minimap2 0.2.30.3 → 1.2.31.0

data/ext/minimap2/tex/ngmlr.eval

@@ -1,38 +0,0 @@
-Q	60	23616	0	0.000000000
-Q	45	3520	1	0.000036851
-Q	41	1840	1	0.000069023
-Q	37	328	2	0.000136500
-Q	36	276	1	0.000169033
-Q	35	480	1	0.000199601
-Q	33	375	2	0.000262855
-Q	31	178	2	0.000326659
-Q	30	153	5	0.000487551
-Q	29	200	1	0.000516696
-Q	27	100	3	0.000611601
-Q	26	93	3	0.000706056
-Q	25	75	2	0.000768393
-Q	24	82	1	0.000798314
-Q	23	80	6	0.000987387
-Q	22	71	6	0.001175835
-Q	21	76	7	0.001394921
-Q	20	63	9	0.001676897
-Q	19	55	4	0.001800322
-Q	18	62	8	0.002048987
-Q	17	55	7	0.002265718
-Q	16	60	10	0.002575539
-Q	15	82	9	0.002850877
-Q	14	67	7	0.003063745
-Q	13	62	11	0.003401042
-Q	12	64	13	0.003799084
-Q	11	56	5	0.003947900
-Q	10	58	17	0.004468303
-Q	9	70	22	0.005139796
-Q	8	23	9	0.005414604
-Q	7	41	17	0.005933068
-Q	6	42	18	0.006480881
-Q	5	33	9	0.006751757
-Q	4	29	9	0.007022948
-Q	3	27	15	0.007478764
-Q	2	23	10	0.007781024
-Q	1	9	2	0.007840364
-Q	0	13	8	0.008083105

data/ext/minimap2/tex/roc.gp

@@ -1,60 +0,0 @@
-set t po eps enh co so "Helvetica,26"
-
-set style line 1 lt 1 pt 1 lc rgb "#e41a1c" lw 2;
-set style line 2 lt 1 pt 2 lc rgb "#377eb8" lw 2;
-set style line 3 lt 1 pt 3 lc rgb "#4daf4a" lw 2;
-set style line 4 lt 1 pt 4 lc rgb "#984ea3" lw 2;
-set style line 5 lt 1 pt 6 lc rgb "#ff7f00" lw 2;
-set style line 6 lt 1 pt 8 lc rgb "#f781bf" lw 2;
-
-set out "roc-color.eps"
-
-set pointsize 2.0
-set size 1.59,1.04
-set multiplot layout 1,2
-
-set label "(a)" at graph -0.245,1.06 font "Helvetica-bold,40"
-set xlab "Error rate of mapped PacBio reads"
-set ylab "Fraction of mapped reads" off +1.8
-set ytics 0.02
-set yran [0.9:1]
-
-set size 0.8,1
-set log x
-set format x "10^{%L}"
-set key bot right
-plot "<./eval2roc.pl blasr-mc.eval" u 2:3 t "blasr-mc" w lp ls 4, \
-     "<./eval2roc.pl bwa.eval" u 2:3 t "bwa-mem" w lp ls 2, \
-     "<./eval2roc.pl graphmap.eval" u 2:3 t "graphmap" w lp ls 3, \
-     "<./eval2roc.pl minialign.eval" u 2:3 t "minialign" w lp ls 1, \
-     "<./eval2roc.pl mm2.eval" u 2:3 t "minimap2" w lp ls 6, \
-     "<./eval2roc.pl ngmlr.eval" u 2:3 t "ngm-lr" w lp ls 5
-unset label
-
-set origin 0.8,0
-set size 0.79,1
-set label "(b)" at graph -0.245,1.06 font "Helvetica-bold,40"
-set xlab "Error rate of mapped short reads"
-
-set key top left
-plot "<./eval2roc.pl -n2e7 bowtie2-s3.sam.eval" u 2:3 t "bowtie2" w lp ls 5, \
-	 "<./eval2roc.pl -n2e7 bwa-s3.sam.eval" u 2:3 t "bwa-mem" w lp ls 2, \
-	 "<./eval2roc.pl -n2e7 mm2-s3.sam.eval" u 2:3 t "minimap2" w lp ls 6, \
-	 "<./eval2roc.pl -n2e7 snap-s3.sam.eval" u 2:3 t "snap" w lp ls 3
-
-#unset log
-#unset format
-#unset key
-#set log y
-#set ylab "Accumulative mapping error rate" off +0
-#set xlab "Mapping quality"
-#set yran [1e-5:0.1]
-#set ytics 1e-5,0.1
-#set format y "10^{%L}"
-#set xran [60:0] reverse
-#plot "<./eval2roc.pl blasr-mc.eval" u 1:2 w lp ls 4, \
-#     "<./eval2roc.pl bwa.eval" u 1:2 t "bwa-mem" w lp ls 2, \
-#     "<./eval2roc.pl graphmap.eval" u 1:2 t "graphmap" w lp ls 3, \
-#     "<./eval2roc.pl minialign.eval" u 1:2 t "minialign" w lp ls 1, \
-#     "<./eval2roc.pl mm2.eval" u 1:2 t "minimap2" w lp ls 6, \
-#     "<./eval2roc.pl ngmlr.eval" u 1:2 t "ngm-lr" w lp ls 5

data/ext/minimap2/tex/snap-s3.sam.eval

@@ -1,62 +0,0 @@
-Q	60	18993268	10320	0.000543350	18993268
-Q	59	33156	216	0.000553756	19026424
-Q	58	29982	295	0.000568365	19056406
-Q	57	9412	278	0.000582666	19065818
-Q	56	11012	228	0.000594281	19076830
-Q	55	9968	235	0.000606283	19086798
-Q	54	8602	292	0.000621301	19095400
-Q	53	6094	259	0.000634662	19101494
-Q	52	5026	257	0.000647946	19106520
-Q	51	4278	224	0.000659522	19110798
-Q	50	3682	178	0.000668708	19114480
-Q	49	2750	156	0.000676772	19117230
-Q	48	2314	112	0.000682548	19119544
-Q	47	2056	96	0.000687495	19121600
-Q	46	1658	62	0.000690677	19123258
-Q	45	1492	74	0.000694493	19124750
-Q	44	1150	56	0.000697379	19125900
-Q	43	1062	48	0.000699850	19126962
-Q	42	976	60	0.000702951	19127938
-Q	41	884	36	0.000704800	19128822
-Q	40	708	52	0.000707493	19129530
-Q	39	870	26	0.000708819	19130400
-Q	38	598	26	0.000710156	19130998
-Q	37	542	34	0.000711913	19131540
-Q	36	846	50	0.000714495	19132386
-Q	35	590	50	0.000717087	19132976
-Q	34	550	42	0.000719261	19133526
-Q	33	2174	66	0.000722628	19135700
-Q	32	876	86	0.000727089	19136576
-Q	31	638	104	0.000732500	19137214
-Q	30	1718	196	0.000742675	19138932
-Q	29	91022	968	0.000789497	19229954
-Q	28	12864	781	0.000829556	19242818
-Q	27	5806	427	0.000851489	19248624
-Q	26	25274	728	0.000888144	19273898
-Q	25	7418	680	0.000923070	19281316
-Q	24	11800	701	0.000958839	19293116
-Q	23	57328	3933	0.001159250	19350444
-Q	22	7662	846	0.001202494	19358106
-Q	21	5924	617	0.001233989	19364030
-Q	20	4623	574	0.001263330	19368653
-Q	19	4988	942	0.001311627	19373641
-Q	18	3968	793	0.001352282	19377609
-Q	17	3630	681	0.001387166	19381239
-Q	16	2921	513	0.001413422	19384160
-Q	15	2716	424	0.001435095	19386876
-Q	14	2366	365	0.001453744	19389242
-Q	13	2169	412	0.001474828	19391411
-Q	12	2077	360	0.001493233	19393488
-Q	11	2016	441	0.001515815	19395504
-Q	10	2292	738	0.001553682	19397796
-Q	9	4165	1832	0.001647772	19401961
-Q	8	3963	1862	0.001743385	19405924
-Q	7	3927	1793	0.001835408	19409851
-Q	6	3572	1639	0.001919497	19413423
-Q	5	3270	1533	0.001998126	19416693
-Q	4	3046	1610	0.002080718	19419739
-Q	3	251447	125550	0.008436553	19671186
-Q	2	24390	13537	0.009113417	19695576
-Q	1	124406	86780	0.013434624	19819982
-Q	0	171254	153874	0.021016609	19991236
-U	8764

data/ext/minimap2.patch

@@ -1,19 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -1,9 +1,9 @@
--CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
-+CFLAGS=		-g -Wall -O2 -Wc++-compat -fPIC #-Wextra
- CPPFLAGS=	-DHAVE_KALLOC
- INCLUDES=
- OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
- 			lchain.o align.o hit.o seed.o jump.o map.o format.o pe.o esterr.o splitidx.o \
--			ksw2_ll_sse.o
-+			ksw2_ll_sse.o cmappy.o
- PROG=		minimap2
- PROG_EXTRA=	sdust minimap2-lite
- LIBS=		-lm -lz -lpthread
-@@ -135,3 +135,4 @@ sdust.o: kalloc.h kdq.h kvec.h sdust.h
- seed.o: mmpriv.h minimap.h bseq.h kseq.h kalloc.h ksort.h
- sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h kseq.h
- splitidx.o: mmpriv.h minimap.h bseq.h kseq.h
-+cmappy.o: cmappy.h

data/lib/minimap2/ffi/constants.rb

@@ -1,267 +0,0 @@
-# frozen_string_literal: true
-
-module Minimap2
-  module FFI
-    # flags
-    NO_DIAG          = 0x001 # no exact diagonal hit
-    NO_DUAL          = 0x002 # skip pairs where query name is lexicographically larger than target name
-    CIGAR            = 0x004
-    OUT_SAM          = 0x008
-    NO_QUAL          = 0x010
-    OUT_CG           = 0x020
-    OUT_CS           = 0x040
-    SPLICE           = 0x080 # splice mode
-    SPLICE_FOR       = 0x100 # match GT-AG
-    SPLICE_REV       = 0x200 # match CT-AC, the reverse complement of GT-AG
-    NO_LJOIN         = 0x400
-    OUT_CS_LONG      = 0x800
-    SR               = 0x1000
-    FRAG_MODE        = 0x2000
-    NO_PRINT_2ND     = 0x4000
-    TWO_IO_THREADS   = 0x8000 # Translator's Note. MM_F_2_IO_THREADS. Constants starting with numbers cannot be defined.
-    LONG_CIGAR       = 0x10000
-    INDEPEND_SEG     = 0x20000
-    SPLICE_FLANK     = 0x40000
-    SOFTCLIP         = 0x80000
-    FOR_ONLY         = 0x100000
-    REV_ONLY         = 0x200000
-    HEAP_SORT        = 0x400000
-    ALL_CHAINS       = 0x800000
-    OUT_MD           = 0x1000000
-    COPY_COMMENT     = 0x2000000
-    EQX              = 0x4000000 # use =/X instead of M
-    PAF_NO_HIT       = 0x8000000 # output unmapped reads to PAF
-    NO_END_FLT       = 0x10000000
-    HARD_MLEVEL      = 0x20000000
-    SAM_HIT_ONLY     = 0x40000000
-    RMQ              = 0x80000000
-    QSTRAND          = 0x100000000
-    NO_INV           = 0x200000000
-    NO_HASH_NAME     = 0x400000000
-    SPLICE_OLD       = 0x800000000
-    SECONDARY_SEQ    = 0x1000000000 # output SEQ field for secondary alignments using hard clipping
-    OUT_DS           = 0x2000000000
-    WEAK_PAIRING     = 0x4000000000
-    SR_RNA           = 0x8000000000
-    OUT_JUNC         = 0x10000000000
-
-    HPC              = 0x1
-    NO_SEQ           = 0x2
-    NO_NAME          = 0x4
-
-    IDX_MAGIC        = "MMI\2"
-
-    MAX_SEG          = 255
-
-    CIGAR_MATCH      = 0
-    CIGAR_INS        = 1
-    CIGAR_DEL        = 2
-    CIGAR_N_SKIP     = 3
-    CIGAR_SOFTCLIP   = 4
-    CIGAR_HARDCLIP   = 5
-    CIGAR_PADDING    = 6
-    CIGAR_EQ_MATCH   = 7
-    CIGAR_X_MISMATCH = 8
-
-    CIGAR_STR        = "MIDNSHP=XB"
-
-    # emulate 128-bit integers
-    class MM128 < ::FFI::Struct
-      layout \
-        :x, :uint64_t,
-        :y, :uint64_t
-    end
-
-    # emulate 128-bit arrays
-    class MM128V < ::FFI::Struct
-      layout \
-        :n, :size_t,
-        :m, :size_t,
-        :a, MM128.ptr
-    end
-
-    # minimap2 index
-    class IdxSeq < ::FFI::Struct
-      layout \
-        :name,   :string,    # name of the db sequence
-        :offset, :uint64_t,  # offset in mm_idx_t::S
-        :len,    :uint32,  # length
-        :is_alt, :uint32
-    end
-
-    class Idx < ::FFI::Struct
-      layout \
-        :b,     :int32,
-        :w,     :int32,
-        :k,     :int32,
-        :flag,  :int32,
-        :n_seq, :uint32,   # number of reference sequences
-        :index, :int32,
-        :n_alt, :int32,
-        :seq,   IdxSeq.ptr,  # sequence name, length and offset
-        :S,     :pointer,    # 4-bit packed sequence
-        :B,     :pointer,    # index (hidden)
-        :I,     :pointer,    # intervals (hidden)
-        :spsc,  :pointer,    # splice score (hidden)
-        :J,     :pointer,    # junctions to create jumps (hidden)
-        :km,    :pointer,
-        :h,     :pointer
-    end
-
-    # minimap2 alignment
-    class Extra < ::FFI::BitStruct
-      layout \
-        :capacity,            :uint32,  # the capacity of cigar[]
-        :dp_score,            :int32,   # DP score
-        :dp_max,              :int32,   # score of the max-scoring segment
-        :dp_max2,             :int32,   # score of the best alternate mappings
-        :dp_max0,             :int32,   # DP score before mm_update_dp_max() adjustment
-        :n_ambi_trans_strand, :uint32,
-        :n_cigar,             :uint32
-      # :cigar,               :pointer  # variable length array (see cigar method below)
-
-      bit_field :n_ambi_trans_strand,
-                :n_ambi, 30,      # number of ambiguous bases
-                :trans_strand, 2  # transcript strand: 0 for unknown, 1 for +, 2 for -
-
-      # variable length array
-      def cigar
-        pointer.get_array_of_uint32(size, self[:n_cigar])
-      end
-    end
-
-    class Reg1 < ::FFI::BitStruct
-      layout \
-        :id,     :int32, # ID for internal uses (see also parent below)
-        :cnt,    :int32, # number of minimizers; if on the reverse strand
-        :rid,    :int32, # reference index; if this is an alignment from inversion rescue
-        :score,  :int32, # DP alignment score
-        :qs,     :int32, # query start
-        :qe,     :int32, # query end
-        :rs,     :int32, # reference start
-        :re,     :int32, # reference end
-        :parent, :int32, # parent==id if primary
-        :subsc,  :int32, # best alternate mapping score
-        :as,     :int32, # offset in the a[] array (for internal uses only)
-        :mlen,   :int32, # seeded exact match length
-        :blen,   :int32, # seeded alignment block length
-        :n_sub,  :int32, # number of suboptimal mappings
-        :score0, :int32, # initial chaining score (before chain merging/spliting)
-        :fields, :uint32,
-        :hash,   :uint32,
-        :div,    :float,
-        :p,      Extra.ptr
-
-      bit_field :fields,
-                :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,
-                :strand_retained, 1,
-                :is_spliced,      1,
-                :dummy,           4
-    end
-
-    # indexing option
-    class IdxOpt < ::FFI::Struct
-      layout \
-        :k,               :short,
-        :w,               :short,
-        :flag,            :short,
-        :bucket_bits,     :short,
-        :mini_batch_size, :int64_t,
-        :batch_size,      :uint64_t
-    end
-
-    # mapping option
-    class MapOpt < ::FFI::Struct
-      layout \
-        :flag,                 :int64_t, # see MM_F_* macros
-        :seed,                 :int,
-        :sdust_thres,          :int,     # score threshold for SDUST; 0 to disable
-        :max_qlen,             :int,     # max query length
-        :bw,                   :int,     # bandwidth
-        :bw_long,              :int,
-        :max_gap,              :int,     # break a chain if there are no minimizers in a max_gap window
-        :max_gap_ref,          :int,
-        :max_frag_len,         :int,
-        :max_chain_skip,       :int,
-        :max_chain_iter,       :int,
-        :min_cnt,              :int,     # min number of minimizers on each chain
-        :min_chain_score,      :int,     # min chaining score
-        :chain_gap_scale,      :float,
-        :chain_skip_scale,     :float,
-        :rmq_size_cap,         :int,
-        :rmq_inner_dist,       :int,
-        :rmq_rescue_size,      :int,
-        :rmq_rescue_ratio,     :float,
-        :mask_level,           :float,
-        :mask_len,             :int,
-        :pri_ratio,            :float,
-        :best_n,               :int,     # top best_n chains are subjected to DP alignment
-        :alt_drop,             :float,
-        :a,                    :int,     # matching score
-        :b,                    :int,     # mismatch
-        :q,                    :int,     # gap-open
-        :e,                    :int,     # gap-ext
-        :q2,                   :int,     # gap-open
-        :e2,                   :int,     # gap-ext
-        :transition,           :int,     # transition mismatch score (A:G, C:T)
-        :sc_ambi,              :int,     # score when one or both bases are "N"
-        :noncan,               :int,     # cost of non-canonical splicing sites
-        :junc_bonus,           :int,     # bonus for a splice site in annotation
-        :junc_pen,             :int,     # penalty for GT- or -AG not scored in --spsc
-        :zdrop,                :int,     # break alignment if alignment score drops too fast along the diagonal
-        :zdrop_inv,            :int,
-        :end_bonus,            :int,
-        :min_dp_max,           :int,     # drop an alignment if the score of the max scoring segment is below this threshold
-        :min_ksw_len,          :int,
-        :anchor_ext_len,       :int,
-        :anchor_ext_shift,     :int,
-        :max_clip_ratio,       :float,   # drop an alignment if BOTH ends are clipped above this ratio
-        :rank_min_len,         :int,
-        :rank_frac,            :float,
-        :pe_ori,               :int,
-        :pe_bonus,             :int,
-        :jump_min_match,       :int32,
-        :mid_occ_frac,         :float,   # only used by mm_mapopt_update(); see below
-        :q_occ_frac,           :float,
-        :min_mid_occ,          :int32,
-        :max_mid_occ,          :int32,
-        :mid_occ,              :int32,   # ignore seeds with occurrences above this threshold
-        :max_occ,              :int32,
-        :max_max_occ,          :int32,
-        :occ_dist,             :int32,
-        :mini_batch_size,      :int64_t, # size of a batch of query bases to process in parallel
-        :max_sw_mat,           :int64_t,
-        :cap_kalloc,           :int64_t,
-        :split_prefix,         :string
-    end
-
-    # index reader
-    class IdxReader < ::FFI::Struct
-      layout \
-        :is_idx,      :int,
-        :n_parts,     :int,
-        :idx_size,    :int64_t,
-        :opt,         IdxOpt,
-        :fp_out,      :pointer, # FILE
-        :seq_or_idx,  :pointer  # FIXME: Union mm_bseq_files or FILE
-    end
-
-    # memory buffer for thread-local storage during mapping
-    class TBuf < ::FFI::Struct
-      layout \
-        :km,       :pointer,
-        :rep_len,  :int,
-        :frag_gap, :int
-    end
-  end
-end

data/lib/minimap2/ffi/functions.rb

@@ -1,239 +0,0 @@
-# frozen_string_literal: true
-
-module Minimap2
-  module FFI
-    attach_function \
-      :main,
-      %i[int pointer],
-      :int
-
-    # int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo);
-    attach_function \
-      :mm_set_opt_raw, :mm_set_opt,
-      [:pointer, IdxOpt.by_ref, MapOpt.by_ref],
-      :int
-
-    private_class_method :mm_set_opt_raw
-
-    def self.mm_set_opt(preset, io, mo)
-      ptr = case preset
-            when 0, nil
-              ::FFI::Pointer.new(:int, 0)
-            else
-              ::FFI::MemoryPointer.from_string(preset.to_s)
-            end
-      mm_set_opt_raw(ptr, io, mo)
-    end
-
-    # int mm_check_opt(const mm_idxopt_t *io, const mm_mapopt_t *mo);
-    attach_function \
-      :mm_check_opt,
-      [IdxOpt.by_ref, MapOpt.by_ref],
-      :int
-
-    # void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi);
-    attach_function \
-      :mm_mapopt_update,
-      [MapOpt.by_ref, Idx.by_ref],
-      :void
-
-    # void mm_mapopt_max_intron_len(mm_mapopt_t *opt, int max_intron_len);
-    attach_function \
-      :mm_mapopt_max_intron_len,
-      [MapOpt.by_ref, :int],
-      :void
-
-    # mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt, const char *fn_out);
-    attach_function \
-      :mm_idx_reader_open,
-      [:string, IdxOpt.by_ref, :string],
-      IdxReader.by_ref
-
-    # mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads);
-    attach_function \
-      :mm_idx_reader_read,
-      [IdxReader.by_ref, :int],
-      Idx.by_ref
-
-    # void mm_idx_reader_close(mm_idx_reader_t *r);
-    attach_function \
-      :mm_idx_reader_close,
-      [IdxReader.by_ref],
-      :void
-
-    # int mm_idx_reader_eof(const mm_idx_reader_t *r);
-    attach_function \
-      :mm_idx_reader_eof,
-      [IdxReader.by_ref],
-      :int
-
-    # int64_t mm_idx_is_idx(const char *fn);
-    attach_function \
-      :mm_idx_is_idx,
-      [:string],
-      :int64_t
-
-    # mm_idx_t *mm_idx_load(FILE *fp);
-    attach_function \
-      :mm_idx_load,
-      [:pointer], # FILE pointer
-      Idx.by_ref
-
-    # void mm_idx_dump(FILE *fp, const mm_idx_t *mi);
-    attach_function \
-      :mm_idx_dump,
-      [:pointer, Idx.by_ref], # FILE pointer
-      :void
-
-    # mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const char **seq, const char **name);
-    attach_function \
-      :mm_idx_str,
-      %i[int int int int int pointer pointer],
-      Idx.by_ref
-
-    # void mm_idx_stat(const mm_idx_t *idx);
-    attach_function \
-      :mm_idx_stat,
-      [Idx.by_ref],
-      :void
-
-    # void mm_idx_destroy(mm_idx_t *mi);
-    attach_function \
-      :mm_idx_destroy,
-      [Idx.by_ref],
-      :void
-
-    # mm_tbuf_t *mm_tbuf_init(void);
-    attach_function \
-      :mm_tbuf_init,
-      [],
-      TBuf.by_ref
-
-    # void mm_tbuf_destroy(mm_tbuf_t *b);
-    attach_function \
-      :mm_tbuf_destroy,
-      [TBuf.by_ref],
-      :void
-
-    # void *mm_tbuf_get_km(mm_tbuf_t *b);
-    attach_function \
-      :mm_tbuf_get_km,
-      [TBuf.by_ref],
-      :pointer
-
-    # mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name);
-    attach_function \
-      :mm_map,
-      [Idx.by_ref, :int, :string, :pointer, TBuf.by_ref, MapOpt.by_ref, :string],
-      Reg1.by_ref
-
-    # void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname);
-    attach_function \
-      :mm_map_frag,
-      [Idx.by_ref, :int, :pointer, :pointer, :pointer, :pointer, TBuf.by_ref, MapOpt.by_ref, :string],
-      :void
-
-    # int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads);
-    attach_function \
-      :mm_map_file,
-      [Idx.by_ref, :string, MapOpt.by_ref, :int],
-      :int
-
-    # int mm_map_file_frag(const mm_idx_t *idx, int n_segs, const char **fn, const mm_mapopt_t *opt, int n_threads);
-    attach_function \
-      :mm_map_file_frag,
-      [Idx.by_ref, :int, :pointer, MapOpt.by_ref, :int],
-      :int
-
-    # int mm_gen_cs(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int no_iden);
-    attach_function \
-      :mm_gen_cs,
-      [:pointer, :pointer, :pointer, Idx.by_ref, Reg1.by_ref, :string, :int],
-      :int
-
-    # int mm_gen_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq);
-    attach_function \
-      :mm_gen_md, :mm_gen_MD, # Avoid uppercase letters in method names.
-      [:pointer, :pointer, :pointer, Idx.by_ref, Reg1.by_ref, :string],
-      :int
-
-    # int mm_idx_index_name(mm_idx_t *mi);
-    attach_function \
-      :mm_idx_index_name,
-      [Idx.by_ref],
-      :int
-
-    # int mm_idx_name2id(const mm_idx_t *mi, const char *name);
-    attach_function \
-      :mm_idx_name2id,
-      [Idx.by_ref, :string],
-      :int
-
-    # int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
-    attach_function \
-      :mm_idx_getseq,
-      [Idx.by_ref, :uint32, :uint32, :uint32, :pointer],
-      :int
-
-    # int mm_idx_alt_read(mm_idx_t *mi, const char *fn);
-    attach_function \
-      :mm_idx_alt_read,
-      [Idx.by_ref, :string],
-      :int
-
-    # int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc);
-    attach_function \
-      :mm_idx_bed_read,
-      [Idx.by_ref, :string, :int],
-      :int
-
-    # int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s);
-    attach_function \
-      :mm_idx_bed_junc,
-      [Idx.by_ref, :int32, :int32, :int32, :pointer],
-      :int
-
-    # int mm_max_spsc_bonus(const mm_mapopt_t *mo);
-    attach_function \
-      :mm_max_spsc_bonus,
-      [MapOpt.by_ref],
-      :int
-
-    # int32_t mm_idx_spsc_read(mm_idx_t *idx, const char *fn, int32_t max_sc);
-    attach_function \
-      :mm_idx_spsc_read,
-      [Idx.by_ref, :string, :int32],
-      :int32
-
-    # int32_t mm_idx_spsc_read2(mm_idx_t *idx, const char *fn, int32_t max_sc, float scale);
-    attach_function \
-      :mm_idx_spsc_read2,
-      [Idx.by_ref, :string, :int32, :float],
-      :int32
-
-    # int64_t mm_idx_spsc_get(const mm_idx_t *db, int32_t cid, int64_t st0, int64_t en0, int32_t rev, uint8_t *sc);
-    attach_function \
-      :mm_idx_spsc_get,
-      [Idx.by_ref, :int32, :int64, :int64, :int32, :pointer],
-      :int64
-
-    # void mm_mapopt_init(mm_mapopt_t *opt);
-    attach_function \
-      :mm_mapopt_init,
-      [MapOpt.by_ref],
-      :void
-
-    # mm_idx_t *mm_idx_build(const char *fn, int w, int k, int flag, int n_threads);
-    attach_function \
-      :mm_idx_build,
-      %i[string int int int int],
-      Idx.by_ref
-
-    # mmpriv.h
-
-    attach_function \
-      :mm_idxopt_init,
-      [IdxOpt.by_ref],
-      :void
-  end
-end