(struct hash *options, char *favorites, char *regions, double fill,
char *thresh_type, char *thresh_s, char *bigfile, char *tmp_dir, char *outputfile)
/* the other kind of finding, based on thresholding. */
{
boolean inverse = (hashFindVal(options, "inverse") != NULL) ? TRUE : FALSE;
enum bw_op_type op= get_bw_op_type(thresh_type, inverse);
struct metaBig *mb = metaBigOpen_check(bigfile, tmp_dir, regions);
double thresh = sqlDouble(thresh_s);
FILE *out = mustOpen(outputfile, "w");
struct bed out_bed;
struct bed *section;
for (section = mb->sections; section != NULL; section = section->next)
{
struct perBaseWig *pbwList = perBaseWigLoadContinue(mb, section->chrom, section->chromStart,
section->chromEnd);
struct perBaseWig *pbw;
int i, len;
if (pbwList)
{
out_bed.chrom = pbwList->chrom;
for (pbw = pbwList; pbw != NULL; pbw = pbw->next)
{
i = 0;
len = pbw->chromEnd - pbw->chromStart;
out_bed.chromStart = out_bed.chromEnd = 0;
while (i < len)
{
while ((i < len) && (!fit_thresh(pbw->data[i], thresh, op)))
i++;
out_bed.chromStart = i + pbw->chromStart;
while ((i < len) && (fit_thresh(pbw->data[i], thresh, op)))
i++;
out_bed.chromEnd = i + pbw->chromStart;
if (out_bed.chromEnd > out_bed.chromStart)
bedTabOutN(&out_bed, 3, out);
}
}
perBaseWigFree(&pbwList);
}
}
metaBigClose(&mb);
carefulClose(&out);
}
/*----------------------------- get_next_scan -------------------------------*/
int get_next_scan( int nscan)
{
if ( nscan != 1)
{ // we don't need to fit and save at the begining
fit_thresh(nscan-1);
save_hist(nscan-1);
print_scan_result(nscan-1);
HDELET(0);
}
init_hist (nscan);
return 0;
}
