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[])
/* 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;
}

boolean gffOpen(struct gff *gff, char *fileName)
/* Initialize gff structure and open file for it. */
{
    dnaUtilOpen();

    /* Initialize structure and open file. */
    zeroBytes(gff, sizeof(*gff));
    gff->memPool = lmInit(16*1024);
    gff->fileSize = fileSize(fileName);
    if (gff->fileSize < 0 ||
       (gff->file = fopen(fileName, "rb")) == NULL)
	    {
            warn("Couldn't find the file named %s\n", fileName);
	    return FALSE;
	    }
    strcpy(gff->fileName, fileName);
    gff->bufSize = ArraySize(gff->buf);

    /* Make sure it's a gff file. */
    _gffSeekDoubleSharpLine(gff);
    if (strncmp(gff->buf, _gffIdent, strlen(_gffIdent)) != 0)
	{
	warn("%s doesn't appear to be a .gff file\n", fileName);
	return FALSE;
	}

    return TRUE;
}

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 *goodName, *badName = NULL;
double profile[16][4];
int alphabatize[4] = {A_BASE_VAL, C_BASE_VAL, G_BASE_VAL, T_BASE_VAL};
int i;

dnaUtilOpen();
if (argc < 2)
    usage();
goodName = argv[1];
if (argc >= 3)
    badName = argv[2];
fragFind(goodName, badName, 7, 2, profile);
printf("\n%s\n", unpacked);
for (i=0; i<4; ++i)
    {
    int baseVal = alphabatize[i];
    printf("%c ", valToNt[baseVal]);
    for (j=0; j<fragSize; ++j)
        printf("%1.3f ", profile[j][baseVal]);
    printf("\n");
    }
return 0;
}

int main(int argc, char *argv[])
/* Process command line. */
{
if (argc != 4)
    usage();
dnaUtilOpen();
pslIntronsOnly(argv[1], argv[2], argv[3]);
return 0;
}

void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
    cart = theCart;
    dnaUtilOpen();
    cartWebStart(cart, NULL, "UCSC In-Silico PCR");
    dispatch();
    cartWebEnd();
}

int main(int argc, char *argv[])
/* Process command line. */
{
if (argc != 5)
    usage();
dnaUtilOpen();
bedDown(argv[1], argv[2], argv[3], argv[4]);
return 0;
}

int main(int argc, char *argv[])
/* Process command line. */
{
if (argc != 3)
    usage();
dnaUtilOpen();
sangPairs(argv[1], argv[2]);
return 0;
}

int main(int argc, char *argv[])
{
char *outDir;
struct cdaAli *cdaList;
struct clonePair *pairList;
struct dlList **goodEntities, **badEntities;  /* Array of lists, one for each chromosome. */
int i;

if (argc != 2)
    {
    errAbort("genieCon - generates constraint GFF files for Genie from cDNA alignments\n"
             "usage\n"
             "      genieCon outputDir\n"
             "genieCon will create one file of form conXX.gff for each chromosome, where\n"
             "the XX is replaced by the chromosome name.");
    }
outDir = argv[1];

dnaUtilOpen();
anyChromNames(&chromNames, &chromCount);

goodEntities = needMem(chromCount * sizeof(goodEntities[0]));
badEntities = needMem(chromCount * sizeof(badEntities[0]));
for (i=0; i<chromCount; ++i)
    {
    goodEntities[i] = newDlList();
    badEntities[i] = newDlList();
    }

cdaList = readAllCda();
printf("Read in %d alignments\n", slCount(cdaList));
cdaCoalesceBlocks(cdaList);
printf("Coalesced blocks\n");
pairList = pairClones(cdaList);
printf("Before weeding genomic had %d clones\n", slCount(pairList));
pairList = weedGenomic(pairList);
printf("after weeding genomic had %d clones\n", slCount(pairList)); 
makeEntities(pairList, goodEntities);
for (i=0; i<chromCount; ++i)
    {
    printf("Made %d gene-like entities on chromosome %s\n",
        dlCount(goodEntities[i]), chromNames[i]);
    }
for (i=0; i<chromCount; ++i)
    {
    if (dlCount(goodEntities[i]) > 0)
        {
        separateEntities(goodEntities[i], badEntities[i]);
        printf("%d good %d bad entities on chromosome %s\n",
            dlCount(goodEntities[i]), dlCount(badEntities[i]), chromNames[i]);
        saveEntities(goodEntities[i], outDir, "ez", chromNames[i]);
        saveEntities(badEntities[i], outDir, "odd", chromNames[i]);
        }
    }
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. */
{
optionInit(&argc, argv, options);
if (argc < 3)
    usage();
dnaUtilOpen();
itsaMake(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();
    dnaUtilOpen();
    txCdsOrfInfo(argv[1], argv[2], argv[3]);
    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)
/* entry */
{
optionInit(&argc, argv, optionSpecs);
if (argc != 3)
    usage("wrong # args");
gNoRc = optionExists("noRc");
dnaUtilOpen();
pslRcFile(argv[1], argv[2]);
return 0;
}

int main(int argc, char *argv[])
/* Process command line. */
{
dnaUtilOpen();
optionInit(&argc, argv, options);
maxSize = optionInt("maxSize", maxSize);
if (argc != 3)
    usage();
itsaDump(argv[1], argv[2]);
return 0;
}

int main(int argc, char *argv[])
/* Process command line. */
{
dnaUtilOpen();
optionInit(&argc, argv, options);
if (argc != 4)
    usage();
hardMask = optionExists("hardMask");
seqFromPsl(argv[1], argv[2], argv[3]);
return 0;
}

void dnaOrAaFilter(char *in, char *out, char filter[256])
/* Run chars through filter. */
{
    char c;
    dnaUtilOpen();
    while ((c = *in++) != 0)
    {
        if ((c = filter[(int)c]) != 0) *out++ = c;
    }
    *out++ = 0;
}

long dnaOrAaFilteredSize(char *raw, char filter[256])
/* Return how long DNA will be after non-DNA is filtered out. */
{
    char c;
    long count = 0;
    dnaUtilOpen();
    while ((c = *raw++) != 0)
    {
        if (filter[(int)c]) ++count;
    }
    return count;
}

int main(int argc, char *argv[])
/* Process command line. */
{
dnaUtilOpen();
optionInit(&argc, argv, options);
if (argc != 6)
    usage();
if (optionExists("conflictLog"))
    conflictLog = mustOpen(optionVal("conflictLog", NULL), "w");
vgLoadMahoney(argv[1], argv[2], argv[3], argv[4], argv[5]);
return 0;
}