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

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

...
 }
close (LINES);