Friday night around 10:45 pm, a sergeant was patrolling the streets near Ellis and Krohn.
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Madera County Sheriff Tyson Pogue says the deputy saw 46-year-old Timothy Bray holding what he believed to be a baseball bat, which turned out to be a hand pump for a bicycle.
Authorities are not releasing many details about what happened between the suspect and the deputy, but say Bray will be charged with assault with a deadly weapon on a peace officer and resisting and obstructing a peace officer.
Bray remains in the hospital after being shot by that deputy, but he is expected to survive and will be booked into the Madera County Jail once released.
"Our sergeant notified dispatch that he was going to be out with a subject with a bat and in pretty quick succession, notified them he had discharged his weapon," Pogue said.
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The sheriff says the suspect has an extensive criminal history, dating back to 1993.
He's been convicted of grand theft, possession of narcotics, trespassing, resisting arrest and felony possession of a firearm.
The Madera Police department is conducting an independent investigation of this shooting, and the sheriff's office is cooperating.