VCF_split_into_scaffolds: Split a VCF file into multiple scaffold-VCFs

In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description

This function splits a VCF file into multiple VCFs including data for exactly one scaffold each.

Usage

VCF_split_into_scaffolds(VCF.file, output.folder)

Arguments

VCF.file	the basepath of the VCF file
output.folder	name of the folder where the VCFs should be stored

Details

The algorithm splits the VCF into multiple scaffold based VCFs and
stores the files in a given folder. This folder can be used as an input for readData(,format="VCF")

Value

TRUE

Examples

# VCF_split_into_scaffolds("VCFfile.vcf","scaffoldVCFs")
# test <- readData("scaffoldVCFs", format="VCF")

Example output

Loading required package: ff
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: 'bit'

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="/work/tmp/tmp/RtmpWUfX6B"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

The following objects are masked from 'package:bit':

    clone, clone.default, clone.list

The following objects are masked from 'package:utils':

    write.csv, write.csv2

The following objects are masked from 'package:base':

    is.factor, is.ordered

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.