R/est_map_hmm.R

In mappoly: Genetic Linkage Maps in Autopolyploids

#' Multipoint analysis using Hidden Markov Models in autopolyploids
#'
#' Performs the multipoint analysis proposed by \cite{Mollinari and
#' Garcia (2019)} in a sequence of markers
#'
#'  This function first enumerates a set of linkage phase configurations
#'  based on two-point recombination fraction information using a threshold
#'  provided by the user (argument \code{thresh}). After that, for each
#'  configuration, it reconstructs the genetic map using the
#'  HMM approach described in Mollinari and Garcia (2019). As result, it returns 
#'  the multipoint likelihood for each configuration in form of LOD Score comparing 
#'  each configuration to the most likely one. It is recommended to use a small number 
#'  of markers (e.g. 50 markers for hexaploids) since the possible linkage 
#'  phase combinations bounded only by the two-point information can be huge. 
#'  Also, it can be quite sensible to small changes in \code{'thresh'}. 
#'  For a large number of markers, please see \code{\link[mappoly]{est_rf_hmm_sequential}}.
#
#' @param input.seq an object of class \code{mappoly.sequence}
#'
#' @param input.ph an object of class \code{two.pts.linkage.phases}. 
#' If not available (default = NULL), it will be computed
#'
#' @param thres LOD Score threshold used to determine if the linkage phases
#'     compared via two-point analysis should be considered. Smaller 
#'     values will result in smaller number of linkage phase 
#'     configurations to be evaluated by the multipoint algorithm. 
#'
#' @param twopt an object of class \code{mappoly.twopt}
#'     containing two-point information
#'
#' @param verbose if \code{TRUE}, current progress is shown; if
#'     \code{FALSE} (default), no output is produced
#'
#' @param tol the desired accuracy (default = 1e-04)
#'
#' @param est.given.0.rf logical. If TRUE returns a map forcing all
#' recombination fractions equals to 0 (1e-5, for internal use only. 
#' Default = FALSE)
#'
#' @param reestimate.single.ph.configuration logical. If \code{TRUE}
#' returns a map without re-estimating the map parameters for cases
#' where there is only one possible linkage phase configuration. 
#' This argument is intended to be used in a sequential map construction
#' 
#' @param high.prec logical. If \code{TRUE} (default) uses high precision 
#' long double numbers in the HMM procedure
#' 
#' @param x an object of the class \code{mappoly.map}
#' 
#' @param detailed logical. if TRUE, prints the linkage phase configuration and the marker 
#' position for all maps. If FALSE (default), prints a map summary 
#' 
#' @param left.lim the left limit of the plot (in cM, default = 0). 
#' 
#' @param right.lim the right limit of the plot (in cM, default = Inf, i.e., 
#'                  will print the entire map)
#' 
#' @param phase logical. If \code{TRUE} (default) plots the phase configuration
#'  for both parents 
#' 
#' @param mrk.names if TRUE, marker names are displayed (default = FALSE)
#' 
#' @param cex The magnification to be used for marker names
#' 
#' @param config should be \code{'best'} or the position of the
#'     configuration to be plotted. If \code{'best'}, plot the configuration
#'     with the highest likelihood
#'
#' @param P a string containing the name of parent P
#' 
#' @param Q a string containing the name of parent Q
#' 
#' @param xlim range of the x-axis. If \code{xlim = NULL} (default) it uses the 
#'             map range. 
#' 
#' @param ... currently ignored
#'
#' @return A list of class \code{mappoly.map} with two elements: 
#' 
#' i) info:  a list containing information about the map, regardless of the linkage phase configuration:
#' \item{ploidy}{the ploidy level}
#' \item{n.mrk}{number of markers}
#' \item{seq.num}{a vector containing the (ordered) indices of markers in the map, 
#'                according to the input file}
#' \item{mrk.names}{the names of markers in the map}
#' \item{seq.dose.p1}{a vector containing the dosage in parent 1 for all markers in the map}
#' \item{seq.dose.p2}{a vector containing the dosage in parent 2 for all markers in the map}
#' \item{chrom}{a vector indicating the sequence (usually chromosome) each marker belongs 
#'                 as informed in the input file. If not available, 
#'                 \code{chrom = NULL}}
#' \item{genome.pos}{physical position (usually in megabase) of the markers into the sequence}
#' \item{seq.ref}{reference base used for each marker (i.e. A, T, C, G). If not available, 
#'                 \code{seq.ref = NULL}}                 
#' \item{seq.alt}{alternative base used for each marker (i.e. A, T, C, G). If not available, 
#'                 \code{seq.ref = NULL}}
#' \item{chisq.pval}{a vector containing p-values of the chi-squared test of Mendelian 
#'                   segregation for all markers in the map}                 
#' \item{data.name}{name of the dataset of class \code{mappoly.data}}
#' \item{ph.thres}{the LOD threshold used to define the linkage phase configurations to test}
#' 
#' ii) a list of maps with possible linkage phase configuration. Each map in the list is also a 
#'    list containing
#' \item{seq.num}{a vector containing the (ordered) indices of markers in the map, 
#'                according to the input file}
#' \item{seq.rf}{a vector of size (\code{n.mrk - 1}) containing a sequence of recombination 
#'               fraction between the adjacent markers in the map}
#' \item{seq.ph}{linkage phase configuration for all markers in both parents}
#' \item{loglike}{the hmm-based multipoint likelihood}
#'
#' @examples
#'     mrk.subset <- make_seq_mappoly(hexafake, 1:10)
#'     red.mrk <- elim_redundant(mrk.subset)
#'     unique.mrks <- make_seq_mappoly(red.mrk)
#'     subset.pairs <- est_pairwise_rf(input.seq = unique.mrks,
#'                                   ncpus = 1,
#'                                   verbose = TRUE)
#'
#'     ## Estimating subset map with a low tolerance for the E.M. procedure
#'     ## for CRAN testing purposes
#'     subset.map <- est_rf_hmm(input.seq = unique.mrks,
#'                              thres = 2,
#'                              twopt = subset.pairs,
#'                              verbose = TRUE,
#'                              tol = 0.1,
#'                              est.given.0.rf = FALSE)
#'     subset.map
#'     ## linkage phase configuration with highest likelihood
#'     plot(subset.map, mrk.names = TRUE, config = "best")
#'     ## the second one
#'     plot(subset.map, mrk.names = TRUE, config = 2)
#' 
#' @author Marcelo Mollinari, \email{mmollin@ncsu.edu}
#'
#' @references
#'     Mollinari, M., and Garcia, A.  A. F. (2019) Linkage
#'     analysis and haplotype phasing in experimental autopolyploid
#'     populations with high ploidy level using hidden Markov
#'     models, _G3: Genes, Genomes, Genetics_. 
#'     https://doi.org/10.1534/g3.119.400378 
#' @rdname est_rf_hmm
#' @export est_rf_hmm
est_rf_hmm <- function(input.seq, 
                       input.ph = NULL,
                       thres = 0.5, 
                       twopt = NULL,
                       verbose = FALSE, 
                       tol = 1e-04,
                       est.given.0.rf = FALSE,
                       reestimate.single.ph.configuration = TRUE,
                       high.prec = TRUE) {
  
  ## checking for correct object
  input_classes <- c("mappoly.sequence", "two.pts.linkage.phases")
  if (!inherits(input.seq, input_classes[1])) {
    stop(deparse(substitute(input.seq)), " is not an object of class 'mappoly.sequence'")
  }
  if(length(input.seq$seq.num)  ==  1)
    stop("Input sequence contains only one marker.", call. = FALSE)
  if (is.null(input.ph)) {
    if (is.null(twopt))
      stop("Two-point analysis not found!")
    if (verbose)
      cat("\nListing all configurations under threshold", thres, "using two-point information...\n")
    input.ph <- ls_linkage_phases(input.seq = input.seq, thres = thres, twopt = twopt)
  }
  if (!inherits(input.ph, input_classes[2])) {
    stop(deparse(substitute(input.ph)), " is not an object of class 'two.pts.linkage.phases'")
  }
  info.par <-detect_info_par(input.seq)
  if(length(input.seq$seq.num)  ==  2 & !est.given.0.rf){
    maps <- vector("list", 1)
    res.temp <- twopt$pairwise[[paste(sort(input.seq$seq.num), collapse = "-")]]
    dp <- get(input.seq$data.name, pos  = 1)$dosage.p1[input.seq$seq.num]
    dq <- get(input.seq$data.name, pos  = 1)$dosage.p2[input.seq$seq.num]
    sh <- as.numeric(unlist(strsplit(rownames(res.temp)[1], split = "-")))
    res.ph <- list(P = c(list(0),list(0)), Q = c(list(0),list(0)))
    if(dp[1] != 0)
      res.ph$P[[1]] <- 1:dp[1]
    if(dq[1] != 0)
      res.ph$Q[[1]] <- 1:dq[1]
    if(dp[2] != 0)
    {
      v <- (rev(res.ph$P[[1]])[1]+1):(dp[2]+rev(res.ph$P[[1]])[1])
      res.ph$P[[2]] <- v-sh[1]
    }
    if(dq[2] != 0)
    {
      v <- (rev(res.ph$Q[[1]])[1]+1):(dq[2]+rev(res.ph$Q[[1]])[1])
      res.ph$Q[[2]] <- v-sh[2]
    }
    names(res.ph$P) <- names(res.ph$Q) <- input.seq$seq.num
    maps[[1]] <- list(seq.num = input.seq$seq.num,
                      seq.rf = res.temp[1,"rf"],
                      seq.ph = res.ph,
                      loglike = 0)
    return(structure(list(info = list(ploidy = input.seq$ploidy,
                                      n.mrk = length(input.seq$seq.num),
                                      seq.num = input.seq$seq.num,
                                      mrk.names = input.seq$seq.mrk.names,
                                      seq.dose.p1 = get(input.seq$data.name, pos  = 1)$dosage.p1[input.seq$seq.mrk.names],
                                      seq.dose.p2 = get(input.seq$data.name, pos  = 1)$dosage.p2[input.seq$seq.mrk.names],
                                      chrom = get(input.seq$data.name, pos  = 1)$chrom[input.seq$seq.mrk.names],
                                      genome.pos = get(input.seq$data.name, pos  = 1)$genome.pos[input.seq$seq.mrk.names],
                                      seq.ref = get(input.seq$data.name, pos  = 1)$seq.ref[input.seq$seq.mrk.names],
                                      seq.alt = get(input.seq$data.name, pos  = 1)$seq.alt[input.seq$seq.mrk.names],
                                      chisq.pval = get(input.seq$data.name, pos  = 1)$chisq.pval[input.seq$seq.mrk.names],
                                      data.name = input.seq$data.name,
                                      ph.thresh = abs(res.temp[2,1])),
                          maps = maps),
                     class = "mappoly.map"))
  }
  n.ph <- length(input.ph$config.to.test)
  ret.map.no.rf.estimation <- FALSE
  if(n.ph  ==  1 && !reestimate.single.ph.configuration)
    ret.map.no.rf.estimation <- TRUE
  maps <- vector("list", n.ph)
  if (verbose){
    txt <- paste0("       ",n.ph, " phase(s): ")
    cat(txt)
  }
  for (i in 1:n.ph) {
    if (verbose) {
      if((i+1)%%40 == 0)
        cat("\n", paste0(rep(" ", nchar(txt)), collapse = ""), sep = "")
      cat(". ")
    }
    if(est.given.0.rf){
      rf.temp <- rep(1e-5, length(input.seq$seq.num) - 1)
      tol = 1
    }
    else{
      rf.temp <- rep(0.001, length(input.seq$seq.num) - 1)
    }
    
    ph <- list(P = input.ph$config.to.test[[i]]$P,
               Q = input.ph$config.to.test[[i]]$Q)
    
    if(info.par == "both")
    {
      maps[[i]] <- est_rf_hmm_single_phase(input.seq = input.seq,
                                           input.ph.single = ph,
                                           rf.temp = rf.temp,
                                           tol = tol,
                                           verbose = FALSE,
                                           ret.map.no.rf.estimation = ret.map.no.rf.estimation, 
                                           high.prec = high.prec)
    }
    else if (info.par == "p1") 
    {
      maps[[i]] <- est_rf_hmm_single_phase_single_parent(input.seq,
                                            input.ph.single = ph,
                                            info.parent = 1,
                                            uninfo.parent = 2,
                                            rf.vec = rf.temp,
                                            tol = tol,
                                            verbose = FALSE,
                                            ret.map.no.rf.estimation = ret.map.no.rf.estimation)
    }
    else if (info.par == "p2")
    {
      maps[[i]] <- est_rf_hmm_single_phase_single_parent(input.seq,
                                                         input.ph.single = ph,
                                                         info.parent = 2,
                                                         uninfo.parent = 1,
                                                         rf.vec = rf.temp,
                                                         tol = tol,
                                                         verbose = FALSE,
                                                         ret.map.no.rf.estimation = ret.map.no.rf.estimation)
      
    }
    else stop("Should not get here.")
  }
  #cat("\n")
  id <- order(sapply(maps, function(x) x$loglike), decreasing = TRUE)
  maps <- maps[id]
  if (verbose)
    cat("\n")
  structure(list(info = list(ploidy = input.seq$ploidy,
                             n.mrk = length(input.seq$seq.num),
                             seq.num = input.seq$seq.num,
                             mrk.names = input.seq$seq.mrk.names,
                             seq.dose.p1 = get(input.seq$data.name, pos  = 1)$dosage.p1[input.seq$seq.mrk.names],
                             seq.dose.p2 = get(input.seq$data.name, pos  = 1)$dosage.p2[input.seq$seq.mrk.names],
                             chrom = get(input.seq$data.name, pos  = 1)$chrom[input.seq$seq.mrk.names],
                             genome.pos = get(input.seq$data.name, pos  = 1)$genome.pos[input.seq$seq.mrk.names],
                             seq.ref = get(input.seq$data.name, pos  = 1)$seq.ref[input.seq$seq.mrk.names],
                             seq.alt = get(input.seq$data.name, pos  = 1)$seq.alt[input.seq$seq.mrk.names],
                             chisq.pval = get(input.seq$data.name, pos  = 1)$chisq.pval[input.seq$seq.mrk.names],
                             data.name = input.seq$data.name, ph.thresh = input.ph$thres),
                 maps = maps),
            class = "mappoly.map")
}

#' Multipoint analysis using Hidden Markov Models: Sequential phase elimination
#'
#' Performs the multipoint analysis proposed by \cite{Mollinari and
#'  Garcia (2019)} in a sequence of markers removing unlikely phases
#' using sequential multipoint information.
#'
#' This function sequentially includes markers into a map given an
#' ordered sequence. It uses two-point information to eliminate
#' unlikely linkage phase configurations given \code{thres.twopt}. The
#' search is made within a window of size \code{extend.tail}. For the
#' remaining configurations, the HMM-based likelihood is computed and
#' the ones that pass the HMM threshold (\code{thres.hmm}) are eliminated.
#'
#' @param input.seq an object of class \code{mappoly.sequence}
#' 
#' @param twopt an object of class \code{mappoly.twopt}
#'     containing the two-point information
#'  
#' @param start.set number of markers to start the phasing procedure (default = 4)      
#'     
#' @param thres.twopt the LOD threshold used to determine if the linkage
#'     phases compared via two-point analysis should be considered 
#'     for the search space reduction (A.K.A. \eqn{\eta} in 
#'     \cite{Mollinari and Garcia (2019)}, default = 5)
#'     
#' @param thres.hmm the LOD threshold used to determine if the linkage
#'     phases compared via hmm analysis should be evaluated in the 
#'     next round of marker inclusion (default = 50)
#'     
#' @param extend.tail the length of the chain's tail that should
#'     be used to calculate the likelihood of the map. If \code{NULL} (default), 
#'     the function uses all markers positioned. Even if \code{info.tail = TRUE}, 
#'     it uses at least \code{extend.tail} as the tail length
#'     
#' @param phase.number.limit the maximum number of linkage phases of the sub-maps defined 
#'     by arguments \code{info.tail} and \code{extend.tail}. Default is 20. If the
#'     size exceeds this limit, the marker will not be inserted. If
#'     \code{Inf}, then it will insert all markers.
#'     
#' @param sub.map.size.diff.limit the maximum accepted length
#'     difference between the current and the previous sub-map defined 
#'     by arguments \code{info.tail} and \code{extend.tail}. If the
#'     size exceeds this limit, the marker will not be inserted. If
#'     \code{NULL}(default), then it will insert all markers.
#'     
#' @param info.tail if \code{TRUE} (default), it uses the complete informative tail
#'     of the chain (i.e. number of markers where all homologous 
#'     (\eqn{ploidy x 2}) can be distinguished) to calculate the map likelihood 
#'     
#'@param reestimate.single.ph.configuration logical. If \code{FALSE} (default)
#'     returns a map without re-estimating the map parameters in cases
#'     where there are only one possible linkage phase configuration
#'      
#' @param tol the desired accuracy during the sequential phase (default = 10e-02)
#'     
#' @param tol.final the desired accuracy for the final map (default = 10e-04)
#'     
#' @param verbose If \code{TRUE} (default), current progress is shown; if
#'     \code{FALSE}, no output is produced
#'     
#' @param detailed.verbose If \code{TRUE}, the expansion of the current 
#'     submap is shown; 
#'     
#' @param high.prec logical. If \code{TRUE} uses high precision 
#' (long double) numbers in the HMM procedure implemented in C++,
#' which can take a long time to perform (default = FALSE)
#' 
#' @return A list of class \code{mappoly.map} with two elements: 
#' 
#' i) info:  a list containing information about the map, regardless of the linkage phase configuration:
#' \item{ploidy}{the ploidy level}
#' \item{n.mrk}{number of markers}
#' \item{seq.num}{a vector containing the (ordered) indices of markers in the map, 
#'                according to the input file}
#' \item{mrk.names}{the names of markers in the map}
#' \item{seq.dose.p1}{a vector containing the dosage in parent 1 for all markers in the map}
#' \item{seq.dose.p2}{a vector containing the dosage in parent 2 for all markers in the map}
#' \item{chrom}{a vector indicating the sequence (usually chromosome) each marker belongs 
#'                 as informed in the input file. If not available, 
#'                 \code{chrom = NULL}}
#' \item{genome.pos}{physical position (usually in megabase) of the markers into the sequence}
#' \item{seq.ref}{reference base used for each marker (i.e. A, T, C, G). If not available, 
#'                 \code{seq.ref = NULL}}
#' \item{seq.alt}{alternative base used for each marker (i.e. A, T, C, G). If not available, 
#'                 \code{seq.ref = NULL}}
#' \item{chisq.pval}{a vector containing p-values of the chi-squared test of Mendelian 
#'                   segregation for all markers in the map}
#' \item{data.name}{name of the dataset of class \code{mappoly.data}}
#' \item{ph.thres}{the LOD threshold used to define the linkage phase configurations to test}
#' 
#' ii) a list of maps with possible linkage phase configuration. Each map in the list is also a 
#'    list containing
#' \item{seq.num}{a vector containing the (ordered) indices of markers in the map, 
#'                according to the input file}
#' \item{seq.rf}{a vector of size (\code{n.mrk - 1}) containing a sequence of recombination 
#'               fraction between the adjacent markers in the map}
#' \item{seq.ph}{linkage phase configuration for all markers in both parents}
#' \item{loglike}{the hmm-based multipoint likelihood}
#'
#' @examples
#'  \donttest{
#'     mrk.subset <- make_seq_mappoly(hexafake, 1:20)
#'     red.mrk <- elim_redundant(mrk.subset)
#'     unique.mrks <- make_seq_mappoly(red.mrk)
#'     subset.pairs <- est_pairwise_rf(input.seq = unique.mrks,
#'                                   ncpus = 1,
#'                                   verbose = TRUE)
#'     subset.map <- est_rf_hmm_sequential(input.seq = unique.mrks,
#'                                         thres.twopt = 5,
#'                                         thres.hmm = 10,
#'                                         extend.tail = 10,
#'                                         tol = 0.1,
#'                                         tol.final = 10e-3,
#'                                         phase.number.limit = 5,
#'                                         twopt = subset.pairs,
#'                                         verbose = TRUE)
#'      print(subset.map, detailed = TRUE)
#'      plot(subset.map)
#'      plot(subset.map, left.lim = 0, right.lim = 1, mrk.names = TRUE)
#'      plot(subset.map, phase = FALSE)
#'      
#'      ## Retrieving simulated linkage phase
#'      ph.P <- maps.hexafake[[1]]$maps[[1]]$seq.ph$P
#'      ph.Q <- maps.hexafake[[1]]$maps[[1]]$seq.ph$Q
#'      ## Estimated linkage phase
#'      ph.P.est <- subset.map$maps[[1]]$seq.ph$P
#'      ph.Q.est <- subset.map$maps[[1]]$seq.ph$Q
#'      compare_haplotypes(ploidy = 6, h1 = ph.P[names(ph.P.est)], h2 = ph.P.est)
#'      compare_haplotypes(ploidy = 6, h1 = ph.Q[names(ph.Q.est)], h2 = ph.Q.est)
#'    }
#'
#' @author Marcelo Mollinari, \email{mmollin@ncsu.edu}
#'
#' @references
#'     Mollinari, M., and Garcia, A.  A. F. (2019) Linkage
#'     analysis and haplotype phasing in experimental autopolyploid
#'     populations with high ploidy level using hidden Markov
#'     models, _G3: Genes, Genomes, Genetics_. 
#'     \doi{10.1534/g3.119.400378} 
#'
#' @importFrom utils head
#' @importFrom cli rule
#' @export est_rf_hmm_sequential
est_rf_hmm_sequential <- function(input.seq,
                                  twopt,
                                  start.set = 4,
                                  thres.twopt = 5,
                                  thres.hmm = 50,
                                  extend.tail = NULL,
                                  phase.number.limit = 20,
                                  sub.map.size.diff.limit = Inf,
                                  info.tail = TRUE,
                                  reestimate.single.ph.configuration = FALSE,
                                  tol = 10e-2,
                                  tol.final = 10e-4,
                                  verbose = TRUE,
                                  detailed.verbose = FALSE,
                                  high.prec = FALSE)
{## checking for correct object
  input_classes <- c("mappoly.sequence", "mappoly.twopt")
  if (!inherits(input.seq, input_classes[1])) {
    stop(deparse(substitute(input.seq)), 
         " is not an object of class 'mappoly.sequence'")
  }
  if (!inherits(twopt, input_classes[2])) {
    stop(deparse(substitute(twopt)), 
         " is not an object of class 'mappoly.twopt'")
  }
  ## Information about the map
  if(verbose) {
    cli::cat_line("Number of markers: ", length(input.seq$seq.num))
    msg("Initial sequence", line = 2)
  }
  if(is.null(extend.tail))
    extend.tail <- length(input.seq$seq.num)
  ##### Map in case of two markers #####
  if(length(input.seq$seq.num)  ==  2)
  {
    cur.map <- est_rf_hmm(input.seq = input.seq, thres = thres.twopt, 
                          twopt = twopt, tol = tol.final, high.prec = high.prec, 
                          verbose = verbose, 
                          reestimate.single.ph.configuration = reestimate.single.ph.configuration)
    return(filter_map_at_hmm_thres(cur.map, thres.hmm))
  } 
  ##### More than 3 markers ####
  ##Starting sequential algorithm for maps with more than 3 markers
  ## First step: test all possible phase configurations under 
  ## a 'thres.twopt' threshold for a sequence of size 'start.set'
  if(start.set > length(input.seq$seq.num))
    start.set <- length(input.seq$seq.num)
  if(verbose) cat(start.set, " markers...\n", sep = "")
  cte <- 0
  rf.temp <- c(Inf, Inf)
  while(any(rf.temp >= sub.map.size.diff.limit))
  {
    cte <- cte+1
    if(length(rf.temp) == 1) {
      ## cat("Impossible build a map using the given thresholds\n")
      ## stop()
      stop("Impossible build a map using the given thresholds\n")
    }
    if(verbose) cat(cli::symbol$bullet, "   Trying sequence:", cte:(start.set+cte-1), ":\n")
    cur.seq <- make_seq_mappoly(input.obj = get(input.seq$data.name, pos = 1), as.vector(na.omit(input.seq$seq.num[cte:(start.set+cte-1)])), data.name = input.seq$data.name)
    input.ph <- ls_linkage_phases(input.seq = cur.seq,
                                  thres = thres.twopt,
                                  twopt = twopt)
    cur.map <- est_rf_hmm(input.seq = cur.seq, thres = thres.twopt, 
                          twopt = twopt, tol = tol, high.prec = high.prec, 
                          verbose = verbose, input.ph = input.ph,
                          reestimate.single.ph.configuration = reestimate.single.ph.configuration)
    cur.map <- filter_map_at_hmm_thres(cur.map, thres.hmm)
    cur.map <- reest_rf(cur.map, tol = tol.final, verbose = FALSE)
    rf.temp <- imf_h(cur.map$maps[[1]]$seq.rf)
  }
  if(verbose)
    msg("Done with initial sequence", line = 2)
  if(start.set >= length(input.seq$seq.num)){
    if(verbose) cat("\nDone phasing", cur.map$info$n.mrk, "markers\nReestimating final recombination fractions.")
    return(reest_rf(cur.map, tol = tol.final))
  }
  ##### More than 'start.set' markers #####
  ## For maps with more markers than 'start.set', include
  ## next makers in a sequential fashion
  ct <- start.set+cte
  all.ph <- update_ph_list_at_hmm_thres(cur.map, thres.hmm)
  if(sub.map.size.diff.limit != Inf & !reestimate.single.ph.configuration){
    if (verbose) message("Making 'reestimate.single.ph.configuration = TRUE' to use map expansion")
    reestimate.single.ph.configuration <- TRUE
  }
  while(ct <= length(input.seq$seq.num))
  {
    ## Number of multipoint phases evaluated in the 
    ## previous round of marker insertion
    hmm.phase.number <- length(cur.map$maps)
    ## Get the map tail containing sufficient markers to 
    ## distinguish among the ploidy*2 possible homologs.
    if(info.tail)
      tail.temp <- get_full_info_tail(input.obj = cur.map)
    input.ph <- NULL
    ## for each linkage phase inherited from HMM 
    ## analysis from previous round, evaluate the
    ## possible linkage phases for the marker inserted 
    ## in the current round using two-point information
    ## under the threshold of thres.twopt
    for(i in 1:length(all.ph$config.to.test))
    {
      seq.num <- NULL
      if(info.tail)
        seq.num <- tail.temp$maps[[i]]$seq.num 
      if(length(seq.num) < extend.tail)
        seq.num <- tail(cur.map$maps[[i]]$seq.num, extend.tail)
      ## If the tail do not contain the marker responsible for carrying 
      ## multiple linkage phases through the rounds of insertion,
      ## extend the tail so it contains that marker
      if(max(check_ls_phase(all.ph)) >= length(seq.num)){
        seq.num <- tail(cur.map$maps[[i]]$seq.num, max(check_ls_phase(all.ph)) + start.set)        
      }
      seq.cur <- make_seq_mappoly(input.obj = get(input.seq$data.name, pos = 1),
                                  arg = seq.num,
                                  data.name = input.seq$data.name)
      all.ph.temp <- get_ph_list_subset(all.ph, seq.num, i)
      input.ph.temp <- ls_linkage_phases(input.seq = seq.cur,
                                         thres = thres.twopt,
                                         twopt = twopt,
                                         mrk.to.add = input.seq$seq.num[ct],
                                         prev.info = all.ph.temp)
      input.ph <- concatenate_ph_list(ph.list.1 = input.ph, ph.list.2 = input.ph.temp)
    }
    ## This is the number of linkage phases to be tested 
    ## combining HMM phases from previous round of mrk
    ## insertion and the linkage phases from the two-point
    ## information obtained in the current round
    twopt.phase.number <- length(input.ph$config.to.test)
    ## If this number is higher than phase.number.limit,
    ## proceed to the next iteration
    if(length(input.ph$config.to.test) > phase.number.limit) {
      if(verbose)
        cat(crayon::italic$yellow(paste0(ct ,": not included (*linkage phases*)\n", sep = "")))
      ct <- ct + 1
      next()
    }
    ## Appending the marker to the numeric 
    ## sequence and making a new sequence
    seq.num <- c(seq.num, input.seq$seq.num[ct])
    seq.cur <- make_seq_mappoly(input.obj = get(input.seq$data.name, pos = 1),
                                arg = seq.num,
                                data.name = input.seq$data.name)
    if(verbose)
      cat_phase(input.seq, input.ph, all.ph, ct, seq.num, twopt.phase.number, hmm.phase.number)
    ## Evaluation all maps using HMM
    cur.map.temp <- est_rf_hmm(input.seq = seq.cur,
                               input.ph = input.ph,
                               twopt = twopt,
                               tol = tol,
                               verbose = FALSE,
                               reestimate.single.ph.configuration = reestimate.single.ph.configuration,
                               high.prec = high.prec)
    cur.map.temp$maps <- unique(cur.map.temp$maps)
    ## Filtering linkage phase configurations under a HMM LOD threshold
    cur.map.temp <- filter_map_at_hmm_thres(cur.map.temp, thres.hmm)
    
    ## Gathering linkage phases of the current map, excluding the marker inserted 
    ## in the current round
    ph.new <- lapply(cur.map.temp$maps, function(x) list(P = head(x$seq.ph$P, -1), 
                                                         Q = head(x$seq.ph$Q, -1)))
    ## Gathering linkage phases of the previous map, excluding the marker inserted 
    ## in the current round
    ph.old <- lapply(cur.map$maps, function(x, id) list(P = x$seq.ph$P[id], 
                                                        Q = x$seq.ph$Q[id]), id = names(ph.new[[1]]$P))

    ## Check in which whole phase configurations the new 
    ## HMM tail should be appended
    MQ <- MP <- matrix(NA, length(ph.old), length(ph.new))
    for(j1 in 1:nrow(MP)){
      for(j2 in 1:ncol(MP)){
        MP[j1, j2] <- identical(ph.old[[j1]]$P, ph.new[[j2]]$P)
        MQ[j1, j2] <- identical(ph.old[[j1]]$Q, ph.new[[j2]]$Q)
      }
    }
    M <- which(MP & MQ, arr.ind = TRUE)
    colnames(M) <- c("old", "new")
    ## Checking for quality (map size and LOD Score)
    submap.length.old <- sapply(cur.map$maps, function(x) sum(imf_h(x$seq.rf)))[M[,1]]
    last.dist.old <- sapply(cur.map$maps, function(x) tail(imf_h(x$seq.rf),1))[M[,1]]
    submap.length.new <- sapply(cur.map.temp$maps, function(x) sum(imf_h(x$seq.rf)))[M[,2]]
    last.dist.new <- sapply(cur.map.temp$maps, function(x) tail(imf_h(x$seq.rf),1))[M[,2]]
    last.mrk.expansion <- submap.expansion <- numeric(nrow(M))
    submap.expansion <- submap.length.new - submap.length.old
    last.mrk.expansion <- last.dist.new - last.dist.old
    
    if(length(M[,2]) == 0) {
      if(verbose) cat(crayon::italic$yellow(paste0(ct ,": not included (~map extension~)\n", sep = "")))
      ct <- ct + 1
      next()
    }
    
    cur.map.temp$maps <- cur.map.temp$maps[M[,2]]
    LOD <- get_LOD(cur.map.temp, sorted = FALSE)
    if(sub.map.size.diff.limit != Inf){
      selected.map <- submap.expansion < sub.map.size.diff.limit & LOD < thres.hmm
      if(detailed.verbose){
        x <- round(cbind(submap.length.new, submap.expansion, last.mrk.expansion),2)
        for(j1 in 1:nrow(x)){
          cat("    ", x[j1,1], ": (", x[j1,2],  "/", x[j1,3],")", sep = "")
          if(j1 != nrow(x)) cat("\n")
        }
        if(all(!selected.map)) cat(paste0(crayon::red(cli::symbol$cross), "\n"))
        else cat(paste0(crayon::green(cli::symbol$tick), "\n"))
      }
      if(all(!selected.map)){
        if(verbose) cat(crayon::italic$yellow(paste0(ct ,": not included (~map extension~)\n", sep = "")))
        ct <- ct + 1
        next()
      }
    } else { selected.map <- LOD < thres.hmm }
    all.ph.temp <- update_ph_list_at_hmm_thres(cur.map.temp, Inf)
    id <- which(selected.map & which(!sapply(cur.map.temp$maps, is.null)))
    if(length(id)  ==  0){
      if(verbose) cat(crayon::italic$yellow(paste0(ct ,": not included (-linkage phases-)\n", sep = "")))
      ct <- ct + 1
      next()
    }
    cur.map.temp$maps <- cur.map.temp$maps[id]      
    if(any(unique(M[id,2,drop = FALSE]) > length(all.ph.temp$config.to.test))){
      if(verbose) cat(crayon::italic$yellow(paste0(ct ,": not included (-linkage phases-)\n", sep = "")))
      ct <- ct + 1
      next()
    }
    if(length(id) > nrow(M))
      all.ph.temp <- add_mrk_at_tail_ph_list(all.ph, all.ph.temp, M[,,drop = FALSE])
    else if(length(id)  ==  nrow(M)){
      M[,2] <- id
      all.ph.temp <- add_mrk_at_tail_ph_list(all.ph, all.ph.temp, M[,,drop = FALSE])
    } else {
      all.ph.temp <- add_mrk_at_tail_ph_list(all.ph, all.ph.temp, M[id,,drop = FALSE])
    }
    all.ph <- all.ph.temp
    cur.map <- cur.map.temp
    ct <- ct + 1
  }
  ##### Re-estimating final map ####
  ## Re-estimating final map with higher tolerance
  seq.final <- make_seq_mappoly(input.obj = get(input.seq$data.name, pos = 1), 
                                arg = as.numeric(names(all.ph$config.to.test[[1]]$P)), 
                                data.name = input.seq$data.name)
  #msg(paste("Done phasing", length(seq.final$seq.num), "markers"))
  if (verbose){
    msg("Reestimating final recombination fractions", line = 2)
    cat("")
  }
  final.map <- est_rf_hmm(input.seq = seq.final,
                          input.ph = all.ph,
                          twopt = twopt,
                          tol = tol.final,
                          verbose = FALSE,
                          reestimate.single.ph.configuration = TRUE,
                          high.prec = TRUE)
  if(verbose) {
    #cat("\n------------------------------------------")
    cat("Markers in the initial sequence: ", length(input.seq$seq.num), sep = "")
    cat("\nMapped markers                  : ", final.map$info$n.mrk, " (", 
        round(100*final.map$info$n.mrk/length(input.seq$seq.num),1) ,"%)\n", sep = "")
    msg("", line = 2)
  }
  return(final.map)
}

#' @rdname est_rf_hmm
#' @export 
print.mappoly.map <- function(x, detailed = FALSE, ...) {
  cat("This is an object of class 'mappoly.map'\n")
  cat("    Ploidy level:\t", x$info$ploidy, "\n")
  cat("    No. individuals:\t", get(x$info$data.name)$n.ind, "\n")
  cat("    No. markers:\t", x$info$n.mrk, "\n")
  cat("    No. linkage phases:\t", length(x$maps), "\n")
  l <- sapply(x$maps, function(x) x$loglike)
  LOD <- round(l - max(l), 2)
  if(detailed)
  {
    for (j in 1:length(x$maps)) {
      cat("\n    ---------------------------------------------\n")
      cat("    Linkage phase configuration: ", j)
      cat("\n       log-likelihood:\t", x$map[[j]]$loglike)
      cat("\n       LOD:\t\t", format(round(LOD[j], 2), digits = 2))
      cat("\n\n")
      M <- matrix("|", x$info$n.mrk, x$info$ploidy * 2)
      M <- cbind(M, "    ")
      M <- cbind(M, format(round(cumsum(c(0, imf_h(x$maps[[j]]$seq.rf))), 1), digits = 1))
      for (i in 1:x$info$n.mrk) {
        if (all(x$maps[[j]]$seq.ph$Q[[i]] != 0))
          M[i, c(x$maps[[j]]$seq.ph$P[[i]], x$maps[[j]]$seq.ph$Q[[i]] + x$info$ploidy)] <- "o" else M[i, x$maps[[j]]$seq.ph$P[[i]]] <- "o"
      }
      M <- cbind(get(x$info$data.name)$mrk.names[x$maps[[j]]$seq.num], M)
      big.name <- max(nchar(M[,1]))
      format_name <- function(y, big.name){
        paste0(y, paste0(rep(" ", big.name-nchar(y)), collapse = ""))
      }
      M <- rbind(c("", letters[1:(ncol(M)-3)], "", ""), M)
      format(apply(M, 1, function(y) cat(c("\t", format_name(y[1], big.name), "\t", y[2:(x$info$ploidy + 1)], rep(" ", 4), y[(x$info$ploidy + 2):(x$info$ploidy * 2 + 3)], "\n"), collapse = "")))
    }
  } else {
    cat("\n    ---------------------------------------------\n")
    cat("    Number of linkage phase configurations: ", length(x$maps))
    cat("\n    ---------------------------------------------\n")
    for (j in 1:length(x$maps)) {
      cat("    Linkage phase configuration: ", j)
      cat("\n       map length:\t", format(round(sum(imf_h(x$map[[j]]$seq.rf)), 2)))
      cat("\n       log-likelihood:\t", format(round(x$map[[j]]$loglike, 2)))
      cat("\n       LOD:\t\t", format(round(LOD[j], 2), digits = 2))
      cat("\n    ~~~~~~~~~~~~~~~~~~\n")
    }
  }
}

#' @rdname est_rf_hmm
#' @importFrom grDevices rgb
#' @importFrom graphics rect
#' @export 
plot.mappoly.map <- function(x, left.lim = 0, right.lim = Inf,
                             phase = TRUE, mrk.names = FALSE, 
                             cex = 1, config = "best", P = "Parent 1",
                             Q = "Parent 2", xlim = NULL, ...) {
  oldpar <- par(no.readonly = TRUE)
  on.exit(par(oldpar))
  if(phase){
    map.info <- prepare_map(x, config)
    if(any(map.info$ph.p == "B")){
      var.col <- c("black", "darkgray")
      var.col <- var.col[1:2]
      names(var.col) <- c("A", "B")
    } else {
      var.col <- c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3")
      names(var.col) <- c("A", "T", "C", "G")
    }
    ploidy <- map.info$ploidy
    if(ploidy  ==  2) {
      d.col <- c(NA, "#1B9E77", "#D95F02")
    }else if(ploidy  ==  4){
      d.col <- c(NA, "#1B9E77", "#D95F02", "#7570B3", "#E7298A")
    }else if(ploidy  ==  6){
      d.col <- c(NA, "#1B9E77", "#D95F02", "#7570B3", "#E7298A", "#66A61E", "#E6AB02")
    }else if(ploidy  ==  8){
      d.col <- c(NA, "#1B9E77", "#D95F02", "#7570B3", "#E7298A", "#66A61E", "#E6AB02", "#A6761D", "#666666") 
    } else d.col <- c(NA, gg_color_hue(ploidy))
    names(d.col) <- 0:ploidy
    d.col[1] <- NA
    x <- map.info$map
    lab <- names(x)
    zy <- seq(0, 0.5, length.out = ploidy) + 1.5
    pp <- map.info$ph.p
    pq <- map.info$ph.q
    dp <- map.info$dp
    dq <- map.info$dq
    x1 <- abs(left.lim - x)
    x2 <- abs(right.lim - x)
    id.left <- which(x1 == min(x1))[1]
    id.right <- rev(which(x2 == min(x2)))[1]
    par(mai = c(1,0.15,0,0), mar = c(4.5,2,1,2))
    curx <- x[id.left:id.right]
    layout(mat  = matrix(c(4,2,3, 1), ncol = 2), heights = c(2, 10), widths = c(1, 10))
    if(is.null(xlim))
      xlim <- range(curx)
    plot(x = curx,
         y = rep(.5,length(curx)),
         type = "n" , 
         ylim = c(.25, 4.5), 
         axes = FALSE, 
         xlab = "Distance (cM)", 
         ylab = "",
         xlim = xlim)
    lines(c(x[id.left], x[id.right]), c(.5, .5), lwd = 15, col = "gray")
    points(x = curx,
           y = rep(.5,length(curx)),
           xlab = "", ylab = "", 
           pch = "|", cex = 1.5, 
           ylim = c(0,2))
    axis(side = 1)
    diplocol1 <- c("#4DAF4A", "#984EA3")
    diplocol2 <- c("#E41A1C", "#377EB8")
    #Parent 2
    x1 <- seq(x[id.left], x[id.right], length.out = length(curx))
    x.control <- diff(x1[1:2])/2
    if(length(x1) < 150)
      x.control <- x.control * .8
    if(length(x1) < 100)
      x.control <- x.control * .8
    if(length(x1) < 75)
      x.control <- x.control * .8
    if(length(x1) < 50)
      x.control <- x.control * .8
    if(length(x1) < 25)
      x.control <- x.control * .8
    for(i in 1:ploidy)
    {
      if(ploidy == 2 && any(map.info$ph.p == "B")){
        lines(range(x1), c(zy[i], zy[i]), lwd = 15, col = diplocol1[i])
      } else {
        lines(range(x1), c(zy[i], zy[i]), lwd = 8, col = "gray")        
      }
      y1 <- rep(zy[i], length(curx))
      pal <- var.col[pq[id.left:id.right,i]]
      rect(xleft = x1 - x.control, ybottom = y1 -.05, xright = x1 + x.control, ytop = y1 +.05, col = pal, border = NA)
    }
    #connecting allelic variants to markers 
    for(i in 1:length(x1))
      lines(c(curx[i], x1[i]), c(0.575, zy[1]-.05), lwd = 0.2)
    points(x = x1,
           y = zy[ploidy]+0.05+dq[id.left:id.right]/20,
           col = d.col[as.character(dq[id.left:id.right])],
           pch = 19, cex = .7)
    #Parent 1
    zy <- zy + 1.1
    for(i in 1:ploidy)
    {
      if(ploidy == 2 && any(map.info$ph.p == "B")){
        lines(range(x1), c(zy[i], zy[i]), lwd = 12, col = diplocol2[i])
      } else {
        lines(range(x1), c(zy[i], zy[i]), lwd = 8, col = "gray")        
      }
      y1 <- rep(zy[i], length(curx))
      pal <- var.col[pp[id.left:id.right,i]]
      rect(xleft = x1 - x.control, ybottom = y1 -.05, xright = x1 + x.control, ytop = y1 +.05, col = pal, border = NA)
    }
    points(x = x1,
           y = zy[ploidy]+0.05+dp[id.left:id.right]/20,
           col = d.col[as.character(dp[id.left:id.right])],
           pch = 19, cex = .7)
    if(mrk.names)
      text(x = x1,
           y = rep(zy[ploidy]+0.05+.3, length(curx)),
           labels = names(curx),
           srt = 90, adj = 0, cex = cex)
    par(mar = c(4.5,1,1,0), xpd = TRUE) 
    plot(x = 0,
         y = 0,
         type = "n" ,
         axes = FALSE, 
         ylab = "",
         xlab = "",
         ylim = c(.25, 4.5))
    zy <- zy - 1.1
    mtext(text = Q, side = 4, at = mean(zy), line = -1, font = 4)
    for(i in 1:ploidy)
      mtext(letters[(ploidy+1):(2*ploidy)][i], line = 0, at = zy[i], side = 4)
    zy <- zy + 1.1
    mtext(text = P, side = 4, at = mean(zy), line = -1, font = 4)
    for(i in 1:ploidy)
      mtext(letters[1:ploidy][i],  line = 0, at = zy[i], side = 4)
    par(mar = c(0,1,2,4), xpd = FALSE)
    plot(x = curx,
         y = rep(.5,length(curx)),
         type = "n" , 
         axes = FALSE, 
         xlab = "", 
         ylab = "")
    if(any(map.info$ph.p == "B")){
      legend("bottomleft", legend = c("A", "B"), 
             fill  = c(var.col), title = "Variants",
             box.lty = 0, bg = "transparent", ncol = 2)
    } else {    
      legend("bottomleft", legend = c("A", "T", "C", "G", "-"), 
             fill  = c(var.col, "white"), title = "Nucleotides",
             box.lty = 0, bg = "transparent", ncol = 4)
    }
    legend("bottomright", legend = names(d.col)[-1], title = "Doses" ,
           col = d.col[-1], ncol = ploidy/2, pch = 19,
           box.lty = 0)
  } else {
    plot_map_list(x) 
  }
}

#' prepare maps for plot 
#' @keywords internal
prepare_map <- function(input.map, config = "best"){
  if (!inherits(input.map, "mappoly.map")) {
    stop(deparse(substitute(input.map)), " is not an object of class 'mappoly.map'")
  }
  ## Choosing the linkage phase configuration
  LOD.conf <- get_LOD(input.map, sorted = FALSE)
  if(config  ==  "best") {
    i.lpc <- which.min(LOD.conf)
  } else if(config  ==  "all"){
    i.lpc <- seq_along(LOD.conf) } else if (config > length(LOD.conf)) {
      stop("invalid linkage phase configuration")
    } else i.lpc <- config
  ## Gathering marker positions
  map <- cumsum(imf_h(c(0, input.map$maps[[i.lpc]]$seq.rf)))
  names(map) <- input.map$info$mrk.names
  ## 
  ph.p <- ph_list_to_matrix(input.map$maps[[i.lpc]]$seq.ph$P, input.map$info$ploidy)
  ph.q <- ph_list_to_matrix(input.map$maps[[i.lpc]]$seq.ph$Q, input.map$info$ploidy)
  dimnames(ph.p) <- list(names(map), letters[1:input.map$info$ploidy])
  dimnames(ph.q) <- list(names(map), letters[(1+input.map$info$ploidy):(2*input.map$info$ploidy)])
  if(is.null(input.map$info$seq.alt))
  {
    ph.p[ph.p == 1] <- ph.q[ph.q == 1] <- "A"
    ph.p[ph.p == 0] <- ph.q[ph.q == 0] <- "B"  
  } else {
    for(i in input.map$info$mrk.names){
      ph.p[i, ph.p[i,] == 1] <- input.map$info$seq.alt[i]
      ph.p[i, ph.p[i,] == 0] <- input.map$info$seq.ref[i]
      ph.q[i, ph.q[i,] == 1] <- input.map$info$seq.alt[i]
      ph.q[i, ph.q[i,] == 0] <- input.map$info$seq.ref[i]
    }
  }
  dp <- input.map$info$seq.dose.p1
  dq <- input.map$info$seq.dose.p2
  list(ploidy = input.map$info$ploidy, map = map, ph.p = ph.p, ph.q = ph.q, dp = dp, dq = dq)
}

#' Get the tail of a marker sequence up to the point where the markers
#' provide no additional information.
#' @keywords internal
get_full_info_tail <- function(input.obj, extend = NULL) {
  ## checking for correct object
  if(!inherits(input.obj, "mappoly.map"))
    stop(deparse(substitute(input.obj)), " is not an object of class 'mappoly.map''")
  if (!is.null(extend))
    if (extend > input.obj$info$n.mrk)
      return(input.obj)
  ploidy <- input.obj$info$ploidy
  i <- ploidy/2
  w1 <- ph_list_to_matrix(input.obj$maps[[1]]$seq.ph$P, ploidy)
  max1 <- length(unique(apply(w1, 2, paste0, collapse = "")))
  w2 <- ph_list_to_matrix(input.obj$maps[[1]]$seq.ph$Q, ploidy)
  max2 <- length(unique(apply(w2, 2, paste0, collapse = "")))
  while (i < input.obj$info$n.mrk) {
    wp <- ph_list_to_matrix(tail(input.obj$maps[[1]]$seq.ph$P, i), ploidy)
    xp <- apply(wp, 2, paste, collapse = "-")
    wq <- ph_list_to_matrix(tail(input.obj$maps[[1]]$seq.ph$Q, i), ploidy)
    xq <- apply(wq, 2, paste, collapse = "-")
    if (length(unique(xp))  ==  max1 && length(unique(xq))  ==  max2)
      break()
    i <- i + 1
  }
  if (!is.null(extend))
    if (i < extend)
      i <- extend
  input.obj$info$n.mrk <- i
  
  
  
  input.obj$info$seq.num <- tail(input.obj$info$seq.num, i)
  input.obj$info$mrk.names <- tail(input.obj$info$mrk.names, i)
  input.obj$info$seq.dose.p1 <- tail(input.obj$info$seq.dose.p1, i)
  input.obj$info$seq.dose.p2 <- tail(input.obj$info$seq.dose.p2, i)
  input.obj$info$chrom <- tail(input.obj$info$chrom, i)
  input.obj$info$genome.pos <- tail(input.obj$info$genome.pos, i)
  input.obj$info$chisq.pval <- tail(input.obj$info$chisq.pval, i)
  
  for (j in 1:length(input.obj$maps)) {
    input.obj$maps[[j]]$loglike <- 0
    input.obj$maps[[j]]$seq.ph$P <- tail(input.obj$maps[[j]]$seq.ph$P, n = i)
    input.obj$maps[[j]]$seq.ph$Q <- tail(input.obj$maps[[j]]$seq.ph$Q, n = i)
    input.obj$maps[[j]]$seq.num <- tail(input.obj$maps[[j]]$seq.num, n = i)
    input.obj$maps[[j]]$seq.rf <- tail(input.obj$maps[[j]]$seq.rf, n = (i - 1))
  }
  return(input.obj)
}

#' Filter MAPpoly Map Configurations by Loglikelihood Threshold
#'
#' This function filters configurations within a `"mappoly.map"` object based on a specified 
#' log-likelihood threshold.
#'
#' @param map An object of class `"mappoly.map"`, which may contain several maps 
#' with different linkage phase configurations and their respective log-likelihoods.
#' @param thres.hmm The threshold for filtering configurations. 
#'
#' @return Returns the modified `"mappoly.map"` object with configurations filtered 
#' based on the log-likelihood threshold.
#'
#' @keywords internal
#' @export
filter_map_at_hmm_thres <- function(map, thres.hmm){
  if (!inherits(map, "mappoly.map")) {
    stop("Input 'map' is not an object of class 'mappoly.map'")
  }
  
  map$info$ph.thresh <- NULL
  map$maps <- map$maps[get_LOD(map, sorted = FALSE) < thres.hmm]
  return(map)
}

#' makes a phase list from map, selecting only 
#' configurations under a certain threshold
#' @keywords internal
update_ph_list_at_hmm_thres <- function(map, thres.hmm){
  temp.map <- filter_map_at_hmm_thres(map, thres.hmm)
  config.to.test <- lapply(temp.map$maps, function(x) x$seq.ph)
  structure(list(config.to.test = config.to.test, 
                 ploidy = map$info$ploidy, seq.num = map$maps[[1]]$seq.num, 
                 thres = map$info$ph.thresh, data.name = map$info$data.name, 
                 thres.hmm = thres.hmm),
            class = "two.pts.linkage.phases")
}

#' subset of a linkage phase list
#' @keywords internal
get_ph_list_subset <- function(ph.list, seq.num, conf){
  config.to.test <- list(lapply(ph.list$config.to.test[[conf]], function(x, seq.num) x[as.character(seq.num)], seq.num))
  structure(list(config.to.test = config.to.test, 
                 ploidy = ph.list$ploidy, seq.num = ph.list$seq.num, 
                 thres = ph.list$ph.thresh, data.name = ph.list$data.name, 
                 thres.hmm = ph.list$thres.hmm),
            class = "two.pts.linkage.phases")
}

#' concatenate two linkage phase lists
#' @keywords internal
concatenate_ph_list <- function(ph.list.1, ph.list.2){
  if(length(ph.list.1) == 0)
    return(ph.list.2)
  config.to.test <- c(ph.list.1$config.to.test, ph.list.2$config.to.test)
  id <- which(!duplicated(config.to.test))
  config.to.test <- config.to.test[id]
  structure(list(config.to.test = config.to.test,
                 ploidy = ph.list.1$ploidy, seq.num = ph.list.1$seq.num, 
                 thres = ph.list.1$ph.thresh, data.name = ph.list.1$data.name, 
                 thres.hmm = ph.list.1$thres.hmm),
            class = "two.pts.linkage.phases")
}

#' add a single marker at the tail of a linkage phase list
#' @keywords internal
add_mrk_at_tail_ph_list <- function(ph.list.1, ph.list.2, cor.index){
  config.to.test <- vector("list", length = nrow(cor.index))
  for(i in 1:nrow(cor.index)){
    config.to.test[[i]] <- list(P = c(ph.list.1$config.to.test[[cor.index[i,1]]]$P, tail(ph.list.2$config.to.test[[cor.index[i,2]]]$P,1)),
                                Q = c(ph.list.1$config.to.test[[cor.index[i,1]]]$Q, tail(ph.list.2$config.to.test[[cor.index[i,2]]]$Q,1)))
  }
  structure(list(config.to.test = config.to.test, 
                 ploidy = ph.list.1$ploidy, seq.num = ph.list.1$seq.num, 
                 thres = ph.list.1$ph.thresh, data.name = ph.list.1$data.name, 
                 thres.hmm = ph.list.1$thres.hmm),
            class = "two.pts.linkage.phases")
}

#' Compare a list of linkage phases and return the 
#' markers for which they are different.
#' @keywords internal
check_ls_phase <- function(ph){
  if(length(ph$config.to.test)  ==  1) return(0)
  id <- rep(1, length(ph$config.to.test[[1]]$P))
  for(i in 1:length(ph$config.to.test[[1]]$P)){
    w <- ph$config.to.test[[1]]$P[i]
    for(j in 2:length(ph$config.to.test))
      id[i] <- id[i] + identical(w, ph$config.to.test[[j]]$P[i])
  }
  names(id) <- names((ph$config.to.test[[1]]$P))
  w <- length(ph$config.to.test[[1]]$P) - which(id < length(ph$config.to.test)) 
  if(length(w) == 0) return(0)
  w
}

#' cat for graphical representation of the phases
#' @keywords internal
print_ph <- function(input.ph){
  phs.P <- lapply(input.ph$config.to.test, 
                  function(x, ploidy) {
                    M <- matrix("|", nrow = 1, ncol = ploidy) 
                    M[unlist(tail(x$P, 1))] <- crayon::red(cli::symbol$bullet)
                    paste(M, collapse = "")}, 
                  ploidy = input.ph$ploidy) 
  phs.Q <- lapply(input.ph$config.to.test, 
                  function(x, ploidy) {
                    M <- matrix("|", nrow = 1, ncol = ploidy) 
                    M[unlist(tail(x$Q, 1))] <- crayon::cyan(cli::symbol$bullet)
                    paste(M, collapse = "")}, 
                  ploidy = input.ph$ploidy) 
  if(length(phs.P)  ==  1)
    return(paste(unlist(phs.P)[1], unlist(phs.Q)[1], "                   "))
  if(length(phs.P)  ==  2)
    return(paste(unlist(phs.P)[1], unlist(phs.Q)[1], "     ", unlist(phs.P)[2], unlist(phs.Q)[2]))
  if(length(phs.P) > 2)
    return(paste(unlist(phs.P)[1], unlist(phs.Q)[1], " ... ", unlist(phs.P)[2], unlist(phs.Q)[2]))
}

#' cat for phase information
#' @keywords internal
cat_phase <- function(input.seq,
                      input.ph,
                      all.ph,
                      ct,
                      seq.num,
                      twopt.phase.number,
                      hmm.phase.number){
  pc <- round(100*ct/length(input.seq$seq.num),1)
  xmax11 <- nchar(length(input.seq$seq.num))
  x11 <- ct
  x11 <- paste0(x11, paste(rep(" ", xmax11-nchar(x11)), collapse = ""))
  x12 <- length(all.ph$config.to.test[[1]]$P) + 1
  x12 <- paste0(x12, paste(rep(" ", xmax11-nchar(x12)), collapse = ""))
  x13 <- pc
  x13 <- paste0(":(",pc,"%)", paste(rep(" ", 5-nchar(x13)), collapse = ""))
  x1 <- paste0(x12,"/",x11, x13)
  xmax21 <- nchar(max(input.seq$seq.num)) 
  x21 <- input.seq$seq.num[ct]
  x21 <- paste0(x21, paste(rep(" ", xmax21-nchar(x21)), collapse = ""))
  x22 <- length(input.ph$config.to.test)
  x22 <- paste0(x22, " ph ", paste(rep(" ", 5-nchar(x22)), collapse = ""))
  x23 <- paste0("(", hmm.phase.number, "/", twopt.phase.number,")  ")
  x23 <- paste0(x23, paste(rep(" ", 10-nchar(x23)), collapse = ""))
  x2 <- paste0( x21, ": ", x22, x23)
  x31 <- length(seq.num)-1
  x31 <- paste0(x31, paste(rep(" ", xmax11-nchar(x31)), collapse = ""))
  x3 <- paste0(" -- tail: ", x31)
  cat(x1, x2, x3, print_ph(input.ph), "\n")
}