int main(int argc, char *argv[])
/* Process command line. */
{
struct tm *tm;
if (argc < 2)
usage();
optionInit(&argc, argv, options);
if (!optionExists("age"))
{
verbose(1,"ERROR: must specify an age argument, e.g.: -age=8\n");
usage();
}
if (time(&timeNow) < 1)
errAbort("can not obtain current time via time() function\n");
tm = localtime(&timeNow);
ageHours = optionFloat("age", 0.0);
time_t ageSeconds = (time_t)(ageHours * 3600); /* age in seconds */
dropTime = timeNow - ageSeconds;
if (ageHours > 0.0)
{
verbose(2,"# specified age = %f hours = %ld seconds\n", ageHours,
(unsigned long)ageSeconds);
verbose(2,"# current time: %d-%02d-%02d %02d:%02d:%02d %ld\n",
1900+tm->tm_year, 1+tm->tm_mon, tm->tm_mday,
tm->tm_hour, tm->tm_min, tm->tm_sec, (unsigned long)timeNow);
tm = localtime(&dropTime);
verbose(2,"# drop time: %d-%02d-%02d %02d:%02d:%02d %ld\n",
1900+tm->tm_year, 1+tm->tm_mon, tm->tm_mday,
tm->tm_hour, tm->tm_min, tm->tm_sec, (unsigned long)dropTime);
}
else
{
verbose(1,"ERROR: specified age %.f must be greater than 0.0\n", ageHours);
usage();
}
drop = optionExists("drop");
historyToo = optionExists("historyToo");
db = optionVal("db",db);
extFileCheck = optionExists("extFile");
extDel = optionExists("extDel");
tableStatus = optionExists("tableStatus");
topDir = optionVal("topDir", topDir);
verbose(2,"# drop requested: %s\n", drop ? "TRUE" : "FALSE");
verbose(2,"# historyToo: %s\n", historyToo ? "TRUE" : "FALSE");
verbose(2,"# extFile: %s\n", extFileCheck ? "TRUE" : "FALSE");
verbose(2,"# extDel: %s\n", extDel ? "TRUE" : "FALSE");
verbose(2,"# tableStatus: %s\n", tableStatus ? "TRUE" : "FALSE");
verbose(2,"# topDir: %s\n", topDir);
verbose(2,"# database: %s\n", db);
dbTrash(db);
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
if (argc != 2)
usage();
bigWigInfo(argv[1]);
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
maxGigs = optionInt("maxGigs", maxGigs);
setMaxAlloc(maxGigs*1000000000L);
blockSize = optionInt("blockSize", blockSize);
itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot);
doCompress = !optionExists("unc");
if (argc != 4)
usage();
bedGraphToBigWig(argv[1], argv[2], argv[3]);
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
clChrom = optionVal("chrom", clChrom);
clStart = optionInt("start", clStart);
clEnd = optionInt("end", clEnd);
maxItems = optionInt("maxItems", maxItems);
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
if (argc != 3)
usage();
bigBedToBed(argv[1], argv[2]);
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
blockSize = optionInt("blockSize", blockSize);
itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot);
clipDontDie = optionExists("clip");
doCompress = !optionExists("unc");
keepAllChromosomes = optionExists("keepAllChromosomes");
fixedSummaries = optionExists("fixedSummaries");
if (argc != 4)
usage();
wigToBigWig(argv[1], argv[2], argv[3]);
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
if (optionExists("fields"))
{
if (argc < 2)
usage();
bigBedFields(argv[1]);
}
else
{
summaryType = optionVal("type", summaryType);
if (argc != 6)
usage();
bigBedSummary(argv[1], argv[2], sqlUnsigned(argv[3]), sqlUnsigned(argv[4]), sqlUnsigned(argv[5]));
}
if (verboseLevel() > 1)
printVmPeak();
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;
}