int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc != 7) { usage(); } tMasked = optionExists("tMasked"); chainToPsl(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6]); return 0; }
static struct chromBins* loadMapChains(char *chainFile) /* read a chain file, convert to mapAln object and chromBins by query locations. */ { struct chromBins* mapAlns = chromBinsNew((chromBinsFreeFunc*)pslFree); struct chain *ch; struct lineFile *chLf = lineFileOpen(chainFile, TRUE); while ((ch = chainRead(chLf)) != NULL) { struct mapAln *mapAln = chainToPsl(ch); chromBinsAdd(mapAlns, mapAln->psl->qName, mapAln->psl->qStart, mapAln->psl->qEnd, mapAln); chainFree(&ch); } lineFileClose(&chLf); return mapAlns; }