Changes from Version 1.1.1 to 1.2.0 [November 3 2020]

* Modifications of vcf2pooldata.R using cpp functions interfaced with Rcpp to improve both speed (about 1 order of magnitude on real life tests) and stability. Parallelisation has been disactivated since it did only provide marginal gain (sequential reading of the file which is not performed in parallel being the main limiting factor).
* Modification of the pooldata.subset.R function to allow subsetting the pooldata object according to SNP indexes (in addition to Pools indexes or not). Additional filtering options included in particular to allow for coverage criteria to be applied on a per-pool basis.
* Fixed a bug that lead to NA in positions not covered by any reads in the subset (i.e., it had no consequence on estimation of statistics) in both the pooldata.subset.R and computePairwiseFSTmatrix.

Changes from Version 1.1.0 to 1.1.1 [October 22 2019]

* Fixed an issue with parsing of vcf files generated by FreeBayes
* Fixed an issue with prefix option and changed writing.dir default value in pooldata2genobaypass an pooldata2selestim functions

Changes from Version 1.0.0 to 1.1.0 [June 23 2019]

* Modified vcf2pooldata function to allows parsing of vcf generated by software other than VarScan (e.g., GATK, BcfTools). Format are automatically detected based on the presence of AD (Bcftools like) or AD and RD fields (VarScan like)
* Modified vcf2pooldata and popsync2pooldata to allow parallelization of some parts of the parsing

Changes from Version 0.0.1 to 1.0.0 [September 14 2018]

* Changed notations in the ComputeFst functions for the MoM method to be consistent with Genetics paper (MoM=>Anova and PiD=>Identity)
* Fixed an issue with missing data in computeFST function (for the MoM method)
* Function pooldata.subset added
* snpdet matrix with dummy values added to the pooldata object created by genobaypass2pooldata and genoselestim2pooldata functions for compatibility with other functions
* Minor corrections
