[Bioc-devel] Why be default 'D' is not dropped from coverage?

[Hervé Pagès]

Hi Leo,

On 10/18/2014 10:50 AM, Leonardo Collado Torres wrote:
> Hi,
>
> A collaborator of mine is working on a new software and we while we were
> doing a sanity check to compare the base-level coverage from BAM files
> and bigWig files generated from his software we realized that by default
> bases corresponding to a 'D' on the CIGAR string get counted when
> reading coverage from BAM files.
>
> That is:
>
>  > getMethod('coverage', 'GAlignments')
> Method Definition:
>
> function (x, shift = 0L, width = NULL, weight = 1L, ...)
> {
>      .local <- function (x, shift = 0L, width = NULL, weight = 1L,
>          method = c("auto", "sort", "hash"), drop.D.ranges = FALSE)
>      coverage(grglist(x, drop.D.ranges = drop.D.ranges), shift = shift,
>          width = width, weight = weight, method = method)
>      .local(x, shift, width, weight, ...)
> }
> <environment: namespace:GenomicAlignments>
>
> Signatures:
>          x
> target  "GAlignments"
> defined "GAlignments"
>  > packageVersion('GenomicAlignments')
> [1] ‘1.2.0’
>
>
> You can see that this is default elsewhere, for example:
>
>  > extractAlignmentRangesOnReference
> function (cigar, pos = 1L, drop.D.ranges = FALSE, f = NULL)
> {
>      if (!isTRUEorFALSE(drop.D.ranges))
>          stop("'drop.D.ranges' must be TRUE or FALSE")
>      if (drop.D.ranges) {
>          ops <- c("M", "=", "X", "I")
>      }
>      else {
>          ops <- c("M", "=", "X", "I", "D")
>      }
>      cigarRangesAlongReferenceSpace(cigar, flag = NULL, pos = pos,
>          f = f, ops = ops, drop.empty.ranges = FALSE, reduce.ranges = TRUE)
> }
> <environment: namespace:GenomicAlignments>
>
>
> What is the rationale for setting `drop.D.ranges` by default to FALSE?

Because last time I checked (but that was 3 or 4 years ago), that's what
Samtools pileup was doing.

Cheers,
H.

>
> Thanks,
> Leo
>
>

-- 
Hervé Pagès

Program in Computational Biology
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