Revered Monks,
This is a working code that generalizes the problem here. It attemps to count the support of a string in a hash, allowing mismatch. The code below already give correct answers. But the problem is that it alters the HoA (with the 'shift' function - see code below). How can I obtain the same result without having have to alter the HoA? I've tried adding label and use "next Label" variation to replace "shift" function, but it doesn't give the desired result.

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

# Explanation for this hash is for $d = 1


my $hash_mismatch = {
    
    # no match because hd($query[0],$hash_mismatch->{'S1'}[0]) > $d
    #  even though  hd($query[1],$hash_mismatch->{'S2'}[1]) < $d
    # i.e in this case only 1 element of query satisfy, 
    # which doesn't count. To be valid, both of query elem must satisf
+y "hd<=$d".

     'S1' => [ 'GGAA', 'GGGG', 'TTTT'  ],
     
    # match because hd($query[0],$hash_mismatch->{'S2'}[0]) = $d
    #          and  hd($query[1],$hash_mismatch->{'S2'}[2]) < $d
     'S2' => [ 'GGGA', 'GTTT', 'GGGG'  ],
     
    # match because hd($query[0],$hash_mismatch->{'S3'}[0]) = $d
    #          and  hd($query[1],$hash_mismatch->{'S3'}[1]) = $d
     'S3' => [ 'GGGA', 'GCGG', 'GTTT'  ], 

    # match because hd($query[0],$hash_mismatch->{'S4'}[0]) < $d
     'S4' => [ 'GGGG', 'AAAA', 'GGGG'  ]
    
};

my $d      = 1; # string mismatch/hamming distance;
#  With $d = 1; the answer is  : Support = 3 (from 'S2,S3,S4);
#  With $d = 0; the answer is  : Support = 1 (from 'S4')

my @query  = ('GGGG','GGGG');  
my $sup = count_support_mismatch($hash_mismatch,\@query,$d);
print "Support = $sup\n";

#------------------Subs-----------
sub count_support_mismatch
{ 
    my ($hashref,$arref,$d) = @_;
    my $counter = 0;

    foreach my $key ( keys %{$hashref}  )
    {
      my $ar = $hashref->{$key};
      my @match_list;
      
      foreach  ( @{$ar} )
      {
          foreach  my $q ( @$arref  )
          {
            my $dist = hd($_,$q);

            if ( $dist <= $d )
            {
                #print "$q - $_\n";
                push @match_list, $_; 
            }
            shift @{$ar};      # Part that alter hash
          }                      
          
      }                              
          if ( @match_list )
          {
             $counter++;
          }
        
    }                 

    return $counter;
}

sub hd 
{
   # Compute hamming distance between two strings 
   # String length is assumed to be equal
    
    my ($a,$b) = @_;
    my $len = length ($a);
    my $num_mismatch = 0;

    for (my $i=0; $i<$len; $i++) 
    { 
     ++$num_mismatch if substr($a, $i, 1) ne substr($b, $i, 1);
    }

    return $num_mismatch;
}
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