if ($B1=~ m/^*/ | $B2=~ m/^*/) {
       my $type;
       $type eq "S";
     } else {
       $type eq "I";
     }

##</code><code>##

my $SNP_FILE="SNP.test.out"; # Will be $out in future, just hardcoded to SNP.report for testing now.


open (LINES,"<$SNP_FILE") || die ("Could not open file! \n"); # Read SNP File
<LINES>;

while ($SNP_FILE=<LINES>) 
  {
    
     my ($contig, $PP, $UPP, $Cons, $Cov, $Conflicts, $B1, $B2)=split('\t', $SNP_FILE); #Split line of SNP File
     my $ratio=sprintf("%.2f",($Conflicts/$Cov)); #Creates new variable of ratio of Conflict Count/Total Coverage

     $PP=$PP+1; # Bump padded position coordinate by 1, as gap4 coordinates are off by 1 base compared to bank file
     $Cons=~ s/-/*/; # Replace - with gap4 pad notation in consensus variable
     $B1=~ s/-/*/;   # Replace - with gap4 pad notation in Base 1 variable
     $B2=~ s/-/*/;   # Replace - with gap4 pad notation in Base 2 variable
     chomp $B2;
     $contig=~ s/Contig/#/; # Replace contig with number sign so gap4 can recognize contig identifier
     if ($B1=~ m/^"*"/ or $B2=~ m/^"*"/) {
       my $type eq "S";
     } else {
       my $type eq "I";
     }
my $type;
     print "$contig $PP $Cons $Cov $Conflicts $B1 $B2 $ratio $type \n";
 }
close (LINES);