mmollina / MAPpoly
Showing 1 of 1 files from the diff.

@@ -514,7 +514,7 @@
Loading
514 514
        seq.num <- tail.temp$maps[[i]]$seq.num 
515 515
      if(length(seq.num) < extend.tail)
516 516
        seq.num <- tail(cur.map$maps[[i]]$seq.num, extend.tail)
517 -
      ## If the tail do not contain the marker responsable for carrying 
517 +
      ## If the tail do not contain the marker responsible for carrying 
518 518
      ## multiple linkage phases through the rounds of insertion,
519 519
      ## extend the tail so it contains that marker
520 520
      if(max(check_ls_phase(all.ph)) >= length(seq.num)){
@@ -537,7 +537,7 @@
Loading
537 537
    ## information obtained in the current round
538 538
    twopt.phase.number<-length(input.ph$config.to.test)
539 539
    ## If this number is higher than phase.number.limit,
540 -
    ## procede to the next iteration
540 +
    ## proceed to the next iteration
541 541
    if(length(input.ph$config.to.test) > phase.number.limit) {
542 542
      if(verbose)
543 543
        cat(crayon::italic$yellow(paste0(ct ,": not included (linkage phases)\n", sep = "")))
@@ -545,7 +545,7 @@
Loading
545 545
      next()
546 546
    }
547 547
    ## Appending the marker to the numeric 
548 -
    ## sequence and makeing a new sequence
548 +
    ## sequence and making a new sequence
549 549
    seq.num <- c(seq.num, input.seq$seq.num[ct])
550 550
    seq.cur <- make_seq_mappoly(input.obj = get(input.seq$data.name, pos=1),
551 551
                                arg = seq.num,
@@ -613,12 +613,14 @@
Loading
613 613
    } else { selected.map <- LOD < thres.hmm }
614 614
    all.ph.temp <- update_ph_list_at_hmm_thres(cur.map.temp, Inf)
615 615
    cur.map.temp$maps <- cur.map.temp$maps[selected.map]
616 +
    id <- !sapply(cur.map.temp$maps, is.null)
617 +
    cur.map.temp$maps <- cur.map.temp$maps[id]
616 618
    cur.map <- cur.map.temp
617 -
    all.ph <- add_mrk_at_tail_ph_list(all.ph, all.ph.temp, M[selected.map,,drop=FALSE])
619 +
    all.ph <- add_mrk_at_tail_ph_list(all.ph, all.ph.temp, M[id,,drop=FALSE])
618 620
    ct <- ct + 1
619 621
  }
620 -
  ##### Reestimating final map ####
621 -
  ## Reestimating final map with higher tolerance
622 +
  ##### Re-estimating final map ####
623 +
  ## Re-estimating final map with higher tolerance
622 624
  seq.final <- make_seq_mappoly(input.obj = get(input.seq$data.name, pos=1), 
623 625
                                arg = as.numeric(names(all.ph$config.to.test[[1]]$P)), 
624 626
                                data.name = input.seq$data.name)
Files Coverage
R 70.18%
src 76.71%
Project Totals (59 files) 71.66%
Sunburst
The inner-most circle is the entire project, moving away from the center are folders then, finally, a single file. The size and color of each slice is representing the number of statements and the coverage, respectively.
Icicle
The top section represents the entire project. Proceeding with folders and finally individual files. The size and color of each slice is representing the number of statements and the coverage, respectively.
Grid
Each block represents a single file in the project. The size and color of each block is represented by the number of statements and the coverage, respectively.
Loading