"They were going to be burned in a special ceremony," said post manager Martha Rowe. "This wasn't what was planned."
The flags are normally disposed of by burning them, but with veterans and Boy Scouts paying tribute to what the flags represent.
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Rowe said she heard the sound of sirens around 2:30 p.m. Wednesday. Smoke was pouring out of the metal shed set far back on the post's property.
The flags had been given to the American Legion for proper disposal.
"The flags are turned over to us, because they're old and weathered," she said. "They've been displayed in front of buildings and houses."
"We also had the little flags we use for holidays like Veterans Day, Memorial Day and July 4th," Rowe said. "We'll have to replace those."
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Electricity was disconnected to the storage shed a long time ago, she said. Vagrants had been found in the building in the past, but not recently.
The Houston Fire Department quickly extinguished the fire. The cause of the fire has not been determined.
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