Merge branch 'devel' of github.com:htgt/LIMS2-WebApp into devel

Changes

@@ -1,5 +1,9 @@
 {{$NEXT}}
 
+0.282     2015-01-22 16:20:36 Europe/London
+
+    Added new front page sponsor report
+
 0.281     2015-01-22 08:41:56 Europe/London
 
 Update public gene report page.

lib/LIMS2/WebApp/Controller/API/Traces.pm

@@ -86,11 +86,21 @@ sub _extract_region {
     for my $i ( $start .. $end ) {
         my $sample_loc = $scf->{index}[$i];
         my $nuc = $scf->{bases}[$i];
-        die "One sample has two base calls??" if exists $sample_to_base{ $sample_loc };
-
-        #we have to lie and reverse complement if we're reversing
-        #$sample_to_base{ $sample_loc } = $nuc;
-        $sample_to_base{ $sample_loc } = $reverse ? revcom( $nuc )->seq : $nuc;
+#        die "One sample has two base calls??" if exists $sample_to_base{ $sample_loc };
+#        Instead of die-ing which causes a valid tracefile to not be displayed,
+#        we accept that the call may be ambiguous and just take the first one as valid
+#        This approach may need to be reviewed - perhaps we should put in an ambiguity code
+#        once we know how often this occurs at a specific location - DP-S 28/01/2015
+        if ( exists $sample_to_base{ $sample_loc } ) {
+            $self->log->debug( "This sample has two base calls:");
+            $self->log->debug( $sample_loc . ' => ' . $sample_to_base{ $sample_loc } . " (already in the hash)");
+            $self->log->debug( $sample_loc . ' => ' . ($reverse ? revcom( $nuc )->seq : $nuc) . " (ready to place in hash)");
+        }
+        else {
+            #we have to lie and reverse complement if we're reversing
+            #$sample_to_base{ $sample_loc } = $nuc;
+            $sample_to_base{ $sample_loc } = $reverse ? revcom( $nuc )->seq : $nuc;
+        }
     }
 
     my ( @series, @labels );