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" <[email protected]> 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 >>> [email protected] >>> 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 >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
