void axtAndBed(char *inAxt, char *inBed, char *outAxt)
/* axtAndBed - Intersect an axt with a bed file and output axt.. */
{
struct hash *tHash = readBed(inBed); /* target keyed, binKeeper value */
struct lineFile *lf = lineFileOpen(inAxt, TRUE);
struct axt *axt;
struct binElement *list = NULL, *el;
FILE *f = mustOpen(outAxt, "w");
struct axtScoreScheme *ss = axtScoreSchemeDefault();
while ((axt = axtRead(lf)) != NULL)
{
struct chromInfo *ci = hashFindVal(tHash, axt->tName);
if (ci != NULL)
{
list = binKeeperFind(ci->bk, axt->tStart, axt->tEnd);
if (list != NULL)
{
/* Flatten out any overlapping elements by projecting them
* onto a 0/1 valued character array and then looking for
* runs of 1 in this array. */
int tStart = axt->tStart;
int tEnd = axt->tEnd;
int tSize = tEnd - tStart;
int i, s = 0;
char c, lastC = 0;
char *merger = NULL;
AllocArray(merger, tSize+1);
for (el = list; el != NULL; el = el->next)
{
int s = el->start - tStart;
int e = el->end - tStart;
int sz;
if (s < 0) s = 0;
if (e > tSize) e = tSize;
sz = e - s;
if (sz > 0)
memset(merger + s, 1, sz);
}
for (i=0; i<=tSize; ++i)
{
c = merger[i];
if (c && !lastC)
{
s = i;
lastC = c;
}
else if (!c && lastC)
{
axtSubsetOnT(axt, s+tStart, i+tStart, ss, f);
lastC = c;
}
}
freez(&merger);
slFreeList(&list);
}
}
axtFree(&axt);
}
}
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);
}
}
}
void addBed(char *file, struct hash *fileHash)
{
char name[128];
if (!endsWith(file, ".bed"))
errAbort("filenames in bed list must end in '.bed'");
splitPath(file, NULL, name, NULL);
hashAdd(fileHash, name, readBed(file));
}
