void netToAxt(char *netName, char *chainName, char *tNibDir, char *qNibDir, char *axtName)
/* netToAxt - Convert net (and chain) to axt.. */
{
Bits *usedBits = findUsedIds(netName);
struct hash *chainHash;
struct chainNet *net;
struct lineFile *lf = lineFileOpen(netName, TRUE);
FILE *f = mustOpen(axtName, "w");
struct dnaSeq *tChrom = NULL;
struct nibTwoCache *qNtc = nibTwoCacheNew(qNibDir);
char *gapFileName = optionVal("gapOut", NULL);
FILE *gapFile = NULL;
if (gapFileName)
gapFile = mustOpen(gapFileName, "w");
lineFileSetMetaDataOutput(lf, f);
chainHash = chainReadUsedSwap(chainName, qChain, usedBits);
bitFree(&usedBits);
while ((net = chainNetRead(lf)) != NULL)
{
verbose(1, "Processing %s\n", net->name);
tChrom = nibTwoLoadOne(tNibDir, net->name);
if (tChrom->size != net->size)
errAbort("Size mismatch on %s. Net/nib out of sync or possibly nib dirs swapped?",
tChrom->name);
rConvert(net->fillList, tChrom, qNtc, qNibDir, chainHash, f, gapFile);
freeDnaSeq(&tChrom);
chainNetFree(&net);
}
nibTwoCacheFree(&qNtc);
}
struct seqPair *readAxtBlocks(char *fileName, struct hash *pairHash, FILE *f)
/* Read in axt file and parse blocks into pairHash */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct dyString *dy = newDyString(512);
struct axt *axt;
struct seqPair *spList = NULL, *sp;
lineFileSetMetaDataOutput(lf, f);
lineFileSetUniqueMetaData(lf);
while ((axt = axtRead(lf)) != NULL)
{
dyStringClear(dy);
dyStringPrintf(dy, "%s%c%s", axt->qName, axt->qStrand, axt->tName);
sp = hashFindVal(pairHash, dy->string);
if (sp == NULL)
{
AllocVar(sp);
slAddHead(&spList, sp);
hashAddSaveName(pairHash, dy->string, sp, &sp->name);
sp->qName = cloneString(axt->qName);
sp->tName = cloneString(axt->tName);
sp->qStrand = axt->qStrand;
}
axtAddBlocksToBoxInList(&sp->blockList, axt);
sp->axtCount += 1;
axtFree(&axt);
}
lineFileClose(&lf);
dyStringFree(&dy);
slSort(&spList, seqPairCmp);
return spList;
}
struct hash *chainReadAllWithMeta(char *fileName, FILE *f)
/* Read chains into a hash keyed by id. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct hash *hash = NULL;
lineFileSetMetaDataOutput(lf, f);
hash = chainReadUsedSwapLf(fileName, FALSE, NULL, lf);
lineFileClose(&lf);
return hash;
}
void liftNet(char *destFile, struct hash *liftHash,
int sourceCount, char *sources[], boolean querySide)
/* Lift up coordinates in .net file. */
{
FILE *f = mustOpen(destFile, "w");
int sourceIx;
int dotMod = dots;
for (sourceIx = 0; sourceIx < sourceCount; ++sourceIx)
{
char *source = sources[sourceIx];
struct lineFile *lf = lineFileOpen(source, TRUE);
struct chainNet *net;
lineFileSetMetaDataOutput(lf, f);
verbose(1, "Lifting %s\n", source);
while ((net = chainNetRead(lf)) != NULL)
{
if (querySide)
{
struct hash *newNameHash = hashNew(6);
liftFillsQ(net->fillList, newNameHash, liftHash, lf);
hashFree(&(net->nameHash));
net->nameHash = newNameHash;
}
else
{
struct liftSpec *spec = findLift(liftHash, net->name, lf);
if (spec == NULL)
{
if (how != carryMissing)
{
chainNetFree(&net);
continue;
}
}
else
{
freeMem(net->name);
net->name = cloneString(spec->newName);
net->size = spec->newSize;
liftFillsT(net->fillList, spec);
}
}
chainNetWrite(net, f);
chainNetFree(&net);
doDots(&dotMod);
}
lineFileClose(&lf);
if (dots)
verbose(1, "\n");
}
}
void chainMergeSort(int fileCount, char *files[], FILE *out, int level)
/* chainMergeSort - Combine sorted files into larger sorted file. */
{
int i;
struct chainFile *cf;
int id = 0;
struct quickHeap *h = NULL;
h = newQuickHeap(fileCount, &cmpChainScores);
/* Open up all input files and read first chain. */
for (i=0; i<fileCount; ++i)
{
AllocVar(cf);
cf->lf = lineFileOpen(files[i], TRUE);
lineFileSetMetaDataOutput(cf->lf, out);
cf->chain = chainRead(cf->lf);
if (cf->chain)
addToQuickHeap(h, cf);
else
cfEof(&cf,level); /* deal with EOF */
}
while (!quickHeapEmpty(h))
{
cf = peekQuickHeapTop(h);
if (!saveId)
cf->chain->id = ++id; /* We reset id's here. */
chainWrite(cf->chain, out);
chainFree(&cf->chain);
if ((cf->chain = chainRead(cf->lf)))
{
quickHeapTopChanged(h);
}
else
{ /* deal with EOF */
if (!removeFromQuickHeapByElem(h, cf))
errAbort("unexpected error: chainFile not found on heap");
cfEof(&cf,level);
}
}
freeQuickHeap(&h);
}
void axtRescore(char *in, char *out)
/* axtRescore - Recalculate scores in axt. */
{
struct lineFile *lf = lineFileOpen(in, TRUE);
FILE *f = mustOpen(out, "w");
struct axt *axt;
lineFileSetMetaDataOutput(lf, f);
axtScoreSchemeDnaWrite(scoreScheme, f, "axtRescore");
for (;;)
{
axt = axtRead(lf);
if (axt == NULL)
break;
axt->score = axtScore(axt, scoreScheme);
axtWrite(axt, f);
axtFree(&axt);
}
}
void chainSplit(char *outDir, int inCount, char *inFiles[])
/* chainSplit - Split chains up by target or query sequence. */
{
struct hash *hash = newHash(0);
int inIx;
char tpath[512];
FILE *meta ;
bool metaOpen = TRUE;
makeDir(outDir);
safef(tpath, sizeof(tpath), "%s/meta.tmp", outDir);
meta = mustOpen(tpath,"w");
for (inIx = 0; inIx < inCount; ++inIx)
{
struct lineFile *lf = lineFileOpen(inFiles[inIx], TRUE);
struct chain *chain;
FILE *f;
lineFileSetMetaDataOutput(lf, meta);
while ((chain = chainRead(lf)) != NULL)
{
char *name = (splitOnQ ? chain->qName : chain->tName);
if (lump > 0)
name = lumpName(name);
if ((f = hashFindVal(hash, name)) == NULL)
{
char path[512], cmd[512];
safef(path, sizeof(path),"%s/%s.chain", outDir, name);
if (metaOpen)
fclose(meta);
metaOpen = FALSE;
safef(cmd,sizeof(cmd), "cat %s | sort -u > %s", tpath, path);
mustSystem(cmd);
f = mustOpen(path, "a");
hashAdd(hash, name, f);
}
chainWrite(chain, f);
chainFree(&chain);
}
lineFileClose(&lf);
}
}
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 liftChain(char *destFile, struct hash *liftHash,
int sourceCount, char *sources[], boolean querySide)
/* Lift up coordinates in .chain file. */
{
FILE *f = mustOpen(destFile, "w");
int sourceIx;
int dotMod = dots;
for (sourceIx = 0; sourceIx < sourceCount; ++sourceIx)
{
char *source = sources[sourceIx];
struct lineFile *lf = lineFileOpen(source, TRUE);
struct chain *chain;
lineFileSetMetaDataOutput(lf, f);
verbose(1, "Lifting %s\n", source);
while ((chain = chainRead(lf)) != NULL)
{
struct liftSpec *spec;
char *seqName = querySide ? chain->qName : chain->tName;
spec = findLift(liftHash, seqName, lf);
if (spec == NULL)
{
if (how != carryMissing)
{
chainFree(&chain);
continue;
}
}
else
{
struct cBlock *b = NULL;
int offset = spec->offset;
if (spec->strand == '-')
{
if (querySide)
{
int qSpan = chain->qEnd - chain->qStart;
if (chain->qStrand == '-')
chain->qStart += spec->offset;
else
{
chain->qStart = spec->newSize - spec->offset
- (chain->qSize - chain->qStart);
}
chain->qEnd = chain->qStart + qSpan;
chain->qStrand = flipStrand(chain->qStrand);
freeMem(chain->qName);
chain->qName = cloneString(spec->newName);
chain->qSize = spec->newSize;
/* We don't need to mess with the blocks here
* since they are all relative to the start. */
}
else
{
/* We try and keep the target strand positive, so we end up
* flipping in both target and query and flipping the target
* strand. */
reverseIntRange(&chain->qStart, &chain->qEnd, chain->qSize);
reverseIntRange(&chain->tStart, &chain->tEnd, chain->tSize);
chain->qStrand = flipStrand(chain->qStrand);
/* Flip around blocks and add offset. */
for (b=chain->blockList; b != NULL; b=b->next)
{
reverseIntRange(&b->qStart, &b->qEnd, chain->qSize);
reverseIntRange(&b->tStart, &b->tEnd, chain->tSize);
b->tStart += offset;
b->tEnd += offset;
}
slReverse(&chain->blockList);
/* On target side add offset as well and update name and size. */
chain->tStart += offset;
chain->tEnd += offset;
freeMem(chain->tName);
chain->tName = cloneString(spec->newName);
chain->tSize = spec->newSize;
}
}
else
{
if (querySide)
{
if (chain->qStrand == '-')
offset = spec->newSize - (spec->offset + spec->oldSize);
freeMem(chain->qName);
chain->qName = cloneString(spec->newName);
chain->qSize = spec->newSize;
chain->qStart += offset;
chain->qEnd += offset;
for (b=chain->blockList; b != NULL; b=b->next)
{
b->qStart += offset;
b->qEnd += offset;
}
}
else
{
freeMem(chain->tName);
chain->tName = cloneString(spec->newName);
chain->tSize = spec->newSize;
chain->tStart += offset;
chain->tEnd += offset;
for (b=chain->blockList; b != NULL; b=b->next)
{
b->tStart += offset;
b->tEnd += offset;
}
}
}
}
chainWrite(chain, f);
chainFree(&chain);
doDots(&dotMod);
}
lineFileClose(&lf);
if (dots)
verbose(1, "\n");
}
}
void liftAxt(char *destFile, struct hash *liftHash,
int sourceCount, char *sources[], boolean querySide)
/* Lift up coordinates in .axt file. */
{
FILE *f = mustOpen(destFile, "w");
int sourceIx;
int dotMod = dots;
for (sourceIx = 0; sourceIx < sourceCount; ++sourceIx)
{
char *source = sources[sourceIx];
struct lineFile *lf = lineFileOpen(source, TRUE);
struct axt *axt;
lineFileSetMetaDataOutput(lf, f);
verbose(1, "Lifting %s\n", source);
while ((axt = axtRead(lf)) != NULL)
{
struct liftSpec *spec;
struct axt a = *axt;
char *seqName;
if (querySide)
seqName = a.qName;
else
seqName = a.tName;
spec = findLift(liftHash, seqName, lf);
if (spec == NULL)
{
if (how != carryMissing)
{
axtFree(&axt);
continue;
}
}
else
{
int offset;
char strand = (querySide ? a.qStrand : a.tStrand);
cantHandleSpecRevStrand(spec);
if (strand == '-')
{
int ctgEnd = spec->offset + spec->oldSize;
offset = spec->newSize - ctgEnd;
}
else
offset = spec->offset;
if (querySide)
{
a.qStart += offset;
a.qEnd += offset;
a.qName = spec->newName;
}
else
{
a.tStart += offset;
a.tEnd += offset;
a.tName = spec->newName;
if (strand == '-')
warn("Target minus strand, please double check results.");
}
}
axtWrite(&a, f);
axtFree(&axt);
doDots(&dotMod);
}
lineFileClose(&lf);
if (dots)
verbose(1, "\n");
}
}
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);
}