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rangelist
2012 May 12
2
range segment exclusion using range endpoints
Hello,
I'm posting this again (with some small edits). I didn't get any replies
last time...hoping for some this time. :)
Currently I'm only coming up with brute force solutions to this issue
(loops). I'm wondering if anyone has a better way to do this. Thank you for
your help in advance!
The problem: I have endpoints of one x range (x_rng) and an unknown number
of s ranges
2012 Dec 17
1
Code works standalone, yet same code fails when part of package
...("qname", "flag",
"rname", "strand", "pos", "qwidth", "mapq", "cigar", "mrnm", "mpos",
"isize", "seq"), tag=c("NM"), removeN=TRUE) {
which <- RangesList(chr = IRanges(start,end))
names(which) <- chr
param <- ScanBamParam(which = which, what = what, tag=tag)
bam <- scanBam(bamfile, param=param)
lst <- lapply(names(bam[[1]]), function(elt) {do.call(c, unname(lapply
(bam, "[[", elt)))})...