bool ContextBase::determineOutputType() {
if (_outputTypeDetermined) {
return true;
}
//test whether output should be BED or BAM.
//If the user explicitly requested BED, then it's BED.
if (getExplicitBedOutput()) {
setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
_outputTypeDetermined = true;
return true;
}
//Otherwise, if the input is BAM, then the output is BAM
if (getFile(0)->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
return true;
}
//Okay, it's bed.
setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
_outputTypeDetermined = true;
return true;
}
bool ContextBase::determineOutputType() {
if (_outputTypeDetermined) {
return true;
}
//test whether output should be BED or BAM.
//If the user explicitly requested BED, then it's BED.
if (getExplicitBedOutput()) {
setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
_outputTypeDetermined = true;
return true;
}
//Otherwise, if there are any BAM files in the input,
//then the output should be BAM.
for (_i = 0; _i < (int)_files.size(); _i++) {
if (_files[_i]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
_bamHeaderAndRefIdx = _i;
_outputTypeDetermined = true;
return true;
}
}
//Okay, it's bed.
setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
_outputTypeDetermined = true;
return true;
}
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();
}
