4/6/2009 committed Version 1.5.12

* Simplified Vignette. 
  - created a data object locusLevelData that has the basic elements required for the HMM
    	    - matrix of genotypes
	    - matrix of copy number
	    - annotation data
* Added function robustSds for computing uncertainty estimates for copy number
  (uses MAD)
* Changed findBreaks function to prevent calling gaps (centromeres) as altered
  - findBreaks is not meant to be called by the user
* Added breaks function that is a wrapper for findBreaks
* The preferred representation of chromosome is an integer.  For the
   sex chromosomes, 23 = X and 24=Y
* Included reference distributions for crlmm confidence scores in the inst/extdata directory

4/6/2009 committed Version 1.5.13

* Added hmm.Rd file

4/9/2009 committed version 1.5.14

* Changed description

4/28/2009 committed version 1.7.1

* Fixed bug in the first figure of the vignette -- for some reason the
  amplified state was not showing up.

4/28/2009 committed version 1.7.2

* edits to copynumberEmission

6/18/2009 committed version 1.7.3

* added 3 additional arguments to the viterbi function that allows one to
  scale the transition probability between the hidden states:
      - normal2altered  (scalar for transition from normal to altered state)
      - altered2normal  (scalar for transitioning from altered to normal state)
      - altered2altered (scalar for transitioning between to states)

* the default is not to scale the transition probability

* the C code now accepts the above arguments and scales the transition
  probability accordingly

* for copynumberEmission, check for zero's in copy number estimates
    when takelog=TRUE...  change zeros to small positive value (0.05)
    to avoid nan's

6/18/2009 committed version 1.7.4

* fixed a few bugs in copynumberEmission
* added warning messages to copynumberEmission -- 
  - inserted stop() if all values in a row are NA or all values in a column are NA

6/25/2009 committed version 1.7.4
* changed imports field require oligoClasses >= 1.6.0

7/07/2009 committed version 1.7.5

* rewrote vignette

* added check that computed transition probabilities sum to one in the
  viterbi function

7/08/2009 committed version 1.7.6

* initialStateProbs argument for viterbi can be missing

* -Inf values in emission probs replaced with small negative value
   (-50) instead of zero

*  use all.equal to check sums of the transition prob. matrix


7/08/2009 committed version 1.7.7

* initialStateProbs argument for viterbi can be missing

* removed sampleNames argument from breaks()

7/16/2009 committed version 1.7.8

* fixed documentation problems, updated vignette

9/22/2009 ----- version 1.7.9

* check that emission probabilities are an array in the viterbi function
* add column for sample in 'breaks' function


9/23/2009 ----- version 1.7.10

* transitionProbability returns an error if the computed tau is
  greater than 1.  We may therefore need to require that one do this
  computation one chromosome at a time.  Need to debug for multiple
  chromosomes.

10/05/2009 ----- version 1.7.11

* added verbose argument to viterbi function

10/05/2009 ----- version 1.7.12

* removed extra verbose argument from viterbi 

10/06/2009 ----- version 1.7.13

* for chromosome arm, define p as <= centromereEnd (instead of centromereStart)
* by default, transitionPr = max(0.5, exp(-2*diff(position)/TAUP)).
* updated transitionProbability help file
svn ci -m "transitionProbability returns tau as max(0.5, exp(-2*d/TAUP)). updated help file"

10/10/2009 ----- version 1.7.14

* fixed bug in transitionProbability.  Returns NA in last index (arbitrary).

11/10/2009 ----- version 1.9.1

* fixed bug in transitionProbability for chromosome X.  

02/20/2010 ----- version 1.9.2

* added hmmOptions function, updated viterbi.  Updated VanillaICE vignette.

* viterbi returns RangedData object (IRanges class) as well as log
  likelihood ratio comparing the viterbi state path to the normal
  state path

04/05/2010 ----- version 1.9.4
* added inst/test/crlmmDownstream.Rnw

04/06/2010 ----- version 1.9.5
* modified vignette.  Added help pages


