readSNP: Read data in .SNP format
In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description Usage Arguments Details Value Examples

This function reads data in .SNP (quality_variant) format, as distributed by the 1001 Genomes project (Arabidopsis).

readSNP(folder,populations=FALSE,outgroup=FALSE,gffpath=FALSE,
	CHR=FALSE,ref.chr=FALSE,snp.window.size=FALSE,
	parallized=FALSE,ffpackagebool=TRUE,
	include.unknown=FALSE
	)

`folder`	the basepath of the variant_calls
`outgroup`	vector of outgroup sequences
`populations`	list of populations
`gffpath`	the corresponding GFF file
`CHR`	which chromosome ?, default: all chromosomes
`ref.chr`	reference chromosome (to classify synonymous/non-synonymous positions)
`snp.window.size`	scan SNP chunks
`parallized`	multicore computation
`ffpackagebool`	use the ff-package to save memory space. (slower)
`include.unknown`	include positions with unknown nucleotides

The ff-package we use to store the SNP information limits the data size to
individuals * (number of SNPs) <= .Machine$integer.max
The text files containing the SNP information of each individual have to be stored in one folder.
The slots transitions, biallelic.sites, and biallelic.substitutions of the class
"regions.data" will be filled.
At this time, if a GFF/GTF is used the data should be organized in a way that
the "CHR" is a numerical value. The prefix "Chr" or "chr" is also supported.

The function creates an object of class "GENOME"

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Following Slots will be filled in the "GENOME" object
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	Slot	Description
1.	`n.sites`	total number of sites
2.	`n.biallelic.sites`	number of biallelic sites
3.	`region.data`	some detailed information about the data read
4.	`region.names`	names of regions

# GENOME.class <- readSNP("...\SNPData")
# GENOME.class <- readSNP("...\SNPData", CHR=1)
# GENOME.class <- readSNP("...\SNPData", CHR=1, gffpath="Gff_file.gff")
# GENOME.class
# GENOME.class <- neutrality.stats(GENOME.class,FAST=TRUE)
# show the result:
# get.sum.data(GENOME.class)
# GENOME.class@region.data