R/get.vcf.R

In MoBPS: Modular Breeding Program Simulator

'#
  Authors
Torsten Pook, torsten.pook@wur.nl

Copyright (C) 2017 -- 2025  Torsten Pook

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 3
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
'#

#' Generate vcf-file
#'
#' Generate a vcf-file for selected groups and chromosome
#' @param population Population list
#' @param path Location to save vcf-file
#' @param database Groups of individuals to consider for the export
#' @param gen Quick-insert for database (vector of all generations to export)
#' @param cohorts Quick-insert for database (vector of names of cohorts to export)
#' @param id Individual IDs to search/collect in the database
#' @param chromosome Limit the genotype output to a selected chromosome (default: "all")
#' @param non.genotyped.as.missing Set to TRUE to replaced non-genotyped entries with "./."
#' @param use.id Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names
#' @param file.append Set extend an existing vcf-file ((without writting a header))
#' @examples
#' data(ex_pop)
#' \donttest{
#' file_path <- tempdir()
#' get.vcf(path=file_path, ex_pop, gen=2)
#' file.remove(paste0(file_path, ".vcf"))
#' }
#' @return VCF-file for in gen/database/cohorts selected individuals
#' @export

get.vcf <- function(population, path=NULL, database=NULL, gen=NULL, cohorts=NULL, id = NULL,
                    chromosome="all",
                    non.genotyped.as.missing=FALSE, use.id = FALSE,
                    file.append = FALSE){

  haplo <- get.haplo(population, database=database, gen=gen, cohorts=cohorts, id = id, chromosome=chromosome, export.alleles=FALSE)
  # haplo <- get.haplo(population, gen=1)
  if(length(path)==0){
    path <- "population.vcf"
  } else{
    path <- paste0(path,".vcf")
  }
  chr.nr <- numeric(sum(population$info$snp))
  start <- 1
  for(index in 1:length(population$info$snp)){
    if(population$info$snp[index]>0){

      if(length(population$info$chromosome.name)>=index){
        chr.nr[start:(start+population$info$snp[index]-1)] <- population$info$chromosome.name[index]
      } else{
        chr.nr[start:(start+population$info$snp[index]-1)] <- index
      }

      start <- start + population$info$snp[index]
    }
  }


  bp <- population$info$bp
  snpname <- population$info$snp.name
  ref <- population$info$snp.base[1,]
  alt <- population$info$snp.base[2,]

  if(chromosome[1]!="all"){

    keep = get.map(population)[,1] %in% chromosome
    bp <- population$info$bp[keep]
    snpname <- population$info$snp.name[keep]
    ref <- population$info$snp.base[1,][keep]
    alt <- population$info$snp.base[2,][keep]

    chr.nr = chr.nr[keep]
  }
  vcfgeno <- matrix(paste0(haplo[,(1:(ncol(haplo)/2))*2-1], "|", haplo[,(1:(ncol(haplo)/2))*2]), ncol=ncol(haplo)/2)

  if(non.genotyped.as.missing){
    is_genotyped <- get.genotyped.snp(population, gen=gen, database = database, cohorts=cohorts, id = id)

    if(sum(!is_genotyped)>0){
      vcfgeno[!is_genotyped] <- "./."
    }

  }


  ref[ref==0] <- "A"
  ref[ref==1] <- "C"
  alt[alt==0] <- "A"
  alt[alt==1] <- "C"
  options(scipen=999)
  vcfgenofull <- cbind(chr.nr, as.numeric(bp), snpname, ref, alt, ".", "PASS", ".", "GT", vcfgeno)

  if(!file.append){
    vcfgenofull <- rbind(c("#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO", "FORMAT", get.pedigree(population, database=database, gen=gen, cohorts = cohorts, id = id, use.id=use.id)[,1]),vcfgenofull)
  }

  headerfile <- rbind(
    "##fileformat=VCFv4.2",
    gsub("-", "", paste0("##filedate=",  Sys.Date())),
    paste0('##source="MoBPS_', utils::packageVersion("MoBPS"),'"'),
    '##FILTER=<ID=PASS,Description="all filters passed">'
  )

  nchr <- unique(chr.nr)

  if(length(population$info$vcf_header)>0){
    contigs <- character(length(population$info$vcf_header[[1]]@header@listData$contig@rownames))
    for(index in 1:length(contigs)){
      contigs[index] <- paste0('##contig=<ID=', population$info$vcf_header[[1]]@header@listData$contig@rownames[index],',length=', population$info$vcf_header[[1]]@header@listData$contig@listData$length[index],'>')
    }
  }else{
    warning("No vcf header present - using last SNP position as end of chromosome for contig dictionary. This may require manual changes for future use of the vcf!")
    contigs <- character(length(nchr))
    for(index in 1:length(nchr)){
      contigs[index] <- paste0('##contig=<ID=', nchr[index],',length=', max(as.numeric(bp)[chr.nr==nchr[index]]),'>')
    }
  }
  headerfile <- rbind(headerfile, t(t(contigs)),     '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">')


  if(!file.append){
    utils::write.table(headerfile, file=path, quote=FALSE, col.names = FALSE, row.names = FALSE)
  }

  if (requireNamespace("data.table", quietly = TRUE)) {
    data.table::fwrite(file=path, vcfgenofull, sep = "\t", col.names = FALSE, append = TRUE)
  } else{
    utils::write.table(vcfgenofull, file=path, quote=FALSE, col.names = FALSE, row.names = FALSE, append = TRUE, sep="\t")
  }
}