Atwater Police arrested 38-year-old Jose Orozco Ceja on Saturday morning on charges including child endangerment and terrorist threats.
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Officers first responded to a home on Fir Avenue near Third Street around 1 in the morning for a call about shots fired.
They say the suspect had threatened family members with a gun.
Two of them made it out of the house, but a 15-year-old boy was still inside.
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The Merced County Sheriff's Office SWAT team arrived and evacuated surrounding homes.
Orozco Ceja finally surrendered around 5 a.m.
The teen was not hurt, but investigators say they did find four handguns -- and evidence that one of them was fired during the incident.