Hmm. It might be best to wait. We've got this other bam_tally pileup generator in gmapR. It has some features that applyPileups lacks. These would include: 1) per-cycle (read position) information 2) per-strand information 3) indels Note that indels are only available from the latest devel with indels=TRUE. Still very much in flux. I like the callback-based applyPileups API. So there are good things about each, as well as a lot of overlap. How hard would it be to add those features to applyPileups? Michael On Mon, Dec 17, 2012 at 1:19 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 12/17/2012 10:13 AM, Michael Lawrence wrote: > >> Do you guys think that pileupAsGRanges should be pushed up somewhere, >> outside of >> ggbio, or is it too high-level? There are clearly many ways that the >> pileup >> output could be coerced to GRanges; maybe Rsamtools or GenomicRanges >> could try >> to support some of the most useful? >> > > I'm ok with moving this (or some similar functionality) to Rsamtools; is > the output of pileupAsGRanges what you're interested in, or could it be > more useful? > > >> Michael >> >> >> >> >> On Mon, Dec 17, 2012 at 9:22 AM, Martin Morgan <mtmorgan@fhcrc.org>> <mailto:mtmorgan@fhcrc.org>> wrote: >> >> On 12/17/2012 03:12 AM, Mark Dunning wrote: >> >> Hi all, >> >> I'm running the pileupAsGRanges function from ggbio, and just >> wondering if there was a limit to the depth it reports? I have >> targeted sequencing data and expect many thousands of reads per >> base >> but the depth seems to be around 250? >> >> >> Hi Mark -- >> >> applyPileups takes a 'PileupParam' argument, which has maxDepth=250L >> as an >> argument, so maxDepth = .Machine$integer.max would get you everything. >> >> The ... arguments of pileupAsGRanges gets passed to PileupParam, so I >> think >> you can add maxDepth=.Machine$integer.max to pileupAsGRanges(). >> >> Martin >> >> >> >> pgr[3:5, >> >> + ] >> GRanges with 3 ranges and 7 metadata columns: >> seqnames ranges strand | A C >> G >> <rle> <iranges> <rle> | <integer> <integer> >> <integer> >> [1] chr17 [7577489, 7577489] + | 1 0 >> 249 >> [2] chr17 [7577490, 7577490] + | 0 6 >> 245 >> [3] chr17 [7577491, 7577491] + | 1 250 >> 0 >> T N depth bam >> <integer> <integer> <numeric> <character> >> [1] 0 0 250 CleanedBams/FLD0097.bam >> [2] 0 0 251 CleanedBams/FLD0097.bam >> [3] 1 0 252 CleanedBams/FLD0097.bam >> >> >> I think that samtools mpileup has a default depth of 250, so is >> it the >> case that the applyPileup function is using the same limit, and >> it is >> possible to change it? >> >> Mark >> >> ______________________________**___________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<http s:="" stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> >> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https="" :="" stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> > >> Search the archives: >> http://news.gmane.org/gmane.__**science.biology.informatics.__** >> conductor<http: news.gmane.org="" gmane.__science.biology.informatics="" .__conductor=""> >> >> <http: news.gmane.org="" gmane.**science.biology.informatics.**="">> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> > >> >> >> >> -- >> 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 <tel:%28206%29%20667-2793> >> >> >> ______________________________**___________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> >> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https:="" s="" tat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> > >> Search the archives: >> http://news.gmane.org/gmane.__**science.biology.informatics.__** >> conductor<http: news.gmane.org="" gmane.__science.biology.informatics="" .__conductor=""> >> <http: news.gmane.org="" gmane.**science.biology.informatics.**="">> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> > >> >> >> > > -- > 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 > [[alternative HTML version deleted]]