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 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: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
