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So I have this query.

SELECT * 
FROM `Comment` 
WHERE `Target` = '".$_GET['pp']."' 
AND `Id` NOT IN (SELECT `Target` 
                 FROM `Delete` 
                 WHERE `Type` = 'comment') 
ORDER BY `Id` DESC;

This selects comments which aren't deleted and displays them to members.

How could I modify it to select everything but with an additional boolean (called Deleted)?

I've heard about IF statements in SQL but don't know whether it's appropriate here or how it works.

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Is this what you are looking for?

    select * 
    FROM Comment cm left join [Delete] del
     on del.[Target]=cm.Id
    where cm.[Target] = '".$_GET[''pp'']."'
    and Type = 'comment'
    and del.[Target] is null
    and deleted=0
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