Filing Taxes - Employee Paid as Independent Contractor (1099)

I have worked for a small electrical company full time for over a year now. I'm definitely an employee - yet I'm paid as an independent contractor (1099). The boss just writes me a check each week. I've expressed in the past that I'd prefer to have deductions taken out, etc. I'm now preparing to file my taxes. I read that I will owe double in taxes if I file as an independent contractor vs. an employee (paying both my share AND employer's share of social security, medicare, etc). However - I'm definitely an employee - the boss runs, controls, and directs everything - every little detail of my job - and my hours. Any advice for filing my taxes? Can I still just file as an employee with the IRS/Dept of Revenue - and let them sort it out?...

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