CHANGES IN VERSION 1.3.9
-------------------------

NEW FEATURES
* InteractionTrack class for plotting interactions with Gviz
* plotAvgViewpoint for plotting summarised interactions around a set of features
* summariseByFeaturePairs: to summarise interactions between all pairs of two feature sets

SIGNIFICANT USER-LEVEL CHANGES
* annotateInteractions is significantly faster
* Data import has been made stricter and more consistent across different file formats. 
  Homer interaction files now have data imported that was previously discarded. 

BUG FIXES
* single viewpoint plotting (plotViewpoint)
* is.dt, is.pt
* calculateDistances
* some import/export issues

CHANGES IN VERSION 1.1.0
-------------------------

NEW FEATURES

* Import method for reading data from two bam files containing paired end reads.
* A function for removing duplicate interactions: 'removeDups'
* Two methods for finding probable distance cutoffs for self ligations: 
  'get_binom_ligation_threshold' and 'get_self_ligation_threshold'. 
* 'countsBetweenAnchors': a function to summarise interactions between a set of 
  genomic regions of interest.

SIGNIFICANT USER-LEVEL CHANGES

* GenomicInteractions objects have been refactored for consistency with GRanges
  objects. Interaction-level metadata such as p-values is now stored as a DataFrame
  accessible using 'mcols'.
* importing data from a file is now done using 'makeGenomicInteractionsFromFile' 
* 'GenomicInteractions' can be used to construct a new object from anchors
  as GRanges objects and metadata.
* 'show' method looks nicer and is faster.

DEPRECATED AND DEFUNCT

* 'FDR', 'pValue', 'normalisedCounts', 'genomeName': no longer needed 
  because of refactoring. Access metadata by 'mcols' instead. 
* 'count' renamed to 'interactionCounts'

BUG FIXES