/*=export_func optionRestore
*
* what: restore option state from memory copy
* arg: tOptions*, pOpts, program options descriptor
*
* doc: Copy back the option state from saved memory.
* The allocated memory is left intact, so this routine can be
* called repeatedly without having to call optionSaveState again.
* If you are restoring a state that was saved before the first call
* to optionProcess(3AO), then you may change the contents of the
* argc/argv parameters to optionProcess.
*
* err: If you have not called @code{optionSaveState} before, a diagnostic is
* printed to @code{stderr} and exit is called.
=*/
void
optionRestore(tOptions* pOpts)
{
tOptions* p = (tOptions*)pOpts->pSavedState;
if (p == NULL) {
char const * pzName = pOpts->pzProgName;
if (pzName == NULL) {
pzName = pOpts->pzPROGNAME;
if (pzName == NULL)
pzName = zNil;
}
fprintf(stderr, zNoState, pzName);
option_exits(EXIT_FAILURE);
}
pOpts->pSavedState = NULL;
optionFree(pOpts);
memcpy(pOpts, p, sizeof(*p));
memcpy(pOpts->pOptDesc, p+1, (size_t)p->optCt * sizeof(tOptDesc));
pOpts->pSavedState = p;
fixupSavedOptionArgs(pOpts);
}
int main(int argc, char *argv[])
{
/* Get all inputs */
optionInit(&argc, argv, options);
if (argc != 4) usage();
double alpha, beta, x;
alpha = atof(argv[1]);
beta = atof(argv[2]);
x = atof(argv[3]);
printf("%f\n", betai(alpha, beta, x));
optionFree();
return 0;
}
int main(int argc, char *argv[])
{
/* Get all inputs */
optionInit(&argc, argv, options);
if (argc != 5) usage();
char *regdomFn, *antigapFn;
int totalRegions, hitRegions;
regdomFn = argv[1];
antigapFn = argv[2];
totalRegions = intExp(argv[3]);
hitRegions = intExp(argv[4]);
calculateBinomialP(regdomFn, antigapFn, totalRegions, hitRegions);
optionFree();
return 0;
}
/**
* This gets called when all is well at the end.
*/
LOCAL void
cleanup(tTemplate* pTF)
{
if (HAVE_OPT(USED_DEFINES))
print_used_defines();
if (pfDepends != NULL)
wrap_up_depends();
optionFree(&autogenOptions);
for (;;) {
tTemplate* pT = pNamedTplList;
if (pT == NULL)
break;
pNamedTplList = (tTemplate*)(void*)(pT->pNext);
unloadTemplate(pT);
}
AGFREE(forInfo.fi_data);
unloadTemplate(pTF);
unloadDefs();
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
blockSize = optionInt("blockSize", blockSize);
itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot);
asFile = optionVal("as", asFile);
doCompress = !optionExists("unc");
sizesIs2Bit = optionExists("sizesIs2Bit");
extraIndex = optionVal("extraIndex", NULL);
tabSep = optionExists("tab");
udcDir = optionVal("udcDir", udcDefaultDir());
if (argc != 4)
usage();
udcSetDefaultDir(udcDir);
if (optionExists("type"))
{
// parse type
char *btype = cloneString(optionVal("type", ""));
char *plus = strchr(btype, '+');
if (plus)
{
*plus++ = 0;
if (isdigit(*plus))
bedP = sqlUnsigned(plus);
}
if (!startsWith("bed", btype))
errAbort("type must begin with \"bed\"");
btype +=3;
bedN = sqlUnsigned(btype);
if (bedN < 3)
errAbort("Bed must be 3 or higher, found %d\n", bedN);
if (bedN > 15)
errAbort("Bed must be 15 or lower, found %d\n", bedN);
}
else
{
if (asText)
errAbort("If you specify the .as file, you must specify the -type as well so that\n"
"the number of standard BED columns is known.");
}
/* If the haven't set bedN and bedP from the type var in the command line, then we sniff it
* out from file. */
char *bedFileName = argv[1];
if (bedN == 0)
{
/* Just read in single line and count fields. */
struct lineFile *lf = lineFileOpen(bedFileName, TRUE);
char *line;
if (!lineFileNextReal(lf, &line))
errAbort("%s is empty", lf->fileName);
int fieldCount;
if (tabSep)
fieldCount = chopByChar(line, '\t', NULL, 0); // Do not use chopString, see GOTCHA
else
fieldCount = chopByWhite(line, NULL, 0);
if (fieldCount > 256)
errAbort("Too many columns in %s, you sure it's a bed file?", lf->fileName);
lineFileClose(&lf);
/* Set up so that it looks like we are straight up bed for that many fields,
* or if more than or maximum defined fields, then for bed15+ */
bedN = fieldCount;
if (bedN > bedKnownFields)
{
bedP = bedN - bedKnownFields;
bedN = bedKnownFields;
}
}
/* Make sure that fields are defined, from bed spec if nowhere else. */
if (asFile)
readInGulp(asFile, &asText, NULL);
else
asText = bedAsDef(bedN, bedN + bedP);
bedToBigBed(bedFileName, argv[2], argv[3]);
optionFree();
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
