#!/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 infile\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";