## Changes in v1.6 ##

TestOverdispersion now prints a helpful suggestion for which overdispersion
parameter to use, as well as returning that value in its output.
The use of qqman has been eliminated from the vignettes.

ExpectedHindHe, ExpectedHindHeMapping, and SimAlleleDepth now have a contamRate
parameter to simulate sample cross contamination when sampling allelic read
depth, and an errorRate parameter to simulate sequencing error.

A bug has been fixed in Export_GWASpoly so that special characters in sample
names are not converted to periods.

## Changes in v1.5 ##

SimGenotypesMapping, ExpectedHindHeMapping, Export_polymapR_probs,
reverseComplement, and readDArTag functions added.

Bug fixed in GetProbableGenotypes when there are multiple possiblePloidies and
multiallelic is set to "na" or "correct".

Bug fixed in process_sam_multi.py for cases where sample names contain spaces.

Bug fixed in HindHeMapping when loci are discarded due to difficulty estimating
parental genotypes.

Vignettes have been updated with a figure to assist in estimating inbreeding.

## Changes in v1.4 ##

Export_GWASpoly can now export posterior mean genotypes.

Export_adegenet_genind function added.

## Changes in v1.3 ##

Added the ExpectedHindHe, SimGenotypes, and SimAlleleDepth functions.  The
first in particular is intended to help the user to select a Hind/He threshold
for filtering markers.

Added the Export_Structure function.

In the variant calling pipeline, process_isoloci.py has been modified so that
the user can set an expected and maximum Hind/He. The previous functionality,
where these thresholds were calculated automatically from inbreeding, remains
available.

Fixed a bug in VCF2RADdata that would occur if expectedAlleles or expectedLoci
were set too low.  VCF2RADdata now also sets the "Variable_sites_only" attribute
to be FALSE if phaseSNPs = FALSE.

Fixed a bug in SubsetByLocus, MergeRareHaplotypes, and MergeIdenticalHaplotypes
that would delete the "Variable_sites_only" attribute, preventing VCF export.

## Changes in v1.2 ##

The functions HindHe and HindHeMapping have been added, to assist with filtering
loci that are behaving in a non-Mendelian fashion, as well as individuals that
do not behave like the expected ploidy.  The function InbreedingFromHIndHe has
been added to facilitate estimating the inbreeding statistic F from the results
of HindHe.

The Python scripts process_sam_multi.py and process_isoloci.py have been added,
to serve as a pipeline for variant calling in highly duplicated genomes.  These
are described in a new vignette, "Variant and Genotype Calling in Highly
Duplicated Genomes" (isolocus_sorting.Rmd).  The functions readProcessSamMulti
and readProcessIsoloci have been added for import of data from the Python
scripts into polyRAD.

The function RADdata2VCF has been added for export to VCF.

A Python script has been added to help identify full tag sequences for alleles
imported from TASSEL-GBSv2 using VCF2RADdata.

The GetProbableGenotypes function has been updated to optionally recognize
genotypes where copy number does not sum to the ploidy across all alleles for a
locus.  It can now either set these genotypes to NA or correct them to sum to
the ploidy.  Some internal Rcpp functions were added for this purpose.

A bug has been fixed in SubsetByPloidy.

MergeTaxaDepth now generates a more useful error if taxa are specified that
do not exist in the object.

If duplicate locus names are passed to SubsetByLocus, it now generates a
warning and deals with the duplicated loci more appropriately.

The AddDepthSamplingPermutations function has been added.  Permutations for
estimating genotype likelihoods are no longer calculated at the time of data
import, but instead are calculated the first time that genotype likelihoods
are calculated.  This is to avoid unnessasary calculation and recalculation
when alleles and taxa are filtered or merged before running genotype calling.
From the user perspective, there isn't any change except faster import.

The EstimateParentalGenotypes function has been added, using code that was
previously in the AddGenotypePriorProb_Mapping2Parents.  This does not
impact anything frin the user's perspective, but makes the code slightly
less unweildy and allows parental genotype estimations to be used for other
purposes.

The MergeIdenticalHaplotypes function has been added.

Internal functions for simulating gametes and calculating their frequencies have
been corrected so that they still work when only one allele is being simulated.

## Changes in v1.1 ##

A plot method has been added for RADdata objects.

The MergeTaxaDepth, RemoveUngenotypedLoci, and SubsetByPloidy utility functions
have been added.

The Export_MAPpoly and Export_GWASpoly functions have been added.

Bug fixes have been made in TestOverdispersion, VCF2RADdata, SubsetByLocus,
and SubsetByTaxon.

Some code in AddAlleleFreqByTaxa has been translated to Rcpp to speed
computation time for IteratePopStruct and IteratePopStructLD.

## Changes in v1.0 ##

Genotype likelihoods are now estimated under a beta-binomial distribution 
rather than the binomial distribution.  This change was made so that real
sequencing data would be accurately modeled; even in diploid heterozygotes,
read depth of two alleles is often very different from a 1:1 ratio, due to
many underlying issues with sequencing data that would be difficult to model.
Under the beta-binomial with respect to the binomial, there is an increased 
probability of read depth ratios that differ from the true allele copy 
ratio.  In a practical sense, this means reduced certainty in the estimation of
allele copy number from read depth alone, and an increased importance of 
genotype prior probabilities.  The exact shape of the beta-binomial 
distribution is determined by an overdispersion parameter, which the user can
optimize using the TestOverdispersion function.

When using linkage disequilibrium to update genotype priors, the square of
Pearson's correlation coefficient is now used for weighting markers, where
Pearson's correlation coefficient was used previously without being squared.
This applies to both mapping populations and diversity panels, and results
in improved genotyping accuracy.

The functions Export_polymapR, readTASSELGBSv2, RemoveHighDepthLoci,
AddGenotypePriorProb_Even, and TestOverdispersion have been added.

This version of polyRAD is incompatible with RADdata objects generated by
previous versions of polyRAD due to a change in format of the 
depthSamplingPermutations slot.  This slot was changed to simplify the
estimation of genotype likelihood.
