Remove redundant code from bedtools intersect for determining the output type.
Remove redundant code from bedtools intersect for determining
the output type as this case is already handled by
ContextBase::determineOutputType() of src/utils/Contexts/ContextBase.cpp
@@ -212,16 +212,7 @@ bool ContextIntersect::determineOutputType() {
_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();
-
}
bool ContextIntersect::handle_a()
