update to add alt_cHGVS fix for gene flanking region too

ltnetcase · Apr 15, 2021 · 0f5cc57 · 0f5cc57
1 parent c619b62
commit 0f5cc57
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/lib/BedAnno.pm b/lib/BedAnno.pm
@@ -2848,13 +2848,17 @@ sub finaliseAnno {
             # 1.23 add standard_cHGVS for gene flanking numbering cHGVS.
             if ( exists $trAnnoEnt->{c} and $trAnnoEnt->{c} =~ /-u|\+d/ ) {
                 $trAnnoEnt->{standard_cHGVS} = $trAnnoEnt->{c};
-
             }
             if ( exists $trAnnoEnt->{standard_cHGVS} ) {
                 $trAnnoEnt->{standard_cHGVS} =~ s/(?<=\*|-)(\d+)(-u|\+d)(\d+)/$1+$3/eg;
                 $trAnnoEnt->{standard_cHGVS} =~ s/\d+-u/-/g;  # for no-5'utr case
                 $trAnnoEnt->{standard_cHGVS} =~ s/\d+\+d/*/g; # for no-3'utr case
             }
+            if ( exists $trAnnoEnt->{alt_cHGVS} and $trAnnoEnt->{alt_cHGVS} =~ /-u|\+d/ ) {
+                $trAnnoEnt->{alt_cHGVS} =~ s/(?<=\*|-)(\d+)(-u|\+d)(\d+)/$1+$3/eg;
+                $trAnnoEnt->{alt_cHGVS} =~ s/\d+-u/-/g;  # for no-5'utr case
+                $trAnnoEnt->{alt_cHGVS} =~ s/\d+\+d/*/g; # for no-3'utr case
+            }
 
             $trAnnoEnt->{trVarName} = _getTrVarName( $tid, $trAnnoEnt );
         }