in reply to SEEKING HELP

Here's an approach to the problem of comparing records. Validity checking stub functions are included just as a suggestion of good practice; there are other ways of handling this. I notice that the  'HG00096.' section in each record pair always seems to be the same. If so, a check for this might be included in the
    m{ \A .{9} (?: \x00\x00){13} \z }xms
regex, but I would prefer to do it in a separate validity check. If the initial sections of each pair up to and including the M/P character are guaranteed to be good, it's only necessary to check for equality of the tail section, e.g., with a
    m{ (?: \x00\x00){13} \z }xms
regex.

File filter_MP_records_1.pl: 

use warnings;
use strict;

<DATA>;  # discard first line/record of data

MP_PAIR:
while (my $m = <DATA>) {

    my $bad;  # badness message from validity checks (empty if ok)

    die qq{bad M record '$m': $bad} if $bad = bad_M_record($m);

    defined(my $p = <DATA>) or die qq{M record '$m' has no P record};
    die qq{bad P record '$p': $bad} if $bad = bad_P_record($p);

    die qq{bad MP pair '$m'/'$p': $bad} if $bad = bad_MP_pair({M => $m
+, P => $p});

    chomp($m, $p);

    my $x = $m ^ $p;  # detect equal sub-regions

    # are ' 0 1 0 0 1 1' sequences at end of records the same?
    next MP_PAIR unless $x =~ m{ \A .{9} (?: \x00\x00){13} \z }xms;

    do_something_with({M => $m, P => $p});

    }  # end while MP_PAIR

# stubs for validity checking functions.
sub bad_M_record { return ''; }
sub bad_P_record { return ''; }
sub bad_MP_pair  { return ''; }

sub do_something_with {

    my ($hr_MP_args,
        ) = @_;

    printf qq{M '%s' \nP '%s' \n\n}, @{ $hr_MP_args }{ qw(M P) };

    }

__DATA__
INDIV 16051347(G-C) 16051497(A-G) 16052239(A-G) 16052513(G-C) 16052618
+(G-A) 16053659(A-C) 16054667(C-G)
HG00096.M 0 0 0 1 1 1 1 1 0 0 0 0 0
HG00096.P 0 0 1 0 0 0 0 1 0 0 0 0 0
HG00097.M 1 1 0 0 0 0 0 0 0 0 0 1 0
HG00097.P 0 0 1 0 0 1 0 1 1 1 0 0 0
HG00099.M 1 1 0 0 0 0 0 0 0 0 0 0 0
HG00099.P 0 0 0 0 1 1 0 0 1 1 0 1 0
HG00100.M 0 0 1 1 1 1 1 1 1 1 1 1 1
HG00100.P 1 1 0 0 0 1 0 0 1 1 0 1 0
HG00101.M 1 1 0 0 0 1 0 0 1 1 0 1 0
HG00101.P 0 0 1 1 1 1 1 1 1 1 1 1 0
HG00102.M 1 1 0 0 0 0 0 0 0 0 0 1 0
HG00102.P 0 0 1 0 0 1 0 1 1 1 0 1 0
EQ99991.M 0 1 0 0 1 1 0 0 0 1 1 1 0
EQ99991.P 0 1 0 0 1 1 0 0 0 1 1 1 0
HG00103.M 0 0 0 0 0 0 0 0 0 0 0 0 0
HG00103.P 1 0 0 0 0 0 0 0 0 0 0 0 0
EQ99992.M 1 0 1 0 1 0 1 0 1 0 1 0 1
EQ99992.P 1 0 1 0 1 0 1 0 1 0 1 0 1

[download]
Output: 
c:\@Work\Perl\monks\A1 Transcendence>perl filter_MP_records_1.pl
M 'EQ99991.M 0 1 0 0 1 1 0 0 0 1 1 1 0'
P 'EQ99991.P 0 1 0 0 1 1 0 0 0 1 1 1 0'

M 'EQ99992.M 1 0 1 0 1 0 1 0 1 0 1 0 1'
P 'EQ99992.P 1 0 1 0 1 0 1 0 1 0 1 0 1'

[download]

Give a man a fish:  <%-{-{-{-<

In Section Seekers of Perl Wisdom