How to avoid OBIEE replacing IN with = in sql query while using data filters?

DBFeatures.ini file under OracleBI\server\Config has the default settings for database features. This file must not be modified.
Each section is identified by the major section [ DATA_SOURCE_FEATURE = database ]
Check whether the database that you are using has the property IS_IN_SUPPORTED set to Yes. If set to No then it won't support what you are looking for.
Check whether the Database Features of the database that you use to query has IN_SUPPORTED checked.

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