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 hash *chainReadAllSwap(char *fileName, boolean swapQ)
/* Read chains into a hash keyed by id. */
{
return chainReadUsedSwap(fileName, swapQ, NULL);
}
