NEWS

CHANGES IN VERSION 1.12.0
------------------------
NEW FEATURES
    o Add function orgKEGGIds2EntrezIDs to fetch the mapping between KEGG IDs
      and Entrez IDs
    o Add function makeAxtTracks
    o Add function addAncestorGO
    
CHANGES IN VERSION 1.10.0
------------------------
NEW FEATURES
    o Updated CNE class for storing all the information about 
      running the pipeline.
    o Add read.rmMask.GRanges to read RepeatMasker .out file.
    o Add read.rmskFasta to read soft repeat masked fasta file.
    o Add the distribution plot of axt alignment matches.
    o Add the distribution plot of CNE length.
    o Add the syntenicDotplot for axt alignment and GRangePairs.
    o When readAxt and readBed, seqinfo is kept when available.
    o New fixCoordinates function makes the coordinates of Axt alignments
      always relative to positive strands.
    o Add parallel subAxt for Axt alignment.
    o Add the plot of genomic distribution of CNE.
    o Add the function to make bed and bigwig files of CNEs.
BUG FIXES
    o Instead of an error, an empty GRangePairs is returned when no CNEs
      identified.
    
CHANGES IN VERSION 1.8.0
------------------------
BUG FIXES
    o Fix a bug caused by "format" in the blat step.

NEW FEATURES
    o Add the pairwise whole genome alignment pipeline
    o Add a new class "GRangePairs"
    o "Axt" class is now based on "GRangePairs" class.
    o readAncora for reading Ancora format CNE files.