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

Tue, Oct 21, 2014 8:10 PM

Thank you Herv?! I failed to realized that this was included in the docs.

Anyhow, we've been discussing internally what default value to use. We
also noted that the `genomecov` tool from BED in it's split mode
ignores the D's:
http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html

Cheers,
Leo

On Mon, Oct 20, 2014 at 5:45 PM, Herv? Pag?s <hpages at fhcrc.org> wrote:

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

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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

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