It happened just after 3 am on Thursday at the Primary Care Pharmacy on Kings Canyon Road and Clovis Avenue.
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Investigators say the burglars cut through the bars over the front door and smashed the glass to get inside.
Deputies believe there is more than one suspect. They are reviewing surveillance footage to help identify the suspects.
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Officials are also taking inventory of the items to determine if anything was taken. Deputies say most of the medications were locked away.