[Bioperl-l] Are Bio::DB::Bam::Alignment objects read-only ?

Lincoln Stein lincoln.stein at gmail.com
Wed Nov 23 17:02:23 EST 2011

I apologize that the qseq() method is only allowing read-only access. I
will attempt to fix this.


On Wed, Nov 23, 2011 at 6:27 PM, Charles Plessy <
charles-listes+bioperl at plessy.org> wrote:

> Dear BioPerl developers,
> I am trying to process some unaligned paired-end reads with Bio::DB::Sam.
>  For
> each pair, I want to detect a sequence index and a unique molecular
> identifier in
> the linker, record them as auxiliary flags, and trim the linker from the
> read.
> I collect the pairs through a features iterator, and can access all their
> data
> through the high-level Bio::DB::Bam::Alignment API.  After modifying them
> (linker trimming and adding flags), I want to write the resulting pairs as
> a
> new unaligned BAM file.
> I apologise if the solution is trivial, but my problem is that I do not
> manage to
> modify the Bio::DB::Bam::Alignment objects.  Typically, attempts such as
> “$pair[0]->qseq("GATACA")” give errors like
> “Usage: Bio::DB::Bam::Alignment::qseq(b) at
> /usr/lib/perl5/Bio/DB/Bam/AlignWrapper.pm line 80”.
> Since I did not find explanations or portsions of source code indicating
> how to
> modify Bio::DB::Bam::Alignment objects, I wonder if they are read-only…
> Have a nice day,
> --
> Charles Plessy
> Tsurumi, Kanagawa, Japan
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Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>

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