mmollina / MAPpoly

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@@ -514,7 +514,7 @@
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        seq.num <- tail.temp$maps[[i]]$seq.num 
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      if(length(seq.num) < extend.tail)
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        seq.num <- tail(cur.map$maps[[i]]$seq.num, extend.tail)
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      ## If the tail do not contain the marker responsable for carrying 
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      ## If the tail do not contain the marker responsible for carrying 
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      ## multiple linkage phases through the rounds of insertion,
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      ## extend the tail so it contains that marker
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      if(max(check_ls_phase(all.ph)) >= length(seq.num)){
@@ -537,15 +537,15 @@
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    ## information obtained in the current round
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    twopt.phase.number<-length(input.ph$config.to.test)
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    ## If this number is higher than phase.number.limit,
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    ## procede to the next iteration
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    ## proceed to the next iteration
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    if(length(input.ph$config.to.test) > phase.number.limit) {
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      if(verbose)
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        cat(crayon::italic$yellow(paste0(ct ,": not included (linkage phases)\n", sep = "")))
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      ct <- ct + 1
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      next()
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    }
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    ## Appending the marker to the numeric 
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    ## sequence and makeing a new sequence
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    ## sequence and making a new sequence
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    seq.num <- c(seq.num, input.seq$seq.num[ct])
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    seq.cur <- make_seq_mappoly(input.obj = get(input.seq$data.name, pos=1),
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                                arg = seq.num,
@@ -613,12 +613,14 @@
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    } else { selected.map <- LOD < thres.hmm }
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    all.ph.temp <- update_ph_list_at_hmm_thres(cur.map.temp, Inf)
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    cur.map.temp$maps <- cur.map.temp$maps[selected.map]
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    id <- !sapply(cur.map.temp$maps, is.null)
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    cur.map.temp$maps <- cur.map.temp$maps[id]
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    cur.map <- cur.map.temp
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    all.ph <- add_mrk_at_tail_ph_list(all.ph, all.ph.temp, M[selected.map,,drop=FALSE])
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    all.ph <- add_mrk_at_tail_ph_list(all.ph, all.ph.temp, M[id,,drop=FALSE])
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    ct <- ct + 1
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  }
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  ##### Reestimating final map ####
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  ## Reestimating final map with higher tolerance
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  ##### Re-estimating final map ####
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  ## Re-estimating final map with higher tolerance
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  seq.final <- make_seq_mappoly(input.obj = get(input.seq$data.name, pos=1), 
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                                arg = as.numeric(names(all.ph$config.to.test[[1]]$P)), 
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                                data.name = input.seq$data.name)

Learn more Showing 1 files with coverage changes found.

Changes in R/filters.R
-1
+1
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Files Coverage
R/cache_twopts.R 57.50%
R/calc_genoprob.R 82.22%
R/calc_genoprob_dist.R 89.23%
R/calc_genoprob_error.R 92.68%
R/check_phase_configurations.R 75.89%
R/eliminate_redundant.R 52.00%
R/est_map_hmm.R 0.06% 83.55%
R/export_map_list.R 87.50%
R/filters.R 0.53% 56.61%
R/get_counts.R 77.14%
R/get_counts_from_web.R 50.00%
R/get_submap.R 66.67%
R/group.R 45.88%
R/haplotype_map_utils.R 78.80%
R/homolog_probs.R 72.50%
R/import_from_polymapR.R 0.00%
R/import_from_updog.R 0.00%
R/loglike_hmm.R 90.48%
R/make_mat.R 80.00%
R/make_pairs.R 78.57%
R/make_seq.R 27.84%
R/marker_info.R 96.30%
R/mds.R 45.53%
R/merge_maps.R 95.77%
R/pairwise_rf.R 63.86%
R/plot_genome_vs_map.R 78.57%
R/plot_map_list.R 90.48%
R/poly_cross_simulate.R 93.10%
R/preferential_pairing.R 63.89%
R/prior_dist_hmm.R 95.24%
R/read_fitpoly.R 65.64%
R/read_mappoly.R 75.31%
R/read_mappoly_csv.R 97.65%
R/read_mappoly_prob.R 71.88%
R/read_mappoly_vcf.R 68.84%
R/reestimate_map.R 70.37%
R/reestimate_map_with_global_genotypic_error.R 84.27%
R/reestimate_map_with_prior_genotypic_probability.R 78.85%
R/rf_list_to_matrix.R 48.91%
R/rf_snp_filter.R 92.00%
R/segreg_poly.R 92.86%
R/sim_homologous.R 94.87%
R/simulation_utils.R 65.56%
R/single_map_hmm.R 92.86%
R/split_and_rephase.R 70.83%
R/utils.R 76.65%
R/zzz.R 100.00%
src/calc_genoprob.cpp 100.00%
src/calc_genoprob_based_on_phased_marker_blocks.cpp 47.95%
src/calc_loglike_given_map.cpp 88.00%
src/combinatorial.cpp 100.00%
src/est_hmm_map_based_on_phased_mrk_blocks.cpp 42.51%
src/est_map_hmm_given_dose.cpp 83.55%
src/est_map_hmm_given_prior.cpp 94.21%
src/genotypic_counts.cpp 100.00%
src/hmm_elements.cpp 80.00%
src/mappoly_init.c 0.00%
src/pairwise_estimation.cpp 100.00%
src/read_mappoly_vcf.cpp 55.83%
Project Totals (59 files) 71.66%
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