[Bioc-devel] Dependency on devtools in biocLite()

2017-01-13 Thread Andrzej Oleś
Dear all, it's great that for some time now `biocLite()` also resolves package dependencies for GitHub hosted packages. However, as this functionality depends on devtools, an attempt to install a GitHub package when devtools is not installed results in an error > library(BiocInstaller) >

Re: [Bioc-devel] readGAlignments Lacks strandMode

2017-01-13 Thread Hervé Pagès
On 01/13/2017 12:36 PM, Hervé Pagès wrote: Hi, No ifelse() statement needed. Just use invertStrand() on your GAlignments object to invert its strand. strandMode is specific to paired-end reads and the supported modes reflect what other software do with paired-end reads (e.g. TopHat, Rsubread,