[Bioperl-l] reading sam files

[Jonas Zierer]

Hi Scott,

no, i didn't find any way to read sam files in the documentation
(http://cpan.uwinnipeg.ca/htdocs/Bio-SamTools/Bio/DB/Sam.html )

the BIO::DB::Sam->new method only takes a -bam argument and give a sam
file to this method it says 
[bam_header_read] EOF marker is
absent.                                                                               
[bam_index_load] fail to load BAM
index.                                                                              
[bam_header_read] EOF marker is
absent.                                                                               
[bam_header_read] EOF marker is absent.  

Jonas


Am Monday, den 13.06.2011, 12:39 -0400 schrieb Scott Cain:
> Hello Jonas,
> 
> When you say it didn't work, what do you mean?  Did you read the
> documentation, and it didn't work the way the documentation indicated?
>  Could you show the code you used and any error messages you got?
> 
> Scott
> 
> 
> On Wed, Jun 8, 2011 at 9:10 AM, Jonas Zierer <jonas.zierer at campus.lmu.de> wrote:
> > Hi,
> >
> > i tried to read a sam file insted of a bam file using DB::BIO::Sam, but
> > that didn't work.
> >
> > Is there any other possibility to read sam files with bioperl?
> >
> > thx, bye
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> 
>