When you assign an array to a scalar like you have below, it assigns the number of elements as you've found.

$bin_file_data{$sampname} = @bindata;
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What you want to do is stuff a reference to the array as the value to the key:

$bin_file_data{$sampname} = \@bindata;

# a different way that copies @bindata as opposed
# to taking a direct reference to it

@{ $bin_file_data{$sampname} } = @bindata;
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Then:

# use the whole array

for (@{ $bin_file_data{$sampname} }){
    ...
}

# get a single element

my $thing = $bin_file_data{$sampname}->[0];
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-stevieb