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
>>
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