int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 6)
usage();
minExp = optionDouble("minExp", minExp);
minAct = optionDouble("minAct", minAct);
regCompanionEnhProCellSpecificPairs(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);
if (argc != 4)
usage();
gStart = optionDouble("start", gStart);
gEnd = optionDouble("end", gEnd);
distributeRgbRainbow(argv[1], argv[2], argv[3]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
maxGap = optionInt("maxGap", maxGap);
minSumScore = optionDouble("minSumScore", minSumScore);
scoreNormFactor = optionDouble("scoreNormFactor", scoreNormFactor);
inNoiseThreshold = optionDouble("inNoiseThreshold", inNoiseThreshold);
if (argc != 3)
usage();
regChromiaMergeWindows(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
eVal = optionDouble("eVal", eVal);
pslxFmt = optionExists("pslx");
convertToNucCoords = optionExists("convertToNucCoords");
forcePsiBlast = optionExists("forcePsiBlast");
char *qNameSrcStr = optionVal("qName", "query-def0");
if (sameString(qNameSrcStr, "query-ID"))
qNameSrc = qNameSrcQueryId;
else if (sameString(qNameSrcStr, "query-def0"))
qNameSrc = qNameSrcQueryDef0;
else
errAbort("invalid value for -qName, expect on of: \"query-ID\", or \"query-def0\", got \"%s\"", qNameSrcStr);
char *tNameSrcStr = optionVal("tName", "Hit_def0");
if (sameString(tNameSrcStr, "Hit_id"))
tNameSrc = tNameSrcHitId;
else if (sameString(tNameSrcStr, "Hit_def0"))
tNameSrc = tNameSrcHitDef0;
else if (sameString(tNameSrcStr, "Hit_accession"))
tNameSrc = tNameSrcHitAccession;
else
errAbort("invalid value for -tName, expect on of: \"Hit_id\", \"Hit_def0\", or \"Hit_accession\", got \"%s\"", tNameSrcStr);
blastXmlToPsl(argv[1], argv[2], optionVal("scores", NULL));
if (errCount > 0)
errAbort("%d invalid PSLs created", errCount);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc < 4)
usage();
clAgree = optionInt("agree", clAgree);
clAdd = optionExists("add");
clGotThreshold = optionExists("threshold");
clThreshold = optionDouble("threshold", clThreshold);
if (optionExists("maxMin"))
{
clGotThreshold = TRUE;
clThreshold = maxMinOfReplicates(argc-2, argv+1, SCORE_COL_IX);
}
if (optionExists("addMin"))
{
clGotThreshold = TRUE;
clThreshold = addMinOfReplicates(argc-2, argv+1, SCORE_COL_IX);
}
if (clGotThreshold)
verbose(2, "Threshold %g\n", clThreshold);
clUniqueName = optionExists("uniqueName");
encodeMergeReplicates(argc-2, argv+1, argv[argc-1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
clThreshold = optionDouble("threshold", clThreshold);
clAdjust = optionDouble("adjust", clAdjust);
clClip = optionDouble("clip", clClip);
clInList = optionExists("inList");
int minArgs = 4;
if (clInList)
minArgs -= 1;
if (argc < minArgs)
usage();
bigWigMerge(argc-2, argv+1, argv[argc-1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 4)
usage();
frag = optionDouble("frag", frag);
txCdsGoodBed(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();
restrictFile = optionVal("restrict", restrictFile);
threshold = optionDouble("threshold", threshold);
bigWigCorrelate(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
eVal = optionDouble("eVal", eVal);
pslxFmt = optionExists("pslx");
if (argc != 3)
usage();
blastToPsl(argv[1], argv[2], optionVal("scores", NULL));
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
dry = optionExists("dry");
minId = optionInt("minId", minId);
maxTime = optionDouble("maxTime", maxTime);
cdwRetryJob(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc < 3)
usage();
if (optionExists("clampMax"))
{
gotClampMax = TRUE;
clampMax = optionDouble("clampMax", clampMax);
}
wigCorrelate(argc-1, argv+1, "stdout");
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2 && argc != 3)
usage();
restrictFile = optionVal("restrict", restrictFile);
threshold = optionDouble("threshold", threshold);
rootNames = optionExists("rootNames");
if (argc == 3)
bigWigCorrelatePair(argv[1], argv[2]);
else
bigWigCorrelateList(argv[1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 5)
usage();
userCount = optionInt("userCount", userCount);
randSeed = optionInt("randSeed", getpid());
srand(randSeed);
cgiDelay = optionInt("cgiDelay", cgiDelay);
hitDelay = optionInt("hitDelay", hitDelay);
iterations = optionInt("iterations", iterations);
newRatio = optionDouble("newRatio", newRatio);
engine = optionVal("engine", engine);
cartSim(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 6)
usage();
makeExceptionHashes();
char *fileName = optionVal("exceptionsOut", NULL);
if (fileName != NULL)
{
exceptionsOut = mustOpen(fileName, "w");
if (!optionExists("exceptionsIn"))
errAbort("Must use exceptionsIn flag with exceptionsOut.");
}
threshold = optionDouble("threshold", threshold);
weightedThreshold = threshold + txCdsPredictWeight;
txCdsPick(argv[1], argv[2], argv[3], argv[4], argv[5]);
carefulClose(&exceptionsOut);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
database = optionVal("database", database);
doAverage = optionExists("average");
transpose = optionExists("transpose");
minAbsVal = optionFloat("minAbsVal", minAbsVal);
minMaxVal = optionInt("minMaxVal", minMaxVal);
c = optionDouble("addConst", c);
clump = optionVal("clump", clump);
doLoad = !optionExists("noLoad");
if (optionExists("tab"))
{
tabDir = optionVal("tab", tabDir);
makeDir(tabDir);
}
limit = optionInt("limit", limit);
hgRatioMicroarray(argv[1], argv[2]);
return 0;
}
