int main(int argc, char *argv[]) /* Process command line. */ { char *task; optionInit(&argc, argv, options); if (argc < 2) usage("must supply a task"); task = argv[1]; gMaxRows = optionInt("maxRows", gMaxRows); gMinRows = optionInt("minRows", gMinRows); gNeedRows = optionInt("minRows", gNeedRows); gWhere = optionVal("where", gWhere); gChrom = optionVal("chrom", gChrom); gOutput = optionVal("output", gOutput); if (sameString(task, "readTable")) { if (argc != 4) usage("readTable task requires two arguments"); readTableTask(argv[2], argv[3]); } else if (sameString(task, "readFile")) { if (argc != 3) usage("readFile task requires one argument"); readFile(argv[2]); } else { usage("invalid task"); } return 0; }
int main(int argc, char *argv[]) { char *altGraphXOutName = NULL; char *altLogFileName = NULL; char *bedViewOutFileName =NULL; if(argc < 6) usage(); optionHash(&argc, argv); doSScores = optionExists("doSScores"); altGraphXOutName = optionVal("altGraphXOut", NULL); minConfidence = optionInt("minConf", 0); altLogFileName = optionVal("altLogFile", NULL); flankingSize = optionInt("flankingSize", 100); bedViewOutFileName = optionVal("bedViewFile", NULL); minControlConf = optionInt("minControlConf", 0); warn("Flanking size is: %d", flankingSize); if(altLogFileName != NULL) altLogFile = mustOpen(altLogFileName, "w"); if(bedViewOutFileName != NULL) bedViewOutFile = mustOpen(bedViewOutFileName, "w"); if(altGraphXOutName) { warn("Writing alts to %s", altGraphXOutName); altGraphXOut = mustOpen(altGraphXOutName, "w"); } altSummary(argv[1], argv[2], argv[3], argv[4], argv[5]); if(altGraphXOut != NULL) carefulClose(&altGraphXOut); if(altLogFile != NULL) carefulClose(&altLogFile); if(bedViewOutFile != NULL) carefulClose(&bedViewOutFile); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { char *command; bzpTime(NULL); dnaUtilOpen(); setMaxAlloc(2LL*1024LL*1024LL*1024LL); optionInit(&argc, argv, options); port = optionInt("port", port); host = optionVal("host", host); netParseSubnet(optionVal("subnet", NULL), subnet); cpuCount = optionInt("cpu", cpuCount); if (argc < 2) usage(); command = argv[1]; if (sameWord(command, "start")) { if (argc < 3) usage(); serverStart(argv+2, argc-2); } else if (sameWord(command, "stop")) { serverStop(); } else if (sameWord(command, "status")) { serverStatus(); } else usage(); return 0; }
int main(int argc, char* argv[]) /* parse command line */ { int numMrnas; int numEsts; char *accList, *selectAccFile; char *database, *relName, *outDir; verboseSetLevel(0); optionInit(&argc, argv, optionSpecs); if (argc != 4) usage(); relName = argv[1]; database = argv[2]; outDir = argv[3]; numMrnas = optionInt("numMrnas", 10); numEsts = optionInt("numEsts", 10); accList = optionVal("accList", NULL); selectAccFile = optionVal("selectAcc", NULL); gbVerbInit(optionInt("verbose", 0)); if (verboseLevel() > 0) setlinebuf(stderr); getTestSubset(numMrnas, numEsts, accList, selectAccFile, relName, database, outDir); return 0; }
int main(int argc, char *argv[]) { char *exclude = NULL; int daysOld = 0; optionInit(&argc, argv, optionSpecs); theTable = optionVal("table", theTable); daysOld = optionInt("daysOld", daysOld); hoursOld = optionInt("hoursOld", hoursOld) + (24 * daysOld); exclude = optionVal("exclude", exclude); ignoreBlocks = optionExists("ignoreBlocks"); verboseBlocks= optionExists("verboseBlocks"); justList = optionExists("justList"); processExcludes(exclude); db = argv[1]; /* Allow "checkTableCoords db table" usage too: */ if (theTable == NULL && argc == 3) { theTable = argv[2]; argc = 2; } if (argc != 2) usage(); verboseSetLogFile("stdout"); return checkTableCoords(argv[1]); }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 3) usage(); clSeq = optionVal("seq", clSeq); clStart = optionInt("start", clStart); clEnd = optionInt("end", clEnd); clSeqList = optionVal("seqList", clSeqList); clBpt = optionVal("bpt", clBpt); clBed = optionVal("bed", clBed); clBedPos = optionExists("bedPos"); noMask = optionExists("noMask"); udcSetDefaultDir(optionVal("udcDir", udcDefaultDir())); if (clBedPos && !clBed) errAbort("the -bedPos option requires the -bed option"); if (clBed != NULL) { if (clSeqList != NULL) errAbort("Can only have seqList or bed options, not both."); if (clSeq != NULL) errAbort("Can only have seq or bed options, not both."); } if ((clStart > clEnd) && (clSeq == NULL)) errAbort("must specify -seq with -start and -end"); if ((clSeq != NULL) && (clSeqList != NULL)) errAbort("can't specify both -seq and -seqList"); dnaUtilOpen(); twoBitToFa(argv[1], argv[2]); return 0; }
int main(int argc, char* argv[]) { char *relName, *updateName, *typeAccPrefix, *database, *sep; struct gbIndex* index; struct gbSelect select; struct gbSelect* prevSelect = NULL; struct gbAlignInfo alignInfo; boolean noMigrate; ZeroVar(&select); optionInit(&argc, argv, optionSpecs); if (argc != 5) usage(); maxFaSize = optionInt("fasize", -1); workDir = optionVal("workdir", "work/align"); noMigrate = optionExists("noMigrate"); createPolyASizes = optionExists("polyASizes"); gbVerbInit(optionInt("verbose", 0)); relName = argv[1]; updateName = argv[2]; typeAccPrefix = argv[3]; database = argv[4]; /* parse typeAccPrefix */ sep = strchr(typeAccPrefix, '.'); if (sep != NULL) *sep = '\0'; select.type = gbParseType(typeAccPrefix); if (sep != NULL) { select.accPrefix = sep+1; *sep = '.'; } select.orgCats = gbParseOrgCat(optionVal("orgCats", "native,xeno")); index = gbIndexNew(database, NULL); select.release = gbIndexMustFindRelease(index, relName); select.update = gbReleaseMustFindUpdate(select.release, updateName); gbVerbMsg(0, "gbAlignGet: %s/%s/%s/%s", select.release->name, select.release->genome->database, select.update->name, typeAccPrefix); /* Get the release to migrate, if applicable */ if (!noMigrate) prevSelect = gbAlignGetMigrateRel(&select); alignInfo = gbAlignGet(&select, prevSelect); /* always print stats */ fprintf(stderr, "gbAlignGet: %s/%s/%s/%s: align=%d, migrate=%d\n", select.release->name, select.release->genome->database, select.update->name, typeAccPrefix, alignInfo.align.accTotalCnt, alignInfo.migrate.accTotalCnt); gbIndexFree(&index); /* print alignment and migrate count, which is read by the driver program */ printf("alignCnt: %d %d\n", alignInfo.align.accTotalCnt, alignInfo.migrate.accTotalCnt); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 3) usage(); minSize = optionInt("minSize", minSize); minTrim = optionInt("minTrim", minTrim); cdwFastqPolyFilter(argv[1], argv[2]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionHash(&argc, argv); if (argc != 5) usage(); maxErr = optionInt("maxErr", maxErr); maxWarn = optionInt("maxWarn", maxWarn); hgClonePos(argv[1], argv[2], argv[3], argv[4]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); dotEvery = optionInt("dots", 0); numThreads = optionInt("threads", DEFTHREADS); if (argc != 5) usage(); hgExpDistance(argv[1], argv[2], argv[3], argv[4]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); testMax = optionInt("testMax", testMax); oneSubmissionSet = optionInt("oneSubmissionSet", oneSubmissionSet); if (argc != 4) usage(); vgLoadJax(argv[1], argv[2], argv[3]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionHash(&argc, argv); if (argc < 4) usage(); chunkSize = optionInt("chunkSize", chunkSize); maxLines = optionInt("maxLines", maxLines); stripVer = optionExists("stripVer"); pslSplit(argv[1], argv[2], &argv[3], argc-3); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); dots = optionInt("dots", dots); pad = optionInt("pad", pad); inclHap = optionExists("inclHap"); if (argc != 5) usage(); chainPreNet(argv[1], argv[2], argv[3], argv[4]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc != 3) usage("wrong # args"); gOutLevels = optionInt("outLevels", gOutLevels); gPartSize = optionInt("partSize", gPartSize); gDropContained = optionExists("dropContained"); pslPartition(argv[1], argv[2]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionHash(&argc, argv); minGapSize = optionInt("minGapSize", minGapSize); scaffoldGapSize = optionInt("scaffoldGapSize", scaffoldGapSize); if (argc != 2) usage(); scaffoldFaToAgp(argv[1]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); clJoinSize = optionInt("joinSize", clJoinSize); clMinCluster = optionInt("minCluster", clMinCluster); clHist = optionExists("hist"); if (argc != 3) usage(); edwClusterMethylBed(argv[1], argv[2]); return 0; }
void netToBed(char *inName, char *outName) /* netToBed - Convert target coverage of net to a bed file.. */ { if (optionExists("maxGap") || optionExists("minFill")) { maxGap = optionInt("maxGap", maxGap); minFill = optionInt("minFill", minFill); netToBedDetailed(inName, outName, maxGap, minFill); } else netToBedSimple(inName, outName); }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); blockSize = optionInt("blockSize", blockSize); itemsPerSlot = optionInt("itemsPerSlot", (blockSize+1)/2); noCheckSort = optionExists("noCheckSort"); if (argc != 3) usage(); crTreeIndexBed(argv[1], argv[2]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); chrom = optionVal("chrom", NULL); minGap = optionInt("minGap", minGap); minRepeat = optionInt("minRepeat", minRepeat); if (argc != 4) usage(); mafSplitPos(argv[1], argv[2], argv[3]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 3) usage(); clChrom = optionVal("chrom", clChrom); clStart = optionInt("start", clStart); clEnd = optionInt("end", clEnd); udcSetDefaultDir(optionVal("udcDir", udcDefaultDir())); bigWigToWig(argv[1], argv[2]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); blockSize = optionInt("blockSize", blockSize); itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot); bedFields = optionInt("bedFields", bedFields); as = optionVal("as", as); if (argc != 4) usage(); bedToBigBed(argv[1], argv[2], argv[3]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc != 6) usage(); minSpace = optionInt("minSpace", minSpace); minFill = optionInt("minFill", minSpace/2); minScore = optionInt("minScore", minScore); inclHap = optionExists("inclHap"); chainNet(argv[1], argv[2], argv[3], argv[4], argv[5]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); maxGap = optionInt("maxGap", maxGap); maxChain = optionInt("maxChain", maxChain); minIdRatio = optionFloat("minId", 0.0)/100.0; minScore = optionFloat("minScore", minScore); bedOut = optionExists("bed"); if (argc != 5) usage(); doIt(argv[1], argv[2], argv[3], argv[4]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionHash(&argc, argv); if (argc != 3) usage(); tStartSize = optionInt("tStartSize", 0); chunkSize = optionInt("chunkSize", 0); if (chunkSize && tStartSize) usage(); tSS = (double)tStartSize; axtSplitByTarget(argv[1], argv[2]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 3) usage(); chromColIx = optionInt("chromColIx", chromColIx); startColIx = optionInt("startColIx", startColIx); endColIx = optionInt("endColIx", endColIx); scoreColIx = optionInt("scoreColIx", scoreColIx); regBedStats(argv[1], argv[2]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 4) usage(); name = optionVal("name", "chrUn"); //vOption = optionExists("v"); //minSize = optionInt("minSize", -1); maxOutputSize = optionInt("maxOutputSize", maxOutputSize); gapSize = optionInt("gapSize", 25); faCat(argv[1],argv[2], argv[3]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionHash(&argc, argv); scale = optionFloat("scale", scale); maxGap = optionInt("maxGap", maxGap); near = optionInt("near", near); sampleList = optionVal("samples", cloneString(sampleList)); if (argc != 2) usage(); calcGap(argv[1]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); test = optionExists("test"); mergeGap = optionInt("mergeGap", mergeGap); minSize = optionInt("minSize", minSize); maxSize = optionInt("maxSize", maxSize); minSeqSize = optionInt("minSeqSize", minSeqSize); if (argc != 4) usage(); database = argv[1]; hgLoadMafSummary(database, argv[2], argv[3]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { warn("Program obsolete - try using alphaAsm instead"); optionInit(&argc, argv, options); if (argc != 4) usage(); maxChainSize = optionInt("size", maxChainSize); outSize = optionInt("outSize", outSize); fullOnly = optionExists("fullOnly"); int seed = optionInt("seed", (int)time(0)); srand(seed); alphaChain(argv[1], argv[2], argv[3]); return 0; }
int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 2) usage(); maxChainSize = optionInt("size", maxChainSize); minUse = optionInt("minUse", minUse); maxNonsenseSize = optionInt("maxNonsenseSize", maxNonsenseSize); lower = optionExists("lower"); unpunc = optionExists("unpunc"); fullOnly = optionExists("fullOnly"); wordChain(argv[1], maxChainSize); return 0; }