[Bioperl-l] reading sam files

[Scott Cain]

Hi Jonas,

Then I think you are correct that there isn't a way to read sam files
directly.  You could convert to bam, or extend Bio::DB::Sam to do what
you want (patches welcome!).

Scott


On Tue, Jun 14, 2011 at 7:47 AM, Jonas Zierer
<jonas.zierer at campus.lmu.de> wrote:
> 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
>> >
>>
>>
>>
>
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research