int main(int argc, char *argv[])
/* Process command line. */
{
char *scoreSchemeFile = NULL;
optionHash(&argc, argv);
if (argc != 5)
usage();
if (optionExists("fa"))
{
qIsFa = TRUE;
qFaList = faReadAllMixed(argv[3]);
}
if (optionExists("tfa"))
{
tIsFa = TRUE;
tFaList = faReadAllMixed(argv[2]);
}
scoreSchemeFile = optionVal("scoreScheme", scoreSchemeFile);
if (scoreSchemeFile != NULL)
scoreScheme = axtScoreSchemeRead(scoreSchemeFile);
else
scoreScheme = axtScoreSchemeDefault();
lavToAxt(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *scoreSchemeName = NULL;
optionHash(&argc, argv);
minScore = optionInt("minScore", minScore);
detailsName = optionVal("details", NULL);
gapFileName = optionVal("linearGap", NULL);
scoreSchemeName = optionVal("scoreScheme", NULL);
if (argc != 5)
usage();
if (scoreSchemeName != NULL)
{
verbose(1, "Reading scoring matrix from %s\n", scoreSchemeName);
scoreScheme = axtScoreSchemeRead(scoreSchemeName);
}
else
scoreScheme = axtScoreSchemeDefault();
dnaUtilOpen();
gapCalc = gapCalcReadOrDefault(gapFileName);
/* testGaps(); */
axtChain(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 9)
usage();
fileCache = newDlList();
maxGap = optionInt("maxGap", maxGap);
verboseSetLogFile("stdout");
ss = axtScoreSchemeDefault();
verbose(1,"Reading alignments from %s\n",argv[3]);
mrnaHash = readPslToBinKeeper(argv[2], argv[3]);
twoBitFile = twoBitOpen(argv[5]);
//verbose(1,"Reading alignments from %s\n",argv[]);
//pseudoHash = readPslToBinKeeper(argv[3], argv[]);
//verbose(1,"Reading mRNA sequences from %s\n",argv[5]);
//mrnaList = faReadAllMixed(argv[5]);
//if (mrnaList == NULL)
//errAbort("could not open %s\n",argv[5]);
//faHash = newHash(0);
//for (el = mrnaList; el != NULL ; el = el->next)
//hashAdd(faHash, el->name, el);
verbose(1,"Reading chains from %s\n",argv[6]);
chainHash = readChainToBinKeeper(argv[2], argv[6]);
outFile = fopen(argv[8],"w");
verbose(1,"Scoring %s\n",argv[1]);
checkExp(argv[1], argv[7], argv[4]);
fclose(outFile);
freeDnaSeqList(&mrnaList);
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. */
{
optionHash(&argc, argv);
if (argc != 4)
usage();
venn(atof(argv[1]), atof(argv[2]), atof(argv[3]));
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 5)
usage();
correctEst(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();
xmfaToMaf(argv[1],argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 4)
usage();
bedCons(argv[1], argv[2], argv[3]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc < 3)
usage();
netStats(argv[1], argc-2, argv+2);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 2)
usage();
axtQueryCount(argv[1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc < 5)
usage();
motifSig(argv[1], argv[2], argv[3], argc-4, argv+4);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 2)
usage();
callGraph(argv[1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc < 2)
usage();
lineCount(argc-1, argv+1);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 3)
usage();
axtIndex(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 5)
usage();
subsetAxt(argv[1], argv[2], argv[3], atoi(argv[4]));
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
uglyTime(NULL);
optionHash(&argc, argv);
if (argc != 4)
usage();
threadExp(argv[1], argv[2], argv[3]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 3)
usage();
organism = optionVal("org", NULL);
emblMatrixToMotif(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
dnaUtilOpen();
if (argc < 2)
usage();
axtCalcMatrix(argc-1, argv+1);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
tabSize = optionInt("tabSize", tabSize);
if (argc != 3)
usage();
detab(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 5)
usage();
dnaUtilOpen();
pickCassettePcrPrimers(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 4)
usage();
initSymToIx();
twinOrfStats(argv[1], argv[2], argv[3]);
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. */
{
optionHash(&argc, argv);
niceSizeList = optionVal("niceSizes", cloneString(niceSizeList));
if (argc != 2)
usage();
faGapSizes(argv[1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
minSize = optionInt("minSize", 100);
listZero = optionVal("listZero", listZero);
if (argc != 3)
usage();
pslMrnaCover(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 3)
usage();
chromHash = newHash(0);
contigNames = newHash(0);
netContigs(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
restrictFile = optionVal("restrict", NULL);
if (argc != 5)
usage();
pushCarefulMemHandler(1000*1000*1000);
ggcPic(argv[1], argv[2], argv[3], argv[4], optionVal("geneParts", NULL));
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. */
{
int options = 0;
optionHash(&argc, argv);
if (optionExists("softMask"))
options = NIB_MASK_MIXED;
if (argc != 3)
usage();
faToNib(options, argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
if (argc != 2)
usage();
if (optionExists("tcp"))
tcpCountServer(argv[1]);
else
udpCountServer(argv[1]);
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;
}