[Bioc-sig-seq] readAligned and SAM format

[Martin Morgan]

Kasper Daniel Hansen wrote:
> 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.

I'm in the same position. I took a snapshot of samtools, extracted the
relevant code to parse SAM / BAM, and used that to parse BAM files in to
R data structures. It was a very first pass, with some problems
including not complete cross-platform portability of the samtools code,
samtools changing rapidly at the time I did this, and not really sure
that the best strategy is to blindly pull the data in to R -- maybe
better, at least for some applications, would be to aim further down
stream, e.g., coverage.

Please feel free, Kasper or others out there, to work on this; I'm happy
to offer my two cents.

Martin

> 
> 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]]
>>>
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>>
>> -- 
>> 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
>>
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>