You can apply for the U visa as long as the law enforcement agency completes their supplement even if the case is still ongoing. As long as you cooperated with them and they are willing to certify this you should be eligible. You should contact a good attorney to help you with this.
I agree, even if the criminal case is ongoing, as long as you can get a certification indicating that you have been "helpful" in the investigation, you will be fine. Consult an experienced immigration attorney on this.
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