CHANGES IN VERSION 1.3.3
-------------------------

NEW FEATURES

    o updates in package vignette

BUG FIXES

    o remove limitation of maximum typecode in the plot, now using rainbow()
    
CHANGES IN VERSION 1.3.2
-------------------------

BUG FIXES

    o fix the returned posterior p

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

BUG FIXES

    o NA bug when model fails
    o using the length of the segment if shorter than maxk

CHANGES IN VERSION 1.1.8
-------------------------

NEW FEATURES

    o add error catching in biomvRhsmm
    o updates in package vignette
    
BUG FIXES

    o fine tuning of memory usage for large count data structure
    o minor bug fixes

CHANGES IN VERSION 1.1.7
-------------------------

NEW FEATURES

    o add support of Rle like sparse data in mcols of large count data structure.
    o add mclapply for parallel processing of different seqnames in biomvRhsmm


CHANGES IN VERSION 1.1.6
-------------------------
    
BUG FIXES

    o fix nbinom emis estimateSegCommonDisp -> nbinomCLLDD

CHANGES IN VERSION 1.1.5
-------------------------

NEW FEATURES

    o update biomvRGviz to have trackList returned when tofile=FALSE
    
BUG FIXES

    o typo fix in function argument
    
CHANGES IN VERSION 1.1.4
-------------------------

NEW FEATURES

    o update biomvRGviz to plot multiple samples in one, and more param
    o plot method now defaults to multiple samples in one, sampleInOne=T
    
BUG FIXES

    o fix states rank when prior.m=cluster 

CHANGES IN VERSION 1.1.3
-------------------------

NEW FEATURES

    o the x slot in the returning object for biomvRhsmm now also contains the probability of associated state for each position
    o the param slot in the returning object for biomvRhsmm now also contains the updated emission and sojourn parameters for each seqname and sample column
 
CHANGES IN VERSION 1.1.2
-------------------------

NEW FEATURES

    o add a new clustering method for emission prior estimation
    o add a new example section of DMR detection in the vignette
    
BUG FIXES

    o switch off several data checking warnings, use normal cat() instead

CHANGES IN VERSION 1.1.1
-------------------------

NEW FEATURES

    o add support of direct input of sojourn parameters as named list.
    
BUG FIXES

    o suppress warnings generated when appending GRanges object for the output

CHANGES IN VERSION 0.99.3
-------------------------

NEW FEATURES

    o add mvt and t to the emis.type and tmvtFit function

BUG FIXES

    o fix shift index (-1) in pois and nbinom fitting	    

CHANGES IN VERSION 0.99.2
-------------------------

NEW FEATURES

    o add log-Vertibi in c
    
    o add normalizing factor for estimation of emis$p and soj$d

    o add avgFunc to be used in average calculation, median and mean with trim, default to median

BUG FIXES

    o fix shift index (-1) in pois and nbinom fitting	
	
CHANGES IN VERSION 0.99.1
-------------------------

NEW FEATURES

    o in Bioc-devel
