[BioC] pileupAsGRanges depth limit

[Mark Dunning]

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?

> 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