Changes in PopGenome 1.2.5
==========================

- fixed PDF problems

Changes in PopGenome 1.2.4
==========================

BUGS FIXED:

- SNP data chunk without corresponding GFF-chunk
- concatenate regions: @gff.info was not set
- positions (type=2) in splitting.data 
  (error, when no SNPs where found)
- readSNP: small BUG in reading all chromosomes
- get_gff_info  
- F_ST.stats: default value is 0.
- linkage.stats: detail=FALSE, calculated wrong Z-statistics

NEW FEATURES:

- sweeps.stats: CLR test
- get.detail(GENOME.class,biallelic.structure=TRUE)
- get.codons()
- get_gff_info(): new parameters
- get.individuals
- mult.linkage.stats (P-value, R2, Distance)
- readMS
- concatenate.regions
- concatenate.classes
- R2.stats
- PG_plot.biallelic.matrix

THX:

- Anna
- JD
- Sebastian
- Thorsten 

Changes in PopGenome 1.2.3
==========================

- removed object files in the src folder (for CRAN)

Changes in PopGenome 1.2.2
=========================

BUGS FIXED:

- readVCF with GFF-file, when chrosomeID includes "Chr"
- readVCF: (GENOME.class@region.names)
- readData (..., FAST=TRUE) # small BUG in computing biallelic.sites
- readData (..., format="HapMap")

NEW FEATURES:

- Phi_ST in the F_ST.stats.2 module
- readSNP and readData(..,FAST=TRUE)  
  calculate now also polyallelic positions (see get.sum.data and 
  GENOME.class@region.stats@polyallelic.sites)
- set.populations() also for diploid data.
- readData(..., format="VCF").
- speed up haplotype-based statistics (unique() now in C )
- diversity.stats()
- get_gff_info() # searching for features

THX:

- Pierre
- Polina

Changes in PopGenome 1.2.1
=========================

BUGS FIXED:

- sliding.window.transform(): BUG in concatenating the regions 
- readSNP(): identifier "1" ... is now also accepted.
- the functon concatenate_to_whole_genome() is now visible
- load.session()


NEW FEATURES:

- scan the data now from a start to an end-position (sliding.window.transform())
- using the bigmemory package for HUGE data sets
- vignettes on CRAN

Changes in PopGenome 1.2.0
=========================

- new implemented C++ functions to read alignments in several formats

- using the ff-package to handle big data

- reading SNP data from 1000/1001 Genome project

- new features (create.PopGenome.method, region.as.fasta ...)

- set.synnonsyn() to verify synonymous/non-synonymous sites of SNP-data 

- new methods (Achaz, ...)

- speed up calculations (C++ functions, multicore computation)

- splitting.data() to analyse subsites like exon, gene, intron ...

 
 
