HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/1	-	1449586	1449619
HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/2	-	1449544	1449577
HWUSI-EAS95L_0025_FC:3:1:6417:1078#0/1	-	4744083	4744113
HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/1	-	4867122	4867157
HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/2	-	4866942	4866977
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/1	+	1930232	1930266
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/2	+	1930354	1930389
##</code><code>##

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

my @result;
my $csv = Text::CSV->new ( { sep_char => "\t" } )  # should set binary attribute.
                or die "Cannot use CSV: ".Text::CSV->error_diag ();
 
my %result;
while ( my $row = $csv->getline( *DATA ) ) {
    my ($key, $index) = $row->[0] =~ m{^(.+)/([12])$}
        or die "Line did not match pattern: @$row";
    
    if ($index == 1) {
        $result{$key}[0] = $row->[2];
    } elsif ($index == 2) {
        $result{$key}[1] = $row->[2];
    } else {
        die "Index was not 1 or 2: @$row"
    }
}
$csv->eof or $csv->error_diag();

# Output results:
for my $key (keys %result) {
    next unless $result{$key}[1];
    print "$key:\t$result{$key}[0]\t$result{$key}[1]\n";
}

__DATA__
HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/1	-	1449586	1449619
HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/2	-	1449544	1449577
HWUSI-EAS95L_0025_FC:3:1:6417:1078#0/1	-	4744083	4744113
HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/1	-	4867122	4867157
HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/2	-	4866942	4866977
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/1	+	1930232	1930266
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/2	+	1930354	1930389
##</code><code>##

HWUSI-EAS95L_0025_FC:3:1:6539:1083#0:	4867122	4866942
HWUSI-EAS95L_0025_FC:3:1:5232:1082#0:	1449586	1449544
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0:	1930232	1930354