#!/usr/bin/perl
use strict;
use warnings;
use Text::CSV_XS;

my $file = $ARGV[0] or die "Usage: $0 <input_file>";

my $csv = Text::CSV_XS->new({binary => 1}) or die "Unable to instantiate CSV object: ", Text::CSV_XS->error_diag();

open(my $fh, '<', $file) or die "Unable to open '$file' for reading: $!\n";
while(my $row = $csv->getline($fh)) {
    # Do something with $row
}

##</code><code>##

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

while (my $in_house_row = $csv->getline($fh)) {
    my $sample_name = $in_house_row->[0];
    next if ! defined $lookup{$sample_name};
}