[Bioperl-l] unaligned sequences breaks hqd analysis

[Andy Nunberg]

I am glad you survived Carnival :)
I can live with gapped sequence, i have a new problem...

the hqd analysis is failing in some ace files...
I get no warnings when parsing the assemblies, or getting the contigs
i do get this
Can't call method "start" on an undefined value at
/loginhome/anunberg/bioperl-1.2/Bio/Assembly/ContigAnalysis.pm line 181
this occurs in this bit of code from Contig Analysis.pm in the hqd_analysis
method
# Scanning the aligned region of each read
	my $seq_ix = 0;
	my $coord =
$self->{'_objref'}->get_seq_feat_by_tag($seq,"_align_clipping:$seqID");
      ***my ($astart,$aend) = ($coord->start,$coord->end);
	$astart = $astart + $ignore; # Redefining limits to evaluate HQDs (jump
$ignore at start)
	$aend   = $aend   - $ignore; # Redefining limits to evaluate HQDs (stop
$ignore before end)

so i looked at each sequence as it was looping,
turns out that the sequence it was breaking on has -1 -1 as the align start
and stop

Ideally, one would check to see which seqs in the contig are aligned before
calling the coordinates of the aligned section
I have inserted
next if !$coord and that seems to work as short term fix

Andy
*******************************************************************
Andy Nunberg, Ph.D
Computational Biologist
Orion Genomics, LLC 
(314) 615-6989
http://www.oriongenomics.com