check number of markers on chromosome arms before fitting hmm.  Arms with fewer than 10 markers are skipped.
check whether multiple genome builds are available in keyOffFirstFile (called by BeadStudioSet constructor)
update DESCRIPTION. Add deprecated-functions.R, hmm-functions.R, viterbi-functions.R, simulation-functions.R, genotype-functions.R
Clean AllGenerics.R and NAMESPACE
Remove viterbi.wrapper, .getArm, getSds, .getSds, getTau, probabilityOutlier
artificialData moved to simulation-functions
Delete logCnStates and initialSigma. Changes to generatorFun:

- b will have fewer rows than r if NP probes present. Only b for SNPs is passed.

- starting value for AAAB and ABBB mean are 0.1 and 0.9, respectively (don't think this makes much difference)
Changes to generatorFun:

- weightedMoments replaces weightedMean, weightedSd in updateBafParams
- insert print(mus) for viewing updates
- the product of the forward/backward variables is passed as a matrix h from viterbi2Wrapper (fv, bv variables no longer passes)
Several changes to updateBafParams and updateCnParams in generatorFun:

updateBafParams:
- estimate the variance for genotypes 'A' and 'B' using the state that has the most support, where support is measured by the column-wise sums of the product of the forward/backward probabilities from viterbi.  Previously, estimates based on hemizygous deletion state are unreliable if there is not any hemizygous deletions.  Use 0 and 1 for the BAF mean of 'A/AA/AAA, ...' and 'B/BB/BBB' genotypes (no update).

- Similarly, the variance of heterozygous genotypes (AB, AAB, ABB) is estimated from states 3, 5, or 6 if the support is greatest for one of these states.  If not, the prior variance is used.

updateCnParams:

- print(mu) added
- matrix h passed from viterbi wrapper (fv * bv)
- if the probability in g1 (product of h and the density) is less than 0.01, 'g1' is zeroed out.
- if there are not at least 10 observations with probability greater than 0.5 for a copy number state, the moments for the copy number state are considered to be not estimable and are not updated.
- The means for state 5 is required to be one standard deviation higher than the mean for state 3.  State 6 must have mean one sd greater than the mean of state 5. State 1 must have a mean at least one standard deviation from state 2.
- Assume that states with at least 1 copy number have the same variance
- Outlier probability for copy number is estimated as the fraction of rows for which the sum of the probabilities across all states (row-wise sums of the g1 matrix) is less than 0.1
Changes to generatorFunG: use 'totalh' instead of 'total.g1'
update functions for gc-wave correction
remove hmm method for CNSet class
Move hmm functions to file hmm-functions.R
remove the commented hmm2 methods. Comment the setvalidity method for class Viterbi. Move fitViterbi to genotype-functions
relocate fitViterbi.  Remove initialize method for Viterbi2 class and setValidity method. Delete pretty much everything for the Viterbi2 class
move simulation functions in methods-matrix to simulation-functions.R
committing methods-matrix before deleting
Removed methods-matrix.R
deleted methods-oligoSnpSet
committing changes to updateBaf.R before deleting