int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
blockSize = optionInt("blockSize", blockSize);
itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot);
bedFields = optionInt("bedFields", bedFields);
as = optionVal("as", as);
if (argc != 4)
usage();
bedToBigBed(argv[1], argv[2], argv[3]);
return 0;
}
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;
}
