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Hi,
As it stands, the WHERE clause isn't supported in command-line SQL Data Compare. It is available through the API, as you've pointed out. -
There is a workaround for this: Create a comparison project in SQL Data Compare containing the databases you want to compare and any table mappings and WHERE clause, then right-click it, select 'locate on disk', and make a copy of the project file in another location on disk.
Next, use SQLDataCompare.exe to run the project using the /pr argument. The command-line version of SQL Data Compare can use the where clause that you'd set in the project.
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Thanks