class

Minimap2::MmMapOpt

Inherits Reference < Object

Mapping / alignment options (mirrors mm_mapopt_t)

Constructors

new

Instance methods

a

a=(a : Int32)

alt_drop

alt_drop=(alt_drop : Float32)

anchor_ext_len

anchor_ext_len=(anchor_ext_len : Int32)

anchor_ext_shift

anchor_ext_shift=(anchor_ext_shift : Int32)

b

b=(b : Int32)

best_n

best_n=(best_n : Int32)

bw

bw=(bw : Int32)

bw_long

bw_long=(bw_long : Int32)

cap_kalloc

cap_kalloc=(cap_kalloc : Int64)

chain_gap_scale

chain_gap_scale=(chain_gap_scale : Float32)

chain_skip_scale

chain_skip_scale=(chain_skip_scale : Float32)

e

e2

e2=(e2 : Int32)

e=(e : Int32)

end_bonus

end_bonus=(end_bonus : Int32)

flag

flag=(flag : Int64)

jump_min_match

jump_min_match=(jump_min_match : Int32)

junc_bonus

junc_bonus=(junc_bonus : Int32)

junc_pen

junc_pen=(junc_pen : Int32)

mask_len

mask_len=(mask_len : Int32)

mask_level

mask_level=(mask_level : Float32)

max_chain_iter

max_chain_iter=(max_chain_iter : Int32)

max_chain_skip

max_chain_skip=(max_chain_skip : Int32)

max_clip_ratio

max_clip_ratio=(max_clip_ratio : Float32)

max_frag_len

max_frag_len=(max_frag_len : Int32)

max_gap

max_gap=(max_gap : Int32)

max_gap_ref

max_gap_ref=(max_gap_ref : Int32)

max_max_occ

max_max_occ=(max_max_occ : Int32)

max_mid_occ

max_mid_occ=(max_mid_occ : Int32)

max_occ

max_occ=(max_occ : Int32)

max_qlen

max_qlen=(max_qlen : Int32)

max_sw_mat

max_sw_mat=(max_sw_mat : Int64)

mid_occ

mid_occ=(mid_occ : Int32)

mid_occ_frac

mid_occ_frac=(mid_occ_frac : Float32)

min_chain_score

min_chain_score=(min_chain_score : Int32)

min_cnt

min_cnt=(min_cnt : Int32)

min_dp_max

min_dp_max=(min_dp_max : Int32)

min_ksw_len

min_ksw_len=(min_ksw_len : Int32)

min_mid_occ

min_mid_occ=(min_mid_occ : Int32)

mini_batch_size

mini_batch_size=(mini_batch_size : Int64)

noncan

noncan=(noncan : Int32)

occ_dist

occ_dist=(occ_dist : Int32)

pe_bonus

pe_bonus=(pe_bonus : Int32)

pe_ori

pe_ori=(pe_ori : Int32)

pri_ratio

pri_ratio=(pri_ratio : Float32)

q

q2

q2=(q2 : Int32)

q=(q : Int32)

q_occ_frac

q_occ_frac=(q_occ_frac : Float32)

rank_frac

rank_frac=(rank_frac : Float32)

rank_min_len

rank_min_len=(rank_min_len : Int32)

rmq_inner_dist

rmq_inner_dist=(rmq_inner_dist : Int32)

rmq_rescue_ratio

rmq_rescue_ratio=(rmq_rescue_ratio : Float32)

rmq_rescue_size

rmq_rescue_size=(rmq_rescue_size : Int32)

rmq_size_cap

rmq_size_cap=(rmq_size_cap : Int32)

sc_ambi

sc_ambi=(sc_ambi : Int32)

sdust_thres

sdust_thres=(sdust_thres : Int32)

seed

seed=(seed : Int32)

split_prefix

split_prefix=(split_prefix : String | Nil)

transition

transition=(transition : Int32)

zdrop

zdrop=(zdrop : Int32)

zdrop_inv

zdrop_inv=(zdrop_inv : Int32)