- RangesList
  - Make GenomicRanges() accept IRanges as 'start' parameter

#+begin_src R
  library("GenomicFeatures")
  library("Rsamtools")
  library("BSgenome")

  st <- system.time
  
  bamFile <- "NA19239.SLX.maq.SRP000033.2009_09.subset.bam"
  tx <- loadFeatures("ucsc-human.sqlite")
  
  ## FIXME: need to align chromosome naming conventions.
  ## bam file uses "1" and tx db uses "chr1".
  ##
  ## one solution is:
  ## runValue(bigPat@unlistData@seqnames) <-
  ##    paste("chr", runValue(bigPat@unlistData@seqnames), sep = "")
  ##
  st(bigTarget <- transcripts(tx))
  
  ## or load serialized?
  st(bigPat <- readBAMasAlignments1(bamFile))
  
  st(olaps <- findOverlaps(bigPat[1:500], bigTarget))
#+end_src
