Prevent inf loop when REF eq ALT

mskcc · Sep 1, 2016 · 0b9fc73 · 0b9fc73
1 parent cccebe6
commit 0b9fc73
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/maf2maf.pl b/maf2maf.pl
@@ -258,7 +258,7 @@
             my $var = (( defined $al1 and $al1 and $al1 ne $ref ) ? $al1 : $al2 );
 
             # Remove any prefixed reference bps from alleles, using "-" for simple indels
-            while( substr( $ref, 0, 1 ) eq substr( $var, 0, 1 )) {
+            while( $ref and $var and substr( $ref, 0, 1 ) eq substr( $var, 0, 1 ) and $ref ne $var ) {
                 ( $ref, $var ) = map{$_ = substr( $_, 1 ); ( $_ ? $_ : "-" )} ( $ref, $var );
                 ++$pos unless( $ref eq "-" );
             }

diff --git a/vcf2maf.pl b/vcf2maf.pl
@@ -433,7 +433,7 @@ sub GetBiotypePriority {
     my ( $ref_length, $var_length ) = ( length( $ref ), length( $var ));
     # Remove any prefixed reference bps from all alleles, using "-" for simple indels
     my $vcf_pos = $pos;
-    while( substr( $ref, 0, 1 ) eq substr( $var, 0, 1 )) {
+    while( $ref and $var and substr( $ref, 0, 1 ) eq substr( $var, 0, 1 ) and $ref ne $var ) {
         ( $ref, $var, @alleles ) = map{$_ = substr( $_, 1 ); ( $_ ? $_ : "-" )} ( $ref, $var, @alleles );
         --$ref_length; --$var_length; ++$pos;
     }