void chainPreNet(char *inFile, char *targetSizes, char *querySizes,
char *outFile)
/* chainPreNet - Remove chains that don't have a chance of being netted. */
{
struct hash *tHash = setupChroms(targetSizes);
struct hash *qHash = setupChroms(querySizes);
struct lineFile *lf = lineFileOpen(inFile, TRUE);
FILE *f = mustOpen(outFile, "w");
struct chain *chain;
double score, lastScore = 9e99;
struct chrom *qChrom, *tChrom;
lineFileSetMetaDataOutput(lf, f);
while ((chain = chainRead(lf)) != NULL)
{
/* Report progress. */
dotOut();
/* Check to make sure it really is sorted by score. */
score = chain->score;
if (score > lastScore)
{
errAbort("%s not sorted by score line %d",
lf->fileName, lf->lineIx);
}
lastScore = score;
/* Output chain if necessary and then free it. */
qChrom = hashMustFindVal(qHash, chain->qName);
tChrom = hashMustFindVal(tHash, chain->tName);
if (chainUsed(chain, qChrom, tChrom) && inclQuery(chain))
{
chainWrite(chain, f);
}
chainFree(&chain);
}
}
void chainNet(char *chainFile, char *tSizes, char *qSizes,
char *tNet, char *qNet)
/* chainNet - Make alignment nets out of chains. */
{
struct lineFile *lf = lineFileOpen(chainFile, TRUE);
struct hash *qHash, *tHash;
struct chrom *qChromList, *tChromList, *tChrom, *qChrom;
struct chain *chain;
double lastScore = -1;
struct lm *lm = lmInit(0);
struct rbTreeNode **rbStack;
FILE *tNetFile = mustOpen(tNet, "w");
FILE *qNetFile = mustOpen(qNet, "w");
lmAllocArray(lm, rbStack, 256);
makeChroms(qSizes, lm, rbStack, &qHash, &qChromList);
makeChroms(tSizes, lm, rbStack, &tHash, &tChromList);
verbose(1, "Got %d chroms in %s, %d in %s\n", slCount(tChromList), tSizes,
slCount(qChromList), qSizes);
lineFileSetMetaDataOutput(lf, tNetFile);
lineFileSetMetaDataOutput(lf, qNetFile);
/* Loop through chain file building up net. */
while ((chain = chainRead(lf)) != NULL)
{
/* Make sure that input is really sorted. */
if (lastScore >= 0 && chain->score > lastScore)
errAbort("%s must be sorted in order of score", chainFile);
lastScore = chain->score;
if (chain->score < minScore)
{
break;
}
verbose(2, "chain %f (%d els) %s %d-%d %c %s %d-%d\n",
chain->score, slCount(chain->blockList),
chain->tName, chain->tStart, chain->tEnd,
chain->qStrand, chain->qName, chain->qStart, chain->qEnd);
qChrom = hashMustFindVal(qHash, chain->qName);
if (qChrom->size != chain->qSize)
errAbort("%s is %d in %s but %d in %s", chain->qName,
chain->qSize, chainFile,
qChrom->size, qSizes);
tChrom = hashMustFindVal(tHash, chain->tName);
if (tChrom->size != chain->tSize)
errAbort("%s is %d in %s but %d in %s", chain->tName,
chain->tSize, chainFile,
tChrom->size, tSizes);
if (!inclQuery(chain))
verbose(2, "skipping chain on query %s\n", chain->qName);
else
{
addChain(qChrom, tChrom, chain);
verbose(2, "%s has %d inserts, %s has %d\n", tChrom->name,
tChrom->spaces->n, qChrom->name, qChrom->spaces->n);
}
}
/* Build up other side of fills. It's just for historical
* reasons this is not done during the main build up.
* It's a little less efficient this way, but to change it
* some hard reverse strand issues would have to be juggled. */
verbose(1, "Finishing nets\n");
finishNet(qChromList, TRUE);
finishNet(tChromList, FALSE);
/* Write out basic net files. */
verbose(1, "writing %s\n", tNet);
outputNetSide(tChromList, tNetFile, FALSE);
verbose(1, "writing %s\n", qNet);
outputNetSide(qChromList, qNetFile, TRUE);
/* prevent SIGPIPE in preceding process if input is a pipe, consume remainder
* of input file since we stop before EOF. */
if (isPipe(lf->fd))
{
char *line;
while(lineFileNext(lf, &line, NULL))
continue;
}
lineFileClose(&lf);
if (verboseLevel() > 1)
printMem(stderr);
}
