[Bioperl-guts-l] [Bug 2669] New: Typo in Bio::Assembly::Contig add_seq()

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Nov 18 00:40:28 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2669

           Summary: Typo in Bio::Assembly::Contig add_seq()
           Product: BioPerl
           Version: 1.5 branch
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Unclassified
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: chad-bioperl-bugzilla at superfrink.net


In the Bio::Assembly::Contig add_seq() routine I just noticed the code:
  $self->{'elem'}
I suspect it should be:
  $self->{'_elem'} 

There are no other references to $self->{'elem'} in the module.

$ grep '[^_]elem[^e]' Contig.pm
    $self->{'_elem'}{$seqID} = {} unless (exists $self->{'elem'}{$seqID});

I am running Ubuntu 8.04.1 with bioperl version 1.5.2.102-1ubuntu1.

A patch is:

$ diff -u Contig.pm.orig Contig.pm
--- Contig.pm.orig      2008-11-17 22:22:30.000000000 -0700
+++ Contig.pm   2008-11-17 22:23:27.000000000 -0700
@@ -1083,7 +1083,7 @@
     }

     my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
-    $self->{'_elem'}{$seqID} = {} unless (exists $self->{'elem'}{$seqID});
+    $self->{'_elem'}{$seqID} = {} unless (exists $self->{'_elem'}{$seqID});

     if (exists( $self->{'_elem'}{$seqID}{'_seq'} ) &&
        ($seq eq $self->{'_elem'}{$seqID}{'_seq'}) ) {


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