#! /usr/bin/perl
open(FILE,$ARGV[0]) || die "Unable to open file";
%nhash =  ();

while(<FILE>)
  {
    @a = split;
    #HWI-ST674_0111:4:2207:13207:103630#0/3
    $a[0] =~ s/\/3$//g; 
    if(($a[1] == 161 || $a[1] == 97) && $a[4] >= 20)
     {
      $id[$i] = $a[0];
      $chr[$i] = $a[2];
      $pos[$i] = $a[3];
      $str[$i] = "+";
      $dist[$i] = $a[8];
      $length[$i] = length($a[9]);
      $i++;
      $idhash{$a[0]} = "aaaa";
     }
   if(($a[1] == 145 || $a[1] == 81) && $idhash{$a[0]} eq "aaaa")
     {
      $key = $a[0];
      $length = length($a[9]);
      $val = "$a[2]\t$a[3]\t-\t$a[8]\t$length";
      $nhash{$key} = $val;
     }
  }
#print "$i \n";
$chr = $chr[$i-1];
  for($j=0;$j<$i;$j++)
    {
       if(($pos[$j] - $pos[$j-1] > 300 ) || ($dist[$j] - $dist[$j-1] > 300 || $dist[$j-1] - $dist[$j] > 300))
        {
          #print "$k $l\n";
          if($k==1 && $l==1)
           {
             @parr = split(/\t/,$ll[0]);
             @narr = split(/\t/,$kk[0]);
           }
          if($k > 1 && $l > 1)
           {
               for($m=0;$m<$k;$m++)
                  {
                    @parr = split(/\t/,$ll[$m]);
                    $ppos[$b] = $parr[2];
                    $pdist[$b] = $parr[4];
                    $plength[$b] = $parr[5];
                    $sum_pdist = $sum_pdist + $parr[4];
                    $b++;
                  }
               for($n=0;$n<$l;$n++)
                  {
                    @narr = split(/\t/,$kk[$n]);
                    $npos[$c] = $narr[2];
                    $ndist[$c] = $narr[4];
                    $nlength[$c] = $narr[5];
                    $c++;
                  }
           @npos = sort(@npos);
           #print "@npos\n";
           $pstart = $ppos[0];
           $pend = $ppos[$b-1];
           $prealend = $ppos[$b-1] + $plength[$b-1];
           $nstart = $npos[0];
           $nend = $npos[$c-1];
           $del_length = $nstart - $prealend;
           $avg_dist = $sum_pdist / $b;
           $real_del_length = $avg_dist - 200;
           if($del_length > 0)
            { 
              print "$chr\t$k\t$pstart\t$pend\t$prealend\t$nstart\t$nend\t$l\t$del_length\t$avg_dist\t$real_del_length\n";
            }
           @ppos=();
           @pdist =();
           @plength = ();
           @npos = ();
           @ndist = ();
           @nlength =();
          }
           $k=0;$l=0;
           $b=0;$c=0;
           $sum_pdist = 0;
            $#ll = -1; 
            $#kk = -1;
        }


          $ll[$k] = "$id[$j]\t$chr[$j]\t$pos[$j]\t$str[$j]\t$dist[$j]\t$length[$j]";
          $k++;
          $nhval = $nhash{$id[$j]};
          
          $kk[$l] = "$id[$j]\t$nhval";
          #print "$kk[$l]\n";
          $l++;
    }