int main(int argc, char *argv[]) {
showCopyright(argv[0]);
dbf = getDatabaseFile();
if (!dbf) {
showError("system variable 'HOME' not valid");
return 1;
}
printf ( "DATABASE:\t%s\n", dbf );
return fuse_main(argc, argv, &nc_oper, NULL);
}
bool ContextIntersect::determineOutputType() {
if (_outputTypeDetermined) {
return true;
}
//determine the maximum number of database fields.
for (int i=0; i < getNumDatabaseFiles(); i++) {
int numFields = getDatabaseFile(i)->getNumFields();
if ( numFields > _maxNumDatabaseFields) {
_maxNumDatabaseFields = numFields;
}
}
//If the query is BAM, and bed output wasn't specified, then the output is BAM.
if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
_outputTypeDetermined = true;
return true;
}
return ContextBase::determineOutputType();
}
