Minimap2 Wrapper

struct Buffer
	handle :: Ptr{Cvoid}
end

Store the untyped address to a minimap2 sequence buffer (working space).

struct Extra
	capacity :: UInt32
	dp_score :: Int32
	dp_max   :: Int32
	dp_max2  :: Int32
	packed   :: UInt32 # n_ambi (30 bits) / strand (2 bits)
	n_cigar  :: UInt32
	cigar UInt32[] (variable length array)
end

Copied from minimap2.h. See mmextrat.

struct Index
	handle :: Ptr{Cvoid}
end

Store the untyped address to a minimap2 sequence index (set of minimizers).

struct IndexOptions
	k    :: Cshort
	w    :: Cshort
	flag :: Cshort
	bucket_bits :: Cshort
	mini_batch_size :: Int64
	batch_size :: UInt64

	IndexOptions() = new()
end

Copied from minimap2.h. See mmidxoptt.

mutable struct MapOptions
	flag :: Int64
	seed :: Cint
	sdust_thres :: Cint

	max_qlen :: Cint

	bw :: Cint; bw_long :: Cint
	max_gap :: Cint; max_gap_ref :: Cint 
	max_frag_len :: Cint
	max_chain_skip :: Cint; max_chain_iter :: Cint
	min_cnt :: Cint
	min_chain_score :: Cint
	chain_gap_scale :: Cfloat
	rmq_size_cap :: Cint; rmq_inner_dist :: Cint
	rmq_rescue_size :: Cint
	rmq_rescue_ratio :: Cfloat

	mask_level :: Cfloat
	mask_len :: Cint
	pri_ratio :: Cfloat
	best_n :: Cint

	alt_drop :: Cfloat

	a :: Cint; b :: Cint; q :: Cint; e :: Cint; q2 :: Cint; e2 :: Cint
	sc_ambi :: Cint
	noncan :: Cint 
	junc_bonus :: Cint
	zdrop :: Cint; zdrop_inv :: Cint
	end_bonus :: Cint
	min_dp_max :: Cint
	min_ksw_len :: Cint
	anchor_ext_len :: Cint; anchor_ext_shift :: Cint
	max_clip_ratio :: Cfloat

	rank_min_len :: Cint
	rank_frac :: Cfloat

	pe_ori :: Cint; pe_bonus :: Cint

	mid_occ_frac :: Cfloat
	min_mid_occ :: Int32; max_mid_occ :: Int32
	mid_occ :: Int32
	max_occ :: Int32; max_max_occ :: Int32; occ_dist :: Int32;
	mini_batch_size :: Int64
	max_sw_mat :: Int64
	cap_kalloc :: Int64

	split_prefix :: Cstring
end

Copied from minimap2.h. See mmmapoptt.

struct Record
	id :: Int32; cnt :: Int32; rid :: Int32; score :: Int32
	qs :: Int32; qe  :: Int32; rs  :: Int32; re :: Int32

	parent :: Int32; subsc :: Int32

	as     :: Int32
	mlen   :: Int32; blen :: Int32
	nsub   :: Int32;
	score0 :: Int32;

	pack :: UInt32 # mapq(8) ; split(2); rev(1); inv(1); sam_pri(1); proper_frag(1); pe_thru(1); seg_split(1); seg_id(8); split_inv(1); is_alt(1); dummy(6)
	hash :: UInt32
	div  :: Cfloat
	p    :: Ptr{Extra}
end

Copied from minimap2.h. See mmreg1t.

align(ref::PanContigs, qry::PanContigs, minblock::Int, preset::String)

Call into minimap to align the set of blocks qry to blocks ref. Preset should be a string ∈ ["asm5","asm10","asm20"]. See minimap2 manual for details. This is probably the function you want. If you call into the function specifically, all memory management is taken care of for you.

freebuffer()

Free memory associated to an opaque handle thread buffer

freeindex()

Free memory associated to an opaque handle to a sequence index.

makebuffer()

Return an opaque handle thread buffer

makeindex(w, k, names, sequence; bucketbits::Int=14)

Given a window size w and kmer length k, return a handle to a minimizer index for sequences sequence.