[Bioc-sig-seq] readAligned and SAM format

[Kasper Daniel Hansen]

Are you working on this now Martin? I have started to implement  
parsing of BAM files but right now my working is stalling a bit due to  
some other commitments, like finishing my thesis.

Kasper

On Jul 24, 2009, at 19:09 , Martin Morgan wrote:

> "Hattem, Gaye" <GLH at stowers.org> writes:
>
>> Does the readAligned function in ShortRead currently support the SAM
>> format? The vignette mentions that Short Read has been extended to
>> include several formats and lists the SAM format but I don't see
>> this option documented anywhere.
>
> Hi Gaye --
>
> SAM is not yet supported, but will be in the next release (my
> preference is for the binary variant, BAM). MAQ and Bowtie-style input
> is available.
>
> Martin
>
>
>> Gaye Hattem
>> Stowers Institute for Medical Research
>> glh at stowers dot org
>>
>>
>>
>>
>> 	[[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing