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#!/usr/bin/perl
use strict;
...
while(my $row = $csv->getline($fh)) {
    # Do something with $row
}

my %lookup;  # The hash that maps "in-house" to "different" and vice v
+ersa

...
    my $sample_name = $in_house_row->[0];
    next if ! defined $lookup{$sample_name};
}