[Bioperl-l] reading sam files

[Jonas Zierer]

i don't want to update the header, but add tags to every single aligned
read!
(in plain text format X[A-Z]:<type>:<value> at the end of the line)

Jonas

Am Wednesday, den 15.06.2011, 10:03 +0100 schrieb Peter Cock:
> On Wed, Jun 15, 2011 at 9:50 AM, Jonas Zierer
> <jonas.zierer at campus.lmu.de> wrote:
> > Hi,
> >
> > the reason is, that i want do add tags to the sam file. as far as i know
> > this is only possible in sam files and not in bam files. now i have to
> > read the sam file analyze the read and add the tag. These tags are
> > written to the sam file which can then be converted to bam.
> > If i have to read a bam file with bioperl i have to convert the sam to
> > bam, read it with bioperl, change the sam file and convert it again.
> >
> > my target was to avoid this second conversion, but i think that's the
> > best solution.
> > thx for your help!
> > bye
> 
> Both SAM and BAM support plain text header text, e.g. @CO lines.
> If you are looking for an efficient way to update this header in a BAM
> file, try the samtools reheader command.
> 
> Peter