CHANGES IN VERSION 1.99.4
------------------------

    o update get_PAscore2.
    
CHANGES IN VERSION 1.99.3
------------------------

    o add rmarkdown as suggests.

CHANGES IN VERSION 1.99.2
------------------------

    o fix a bug if utr3 list is empty.
    
CHANGES IN VERSION 1.99.1
------------------------

    o add dontrun for getGCandMappability doc.
    
CHANGES IN VERSION 1.99.0
------------------------

    o merge Haibo's code.
    
CHANGES IN VERSION 1.19.1
------------------------

    o replace all `class` by `is`.

CHANGES IN VERSION 1.17.3
------------------------

    o update documentation.
    
CHANGES IN VERSION 1.17.2
------------------------

    o add citation of cleanUpdTSeq.
    
CHANGES IN VERSION 1.15.2
------------------------

    o update author's email.
    
CHANGES IN VERSION 1.15.1
------------------------

    o add the new biocViews tag "ImmunoOncology"
    
CHANGES IN VERSION 1.11.4
------------------------

    o fix the warning for help files in windows

CHANGES IN VERSION 1.11.3
------------------------

    o add utr3.danRer10.
    
    
CHANGES IN VERSION 1.11.2
------------------------

    o fix the error by the change of GRanges.
    
CHANGES IN VERSION 1.7.5
------------------------

    o add Julie as co-maintainer.

CHANGES IN VERSION 1.7.4
------------------------
BUG FIXES
    o fix the bug if there is NA values for proximal site to be adjusted.
    
CHANGES IN VERSION 1.7.3
------------------------
BUG FIXES
    o remove the code modified from voom. And directly use diffSplice.
    
CHANGES IN VERSION 1.7.2
------------------------
BUG FIXES
    o Fix the memory trap if the dataset is huge when call CPsites.

CHANGES IN VERSION 1.7.1
------------------------
BUG FIXES
    o Fix the bug for empty bedgraph.

CHANGES IN VERSION 1.5.7
------------------------
NEW FEATURE
    o decrease the memory to run InPAS.
    
CHANGES IN VERSION 1.5.6
------------------------
NEW FEATURE
    o Add a parameter to control search the proximal site from both 
    direction or not.
    
CHANGES IN VERSION 1.5.5
------------------------
NEW FEATURE
    o search the proximal site from both direction.
    
CHANGES IN VERSION 1.5.4
------------------------
NEW FEATURE
    o Categorize novel distal events into "novel distal" and "truncated distal"
    
BUG FIXES
    o fix the bug in proximalAdjByCleanUpdTSeq.
    
CHANGES IN VERSION 1.5.1
------------------------
NEW FEATURE
    o new function coverageRate for quality control.
BUG FIXES
    o fix the error when not all the seqnames is in bedgraphs for CPsites.

CHANGES IN VERSION 1.3.2
------------------------
BUG FIXES
    o re-run coverage when worker is died for bpapply

CHANGES IN VERSION 1.3.1
------------------------

    o suppress the error not needed in phmm

CHANGES IN VERSION 1.1.9
------------------------

    o update documentation

CHANGES IN VERSION 1.1.8
------------------------
BUG FIXES
    o improve the distCP site search.

CHANGES IN VERSION 1.1.7
------------------------
BUG FIXES
    o typo "novel distal".

CHANGES IN VERSION 1.1.6
------------------------
BUG FIXES
    o fix the seqlevels style issue.

CHANGES IN VERSION 1.1.5
------------------------
BUG FIXES
    o improve limmaAnalyze algorithm

CHANGES IN VERSION 1.1.4
------------------------
BUG FIXES
    o improve the CP sites adjustment algorithm.

CHANGES IN VERSION 1.1.3
------------------------
BUG FIXES

    o shorten the CPU time of CP sites prediction

CHANGES IN VERSION 1.1.2
------------------------
BUG FIXES

    o update description

CHANGES IN VERSION 1.1.1
------------------------
BUG FIXES

    o fix the bug in FFT smooth when length of 3UTR is shorter than smooth power


CHANGES IN VERSION 0.99.7
------------------------
NEW FEATURES

    o compensation by last CDS but not by ratio.


CHANGES IN VERSION 0.99.6
------------------------
BUG FIXES

    o fix the bug in utr3UsageEstimation in calculating of PDUI

CHANGES IN VERSION 0.99.5
------------------------
BUG FIXES

    o fix the bug in utr3Annotation when multiple transcripts sharing same
    transcript name by Gviz::GeneRegionTrack

CHANGES IN VERSION 0.99.4
------------------------
BUG FIXES

    o fix the bug in documentation of utr3Annotation

CHANGES IN VERSION 0.99.3
------------------------
BUG FIXES

    o fix the output ranges from short form to whole 3UTR

CHANGES IN VERSION 0.99.2
------------------------
BUG FIXES

    o clear warnings when run check. 
      Warning: multiple methods tables found for 'species'
      Warning: multiple methods tables found for ‘organism’


CHANGES IN VERSION 0.99.1
------------------------
BUG FIXES

    o errors when run BioCheck. import all the package should be import.
