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




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 ...