NEWS

Changes in PopGenome 2.7.2
===========================

NEW FEATURES:
- include df introgression statistic 
  from https://doi.org/10.1186/s12859-019-2747-z 

Changes in PopGenome 2.6.0
===========================

NEW FEATURES:
- weighted jackknife
- BDF (introgression.stats)

Changes in PopGenome 2.2.8
===========================

NEW FEATURES:
- jacknife for Bdf (introgression.stats())
- diversity.stats(, keep.site.info=TRUE)
- split_data_into_GFF_features()

BUG FIXED:
- jacknife in introgression.stats()
- GFF parsing: '#' comment lines caused a 'segfault' 
- regions containing only NaN's crashed neutrality.stats()
- C-code (crashed calculating pi) 

toDo:
- set.outgroup on slide objects
- 

Changes in PopGenome 2.2.4
===========================

NEW FEATURES:

- introgression.stats
-- Bd-fraction and Bd-bayes-factor

see: 
"Estimates of Introgression as a Function of Pairwise Distances"
bioRxiv
doi: https://doi.org/10.1101/154377 

BUG FIXED:

- Tajima.D for missing data included.

THX:
Ari
Durrell

Changes in PopGenome 2.2.1
===========================

- fixed some warnings and errors 

-- bgzf.c fixes (inline -> static inline)
-- "whopgenome/whop_rsupport.h", line 58: Error: The function "strcasecmp" must have a prototype.

Changes in PopGenome 2.2.0
===========================

NEW FEATURES:

- calc.fixed.shared()
- diversity.stats.between()
- set.filter()
- set.populations() # now also works on transformed objects

Changes in PopGenome 2.1.7
===========================

BUG FIXED:

- diversity.stats()
- introgression.stats: f-statistic
- count.unknowns: GENOME.class@region.data@missing.freqs
  not correctly displayed the values in a 'per population' fashion

NEW FEATURES:

- diversity.stats.between (with additional parameter)
- introgression.stats (new parameter)
	- jacknife; Z & P-values
- calc.R2 now also saves the genomic position of the SNPs
- new function set.filter() to filter data by missing data or SFS
- new slot GENOME.class@region.data@included

Changes in PopGenome 2.1.6
===========================

BUG FIXED:

- readData(,format="VCF") didn't handle insertions.
  Those positions are now treated as unknowns
- MS() failed for low theta values   
- minor issue in set.synnonsyn()

NEW FEATURES:

- region.as.fasta(,type=2) now uses the information 
  stored in the slot GENOME.class.split@region.names 
  to extract the FASTA.
- VCF_split_into_scaffolds()
- GFF_split_into_scaffolds()
- count.unknowns()
- new manual on CRAN 
- split_data_into_GFF_attributes()
- get.feature.names()

THX:

- Mara
- Tina
- Tony

Changes in PopGenome 2.1.0
===========================

BUG FIXED:

- readVCF: polyallelic sites were not stored
- misleading results in the module linkage.stats 
  and calc.R2 when unknown nucleotides are included
  (NaNs in the biallelic matrix)
- get.codons() did not worked correctly for data
  in alignment format
- readData: PopGenome now correctly opens and close
  ff-objects. As a consequence more data (data chunks) can 
  be read in without a write error reported by the ff-package.

NEW FEATURES:

- MKT: new parameter
- detail.stats(,site.FST) now computes SNP-wise FST
- jack.knife.transform()

Changes in PopGenome 2.0.9
===========================

BUG FIXED:

- concatenate.regions (small BUG)

NEW FEATURES:

- readVCF: faster computation + better GFF support


Changes in PopGenome 2.0.8
===========================

BUG FIXED:

- 

NEW FEATURES:

- The function readData(..., format="VCF") is now faster and 
  is able to handle any kind of polyploid data. 
- set.populations: new parameter.
- save and loading "GENOME" objects: much easier.
- readVCF(): can handle unknown positions like ./.
- introgression.stats()

THX:
Durrell

Changes in PopGenome 2.0.7
===========================

IMPORTANT BUG FIXED:

- PopGenome still not correctly specified syn/nonsyn SNPs
  for reverse strands.

NEW FEATURES:

- get.codons works now also for SNP data.

THX:
Mara

Changes in PopGenome 2.0.6
===========================

NEW FEATURES:
- documentation updates

BUG FIXED:
- pairwise MKT test

THX:
Mara

Changes in PopGenome 2.0.5
===========================

BUG FIXED:
- include.unknown was bugy when the very first individual was unknown.

NEW FEATURES:
- splitting.data(..., whole.data=FALSE)
  works now for multiple regions when the 
  regions cannot be concatenated.


Changes in PopGenome 2.0.4
===========================

-

Changes in PopGenome 2.0.3
===========================

IMPORTANT BUG FIXED:

- PopGenome did not correctly specified syn/non-syn
  SNPs for coding regions on reverse ("-") strands.

THX:
- Romain

Changes in PopGenome 2.0
==========================

BUGS FIXED:

- U,u was not accepted as a nucleotide (readData)

NEW FEATURES:

- PopGenome no longer depends on the ape package
- Whop_readVCF (an interface to the WhopGenome package)


Changes in PopGenome 1.3.0
==========================

BUGS FIXED:

- 

NEW FEATURES:
 
- new Vignette
- readMS(..., big.data=TRUE)
- MS(..., big.data=TRUE)
- MS_getStats
- readData(..., progress_bar_switch)
- get.codons(..., SNP.DATA=TRUE/FALSE)
- read.big.fasta now much faster.
- codontable() to define your own genetic code
- PopGplot 

Changes in PopGenome 1.2.6
==========================

BUGS FIXED:

- MKT Test failed with only one sequence as an outgroup
- diversity.stats/get.diversity works
- example files (subdirectory "data")

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 ...