o Complete vignette (get rid of all TODO from it).

o Complete man pages (get rid of all TODO from them).

o Add 'drop.ambiguous.hits' arg to countReads() for dropping reads that are
  assigned to multiple edges (when by="sgedge"), to multiple reduced edges
  (when by="rsgedge"), to multiple transcripts (when by="tx"), or to
  multiple genes (when by="gene"). Default value for 'drop.ambiguous.hits'
  should be FALSE. But the exact effect of dropping ambiguous hits when
  by="sgedge" (or by="rsgedge") needs to be closely examined first. For
  example, that would mean always dropping junction reads since they are
  always assigned to more than 1 edge (they're assigned to an intron + its
  2 flanking exons).

  Counting the nb of "unambiguous compatible hits" per transcript is currently
  done "by hand" in the man page for txweight(). Do it again with
  countReads(sg, by="tx", drop.ambiguous.hits=TRUE) and compare. Should
  produce the same result.

o Fix issue with calls to plotting functions requiring 1 more key-stroke than
  necessary before they actually start to plot something.

o Implement rsgedgesByTranscript().

o Move vignette to vignettes/


