I've been playing with mapToTranscripts(), which is a great addition BTW. It's already useful for me.
It would be nice to give a little more description in the help file on the behavior regarding the positions in the returned object and the strand of 'transcripts'. I scanned the man page and found:
"Transcriptome-based coordinates start counting at 1 at the beginning of the ‘transcripts’ range and return positions where ‘x’ was aligned."
But from this it was not totally obvious that 1 starts from the left regardless of the strand. E.g.:
transcripts <- GRangesList(foo=GRanges("1", IRanges(c(101,201),width=50), strand="-")) x <- GRanges("1", IRanges(248,width=1)) mapToTranscripts(x, transcripts) GRanges object with 1 range and 2 metadata columns: seqnames ranges strand | xHits transcriptsHits <Rle> <IRanges> <Rle> | <integer> <integer>  foo [98, 98] - | 1 1 ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths
I believe this is not the same behavior as getSeq() for example, which would consider the rightmost position of a negative strand GRanges(List) to be position 1 in the returned DNAStringSet(List).
just to be clear, I'm not suggesting a change in behavior, just a bit more description in the man page.
R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite) locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  splines stats4 parallel stats graphics grDevices datasets utils methods  base other attached packages:  alpine_0.1 BiocParallel_1.2.1  speedglm_0.2-1.0 Matrix_1.2-0  TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2 GenomicFeatures_1.20.1  AnnotationDbi_1.30.1 Biobase_2.28.0  BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.36.0  rtracklayer_1.28.2 GenomicAlignments_1.4.1  Rsamtools_1.20.1 Biostrings_2.36.1  XVector_0.8.0 GenomicRanges_1.20.3  GenomeInfoDb_1.4.0 IRanges_2.2.1  S4Vectors_0.6.0 BiocGenerics_0.14.0  testthat_0.9.1 devtools_1.8.0  knitr_1.10.5 BiocInstaller_1.18.2 loaded via a namespace (and not attached):  Rcpp_0.11.6 compiler_3.2.0 git2r_0.10.1 futile.logger_1.4.1  bitops_1.0-6 futile.options_1.0.0 tools_3.2.0 zlibbioc_1.14.0  biomaRt_2.24.0 digest_0.6.8 memoise_0.2.1 RSQLite_1.0.0  lattice_0.20-31 DBI_0.3.1 stringr_1.0.0 roxygen2_4.1.1  rversions_1.0.0 grid_3.2.0 XML_3.98-1.1 magrittr_1.5  lambda.r_1.1.7 stringi_0.4-1 RCurl_1.95-4.6