6 Example inputs

• Parameter-name Default Other option:
• prefilter FALSE TRUE
• maf 0.00 Value between 0 and 0.5
• equal_remove FALSE TRUE
• window_sequence NULL (automatic generated)
• window_size 20 Natural number (1,2,3,…)
• merging_error 1 Natural number (1,2,3,…) - lower than window_size!
• max_groups 0 to active: Natural number >= 2
• bp_map NULL
• window_anchor_gens NULL
• blockinfo_mode 0 1 to minimize groups per window
• at_least_one TRUE FALSE
• multi_window_mode FALSE TRUE (use e.g. window_size=c(5,10,20,50))
• blockinfo_mode_na FALSE TRUE (adjust merging_error ! )
• na_snp_weight 2 Numeric value >0
• na_seq_weight 0 Numeric value > 0
• actual_snp_weight 5 Numeric value > 0
• gap 10 Natural number (1,2,3,…)
• min_share 0.975 Value between 0.5 and 1 (highly recommend to not use small values!
• node_min 5 Natural number (1,2,3,…)
• edge_min 5 Natural number (1,2,3,…)
• multi_min 5 Natural number (1,2,3,…)
• consider_nodes TRUE FALSE
• consider_edge TRUE FALSE
• consider_multi FALSE TRUE
• subgroups NULL (automatic generated) List(1:500, 1:200, 1:300)
• Subpopulation 1 in first 200 colums
• Subpopulation 2 in last 300 colums
• min_per_subgroup 0 Natural number (1,2,3,…) Only when one is explicitly interested in the overlap between both populations!
• min_majorblock 5’000 Non-negativ-number (0,1,2,…)

• min_majorblock_steps 4 Non-negativ-number (0,1,2,…)
• min_similarity 0.99 Value between 0 and 1 (highly recommend to not use values below 0.9!
• save_allblock TRUE FALSE
• consider_all TRUE FALSE
• merge_closeblock FALSE TRUE
• max_diff_i 1 Non-negative-number (0,2,3,…)
• max_diff_l 1 Non-negative-number (0,2,3,…)
• off_lines 5 Natural number (1,2,3,…)
• Weighting_length 1 Numeric value (<0 not recommended)
• Weighting_size 1 Numeric value (<0 not recommended)
• block_extending TRUE FALSE
• snp_extending TRUE FALSE
• max_extending_diff 1 Non-negative-number (0,2,3,…)
• max_extending_diff_snp 0 Non-negative-number (1,2,3,…)
• extending_ratio 20 Natural number (1,2,3,…) Avoid low values
• extending_ratio_snp Inf Naturual number (1,2,3,…) Only change for long windows and high number of haplotypes in *blocks
• off_node_addition FALSE TRUE
• raster 5 Natural number (1,2,3,…)
• recoding FALSE TRUE
• recoding_notneeded FALSE TRUE
• fast_compiler TRUE FALSE
• intersect_func TRUE FALSE (base::intersect), usage of HaploBlocker::intersect requires that vector in an ascending *sequence of numbers
• c_dhm_mode TRUE FALSE
• big_output FALSE TRUE
• target_coverage NULL Value between 0 and 1
• max_iteration 10 Natural number (1,2,3,…)
• min_step_size 25 Natural number (1,2,3,…)
• target_stop 0.001 Value between 0 and 1 (recommend close to 0)
• multi_window_mode FALSE TRUE;
• Can be actived by using a vector for window_size; merging_error or min_share
• adaptive_mode FALSE TRUE;
• Sets window_size = c(5,10,20,50) and
• Target_coverage = 0.9
• developer_mode FALSE TRUE
• parallel_window Inf Natural number – bigger than the biggest blocks one wants to identify
• window_overlap 0 Natural number – nothing bigger than the size of the largest block is needed
• window_cores 1 Natural number (2,3,4,…)
• double_share 1 Value between 0 and 1 (nothing below 0.5 is recommended)
• min_reduction_cross -Inf Non-negative-number (0,1,2,3,…)
• min_reduction_neglet -Inf Non-negative-number (0,1,2,3,…)
• early_remove FALSE TRUE
• node_min_early NULL Natural number (1,2,3,…) – e.g. node_min / edge_min