[Bioperl-l] Bio::Assembly::Contig object does not contain reads in opposite orientation

[Mark A. Jensen]

Thanks Jiri, I've created a bug report and assigned it to myself. See
http://bugzilla.open-bio.org/show_bug.cgi?id=3088
cheers, Mark
----- Original Message ----- 
From: "Jiri Stiller" <j.stiller at uq.edu.au>
To: <bioperl-l at bioperl.org>
Sent: Tuesday, June 01, 2010 4:03 AM
Subject: [Bioperl-l] Bio::Assembly::Contig object does not contain reads in 
opposite orientation


> Hi,
> I am trying to process bam file using Bio::Assembly::IO. I attached test
> script and output.
> When I am retrieving contigs I get correct contig number and position
> but contig objects build from reads of different orientation  don't
> contain any read sequences. Contigs built from the reads of the same
> orientations are fine.
>
> Your help/advice would be greatly appreciated.
>
> Cheers,
>
> -- 
> Jiri Stiller
> Senior Bioinformatics Researcher
> Australian Centre for Plant Functional Genomics
> School of Land, Crop and Food Sciences
> University of Queensland
> Brisbane QLD 4072
>
> j.stiller at uq.edu.au
> Phone: +61 (0)7 3346 7082
> Mobile: +61 (0) 422 941 581
> Fax: +61 (0)7 3365 1177
>
>
>


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