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_;
}
