My general approach in this type of situation is to build a hash, or more specifically a hash of lists. I am not familiar with your particular input, and figuring out the patterns and how to parse them is usually where most of the effort in writing a script of this type falls. Taking the input from your original post:

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
[download]

And fitting the most general pattern that seems to match, I would use code like

#!/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
[download]

to get the output

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
[download]

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