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0
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1 @genomes=();
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2 $ofile=shift;
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3 open(OUT,">$ofile");
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4 foreach $f (@ARGV)
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5 {
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6 open(IN,$f);
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7 %ldata=();
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8 $genome="";
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9 while(<IN>)
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10 {
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11 chomp();
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12 ($pos,$b1,$b2,$gen)=(split(/\s+/))[1,2,3,-1];
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13 next unless $b1=~/[ACTG]/ && $b2=~/[ACTG]/;
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14 $ldata{$pos}=[$b1,$b2];
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15 if ($genome eq "")
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16 {
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17 $genome=$gen;
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18 push(@genomes,$genome);
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19 }
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20 }
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21 $prev_pos=0;
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22 $prev_ref="na";
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23 $prev_alt="na";
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24 foreach $pos (sort{$a<=>$b} keys %ldata)
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25 {
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26 $dist=$pos-$prev_pos;
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27 if ($dist>1)
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28 {
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29 $pos_append=$prev_pos-length($prev_alt)+1;
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30 $dat_final{"$pos_append\_$prev_ref|$prev_alt"}{$genome}=1 unless $prev_ref eq "na";
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31 $prev_ref=$ldata{$pos}[0];
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32 $prev_alt=$ldata{$pos}[1];
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33 }else{
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34 $prev_ref.=$ldata{$pos}[0];
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35 $prev_alt.=$ldata{$pos}[1];
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36 }
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37 $prev_pos=$pos;
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38 }
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39 $pos_append=$prev_pos-length($prev_alt)+1;
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40 $dat_final{"$pos_append\_$prev_ref|$prev_alt"}{$genome}=1 if $prev_ref ne "na";
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41
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42 }
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43
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44 print OUT " @genomes\n";
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45 foreach $pos (sort{$a<=>$b} keys %dat_final)
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46 {
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47 $line="$pos ";
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48 foreach $g (@genomes)
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49 {
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50 $val=$dat_final{$pos}{$g} ? 1 : 0;
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51 $line.="$val ";
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52 }
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53 chop($line);
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54 print OUT "$line\n";
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55 }
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