@total = (); #this is an array of arrays 
@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];<p>
 
  } elsif (/segsites: (\d+)/) {
     $currentPop++;
     push @total, $currentPop;
  }    
}

foreach $_ (@total) { 
  for($i = 0; $i < $sampleSize{$currentPop}; $i++){
    $Rand=rand(int(@{$haplotypes{$_}}));
    $temp=splice (@{$haplotypes{$_}}, $Rand, 1);
    push @{$RandHapl{$_}}, $temp;
  }
}