I have adopted some suggestions that were given before. My code still blows off the memory when I use a very large infile. Can somebody please help me in optimizing this? Thanks a lot

#!/usr/bin/perl -w
#This code joins randomly haplotypes two by two from the output given 
+by Eli's program with an arbitrary number of populations. It needs a 
+2 allele output. It is  the infile for R calculation.

if ( @ARGV != 1 ) {
    print "incorrect usage ---- TYPE IN COMMAND LINE: perl eli+.pl inf
+ile\n";
    exit();
}

print "What's the OUTFILE?\n";
$OUTFILE = <STDIN>;

open (OUT, ">$OUTFILE") or die "could not create $OUTFILE\n";
open (IN, $ARGV[0]);    #open the first argument

#transform the input list in an array of arrays

@total = ();
@haplotypes=();
$currentPop = 0;
$sampleSize={};  # This will hold the sample size for each population 
+               

while(<IN>) {
               chomp;
           if (/^(\-{0,1}\d+\t-{0,1}\d+)/) {  
                        $sampleSize{$currentPop}++;
                         @temp = split;
                          push @{$haplotypes{$currentPop}}, [@temp];
       
        }elsif (/segsites: (\d+)/) {
                          @{$TempList{$currentPop}}=();
                          while(@{$haplotypes{$currentPop}}) {
                           push(@{$TempList{$currentPop}},            
+                        
                           splice(@{$haplotypes{$currentPop}},       
                           rand(@{$haplotypes{$currentPop}}), 1))
                                                                      
+            }
             @{$haplotypes{$currentPop}} =  @{$TempList{$currentPop}};
                     push @total, $currentPop;
                     $currentPop++;
                                                                      
+         } 
                                                                      
+             }
         foreach $_ (@total) { 
                           print "Population $_\n";
                           print OUT "Population $_\n";
                           print "$sampleSize{$_}\n";
                               
                    for($i = 0; $i <  $sampleSize{$_}/2; $i++) {
                            @pair =();
                            @pair = splice @{$haplotypes{$_}}, 0, 2;
print "$pair[0][0]\t$pair[1][0]\t$pair[0][1]\t$pair[1][1]\t\n";
print OUT "$pair[0][0]\t$pair[1][0]\t$pair[0][1]\t$pair[1][1]\t\n";
                                                                      
+               }
                                                                      
+                 }
 print "$currentPop\n";
[download]

The infile looks like this with hundreds of thousands of repeats

segsites: 2    tMRCA: 0.6398829    
Fsense 1    founders: 2    
-4    0
-4    0
-1    1
-4    0
-segsites: 2    tMRCA: 0.3395337    
Fsense 1    founders: 2    
0    0
0    0
-3    -1
0    0
[download]

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