int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
if (argc < 4)
usage();
noBin = optionExists("noBin") || optionExists("nobin");
noSort = optionExists("noSort");
strictTab = optionExists("tab");
oldTable = optionExists("oldTable");
sqlTable = optionVal("sqlTable", sqlTable);
renameSqlTable = optionExists("renameSqlTable");
trimSqlTable = optionExists("trimSqlTable");
hasBin = optionExists("hasBin");
noLoad = optionExists("noLoad");
noHistory = optionExists("noHistory");
bedGraph = optionInt("bedGraph",0);
bedDetail = optionExists("bedDetail");
minScore = optionInt("minScore",100);
if (minScore<0 || minScore>1000)
errAbort("minScore must be between 0-1000\n");
notItemRgb = optionExists("notItemRgb");
if (notItemRgb) itemRgb = FALSE;
maxChromNameLength = optionInt("maxChromNameLength",0);
noStrict = optionExists("noStrict") || optionExists("nostrict");
allowStartEqualEnd = optionExists("allowStartEqualEnd");
tmpDir = optionVal("tmpDir", tmpDir);
nameIx = ! optionExists("noNameIx");
ignoreEmpty = optionExists("ignoreEmpty");
allowNegativeScores = optionExists("allowNegativeScores");
customTrackLoader = optionExists("customTrackLoader");
/* turns on: noNameIx, ignoreEmpty, allowStartEqualEnd, allowNegativeScores
* -verbose=0 */
if (customTrackLoader)
{
ignoreEmpty = TRUE;
noHistory = TRUE;
nameIx = FALSE;
allowStartEqualEnd = TRUE;
allowNegativeScores = TRUE;
verboseSetLevel(0);
}
fillInScoreColumn = optionVal("fillInScore", NULL);
hgLoadBed(argv[1], argv[2], argc-3, argv+3);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *chromInfo;
optionInit(&argc, argv, optionSpecs);
if (argc < 4)
usage();
noBin = optionExists("noBin") || optionExists("nobin");
noSort = optionExists("noSort");
strictTab = optionExists("tab");
oldTable = optionExists("oldTable");
sqlTable = optionVal("sqlTable", sqlTable);
renameSqlTable = optionExists("renameSqlTable");
trimSqlTable = optionExists("trimSqlTable");
as = optionVal("as", as);
type = optionVal("type", type);
hasBin = optionExists("hasBin");
noLoad = optionExists("noLoad");
noHistory = optionExists("noHistory");
bedGraph = optionInt("bedGraph",0);
bedDetail = optionExists("bedDetail");
minScore = optionInt("minScore",100);
if (minScore<0 || minScore>1000)
errAbort("minScore must be between 0-1000\n");
notItemRgb = optionExists("notItemRgb");
if (notItemRgb) itemRgb = FALSE;
maxChromNameLength = optionInt("maxChromNameLength",0);
dotIsNull = optionInt("dotIsNull",dotIsNull);
noStrict = optionExists("noStrict") || optionExists("nostrict");
allowStartEqualEnd = optionExists("allowStartEqualEnd");
tmpDir = optionVal("tmpDir", tmpDir);
nameIx = ! optionExists("noNameIx");
ignoreEmpty = optionExists("ignoreEmpty");
allowNegativeScores = optionExists("allowNegativeScores");
customTrackLoader = optionExists("customTrackLoader");
parseType();
/* turns on: noNameIx, ignoreEmpty, allowStartEqualEnd, allowNegativeScores
* -verbose=0 */
if (customTrackLoader)
{
type = NULL; /* because customTrack/Factory has already validated the input */
ignoreEmpty = TRUE;
noHistory = TRUE;
nameIx = FALSE;
allowStartEqualEnd = TRUE;
allowNegativeScores = TRUE;
verboseSetLevel(0);
expireSeconds = 1200; /* 20 minutes */
(void) signal(SIGALRM, selfApoptosis);
(void) alarm(expireSeconds); /* CGI timeout */
}
fillInScoreColumn = optionVal("fillInScore", NULL);
chromInfo=optionVal("chromInfo", NULL);
if (chromInfo)
{
if (!type)
errAbort("Only use chromInfo with type for validate");
// Get chromInfo from file
chrHash = chromHashFromFile(chromInfo);
}
else if (type)
{
// Get chromInfo from DB
chrHash = chromHashFromDatabase(argv[1]);
}
hgLoadBed(argv[1], argv[2], argc-3, argv+3);
return 0;
}
