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); }