[BioC] pileupAsGRanges depth limit

[Martin Morgan]

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 at fhcrc.org
> <mailto:mtmorgan at 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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