void bedIntersect(char *aFile, char *bFile, char *outFile) /* bedIntersect - Intersect two bed files. */ { struct lineFile *lf = lineFileOpen(aFile, TRUE); struct hash *bHash = readBed(bFile); FILE *f = mustOpen(outFile, "w"); char *row[40]; int wordCount; while ((wordCount = (strictTab ? lineFileChopTab(lf, row) : lineFileChop(lf, row))) != 0) { char *chrom = row[0]; int start = lineFileNeedNum(lf, row, 1); int end = lineFileNeedNum(lf, row, 2); if (start > end) errAbort("start after end line %d of %s", lf->lineIx, lf->fileName); if (start == end && !allowStartEqualEnd) lineFileAbort(lf, "start==end (if this is legit, use -allowStartEqualEnd)"); struct binKeeper *bk = hashFindVal(bHash, chrom); if (bk != NULL) { struct binElement *hitList = NULL, *hit; if (allowStartEqualEnd && start == end) hitList = binKeeperFind(bk, start-1, end+1); else hitList = binKeeperFind(bk, start, end); if (aHitAny) { for (hit = hitList; hit != NULL; hit = hit->next) { float cov = getCov(start, end, hit->val); if (cov >= minCoverage) { outputBed(f, row, wordCount, start, end, hit->val); break; } else { struct bed5 *b = hit->val; verbose(1, "filter out %s %d %d %d %d overlap %d %d %d %.3f\n", chrom, start, end, b->start, b->end, positiveRangeIntersection(start, end, b->start, b->end), end-start, b->end-b->start, cov); } } } else { for (hit = hitList; hit != NULL; hit = hit->next) { if (getCov(start, end, hit->val) >= minCoverage) outputBed(f, row, wordCount, start, end, hit->val); } } slFreeList(&hitList); } } }
/** * Get the vector and covariance matrix * \param[out] x vector * \param[out] Sx uncertainty */ void get( VecType &x, MatType &Sx) const { get(x); getCov(Sx); }
/** * Get the vector, covariance matrix, and time * \param[out] x vector * \param[out] Sx uncertainty * \param[out] t time */ void get( VecType &x, MatType &Sx, TimeStamp &t) const { get(x); getCov(Sx); t = t_; }
/** * Get the vector, covariance matrix, and time * \param[out] x vector * \param[out] Sx uncertainty * \param[out] t time */ void get( VecType &x, MatType &Sx, double &t){ get(x); getCov(Sx); t = t_; }