int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
if (argc != 6)
usage();
if (optionExists("prot"))
qType = tType = "prot";
qType = optionVal("q", qType);
tType = optionVal("t", tType);
if (sameWord(tType, "prot") || sameWord(tType, "dnax") || sameWord(tType, "rnax"))
minIdentity = 25;
minIdentity = optionFloat("minIdentity", minIdentity);
minScore = optionInt("minScore", minScore);
dots = optionInt("dots", 0);
outputFormat = optionVal("out", outputFormat);
/* set global for fuzzy find functions */
setFfIntronMax(optionInt("maxIntron", ffIntronMaxDefault));
gfClient(argv[1], argv[2], argv[3], argv[4], argv[5], tType, qType);
return 0;
}
int main(int argc, char *argv[])
/* Process command line into global variables and call blat. */
{
boolean tIsProtLike, qIsProtLike;
#ifdef DEBUG
{
char *cmd = "blat hCrea.geno hCrea.mrna foo.psl -t=dnax -q=rnax";
char *words[16];
printf("Debugging parameters\n");
cmd = cloneString(cmd);
argc = chopLine(cmd, words);
argv = words;
}
#endif /* DEBUG */
optionInit(&argc, argv, options);
if (argc != 4)
usage();
/* Get database and query sequence types and make sure they are
* legal and compatable. */
if (optionExists("prot"))
qType = tType = gftProt;
if (optionExists("t"))
tType = gfTypeFromName(optionVal("t", NULL));
trimA = optionExists("trimA") || optionExists("trima");
trimT = optionExists("trimT") || optionExists("trimt");
trimHardA = optionExists("trimHardA");
switch (tType)
{
case gftProt:
case gftDnaX:
tIsProtLike = TRUE;
break;
case gftDna:
tIsProtLike = FALSE;
break;
default:
tIsProtLike = FALSE;
errAbort("Illegal value for 't' parameter");
break;
}
if (optionExists("q"))
qType = gfTypeFromName(optionVal("q", NULL));
if (qType == gftRnaX || qType == gftRna)
trimA = TRUE;
if (optionExists("noTrimA"))
trimA = FALSE;
switch (qType)
{
case gftProt:
case gftDnaX:
case gftRnaX:
minIdentity = 25;
qIsProtLike = TRUE;
break;
default:
qIsProtLike = FALSE;
break;
}
if ((tIsProtLike ^ qIsProtLike) != 0)
errAbort("t and q must both be either protein or dna");
/* Set default tile size for protein-based comparisons. */
if (tIsProtLike)
{
tileSize = 5;
minMatch = 1;
oneOff = FALSE;
maxGap = 0;
}
/* Get tile size and related parameters from user and make sure
* they are within range. */
tileSize = optionInt("tileSize", tileSize);
stepSize = optionInt("stepSize", tileSize);
minMatch = optionInt("minMatch", minMatch);
oneOff = optionExists("oneOff");
fastMap = optionExists("fastMap");
minScore = optionInt("minScore", minScore);
maxGap = optionInt("maxGap", maxGap);
minRepDivergence = optionFloat("minRepDivergence", minRepDivergence);
minIdentity = optionFloat("minIdentity", minIdentity);
gfCheckTileSize(tileSize, tIsProtLike);
if (minMatch < 0)
errAbort("minMatch must be at least 1");
if (maxGap > 100)
errAbort("maxGap must be less than 100");
/* Set repMatch parameter from command line, or
* to reasonable value that depends on tile size. */
if (optionExists("repMatch"))
repMatch = optionInt("repMatch", repMatch);
else
repMatch = gfDefaultRepMatch(tileSize, stepSize, tIsProtLike);
/* Gather last few command line options. */
noHead = optionExists("noHead");
ooc = optionVal("ooc", NULL);
makeOoc = optionVal("makeOoc", NULL);
mask = optionVal("mask", NULL);
qMask = optionVal("qMask", NULL);
repeats = optionVal("repeats", NULL);
if (repeats != NULL && mask != NULL && differentString(repeats, mask))
errAbort("The -mask and -repeat settings disagree. "
"You can just omit -repeat if -mask is on");
if (mask != NULL) /* Mask setting will also set repeats. */
repeats = mask;
outputFormat = optionVal("out", outputFormat);
dotEvery = optionInt("dots", 0);
/* set global for fuzzy find functions */
setFfIntronMax(optionInt("maxIntron", ffIntronMaxDefault));
setFfExtendThroughN(optionExists("extendThroughN"));
/* Call routine that does the work. */
blat(argv[1], argv[2], argv[3]);
return 0;
}
