New findOverlaps,GTuples,GTuples-method when type = "equal" gives 10-100x speedup by using data.table.
After being deprecated from GenomicRanges in BioC 3.1, mapCoords() and pmapCoords() are now defunct.
After being deprecated in BioC 3.1, the "intervaltree" algorithm in findOverlaps() is now defunct.
Switched to a html vignette from a pdf one.
Added missing Value sections to GTuples-comparison.Rd and
intra-tuple-methods.Rd.
Improved description of findOverlaps,GTuples,GTuples-method and
what it means for two tuples to overlap. In particular, included a reference to
the vignette which uses examples to explain these definitions.
Included in the vignette my motivation for creating the
GenomicTuples package.
Initial version submitted to Bioconductor.