minimap2 0.2.23.1 → 0.2.24.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: f9729fda39fc510adf028d0aea9736ef247201d850f22cfad4821e40253ec26e
+  data.tar.gz: ef6d69949647da93a9a971cfe001060c18053c6075b3a3facff21c80634a835f
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data/ext/Rakefile

@@ -1,40 +1,52 @@
-require 'rake'
+# frozen_string_literal: true
 
-libsuffix = RbConfig::CONFIG['SOEXT']
-minimap2_dir = File.expand_path('minimap2', __dir__)
-target_dir = '../../vendor'
-target_fname = "libminimap2.#{libsuffix}"
+require "rake"
+require "fileutils"
+require "ffi"
+
+minimap2_dir = File.expand_path("minimap2", __dir__)
+target_dir = "../../vendor"
+target_fname = FFI.map_library_name("minimap2")
 target_path = File.join(target_dir, target_fname)
 
-task default: 'minimap2:build'
+task default: ["minimap2:build", "minimap2:clean"]
 
 namespace :minimap2 do
-  desc 'Compile Minimap2'
+  desc "Compile Minimap2"
   task :build do
     Dir.chdir(minimap2_dir) do
       # Add -fPIC option to Makefile
-      sh 'git apply ../minimap2.patch'
-      sh 'cp ../cmappy/cmappy.h ../cmappy/cmappy.c .'
-      sh 'make'
-      case RbConfig::CONFIG['host_os']
+      sh "git apply ../minimap2.patch"
+      sh "cp ../cmappy/cmappy.h ../cmappy/cmappy.c ."
+      sh "make"
+      case RbConfig::CONFIG["host_os"]
       when /mswin|msys|mingw|cygwin|bccwin|wince|emc/
-        warn 'windows not supported'
+        sh "cc *.o -shared -o #{target_fname} -lm -lz -lpthread"
       when /darwin|mac os/
         sh "clang -dynamiclib -undefined dynamic_lookup -o #{target_fname} *.o"
       else
-        sh "cc -shared -o #{target_fname} *.o"
+        sh "cc -shared -o #{target_fname} -lm -lz -lpthread *.o"
       end
-      sh 'rm cmappy.h cmappy.c'
-      sh 'git apply -R ../minimap2.patch'
-      sh "mkdir -p #{target_dir}"
+      sh "rm cmappy.h cmappy.c"
+      sh "git apply -R ../minimap2.patch"
+      FileUtils.mkdir_p(target_dir)
+      warn "mkdir -p #{target_dir}"
       sh "mv #{target_fname} #{target_path}"
     end
   end
 
-  desc 'Cleanup'
+  desc "Clean"
   task :clean do
     Dir.chdir(minimap2_dir) do
-      sh 'make clean'
+      sh "make clean"
+    end
+  end
+
+  task cleanall: [:clean]
+
+  desc "Clean all"
+  task :cleanall do
+    Dir.chdir(minimap2_dir) do
       sh "rm #{target_path}" if File.exist?(target_path)
     end
   end

data/ext/minimap2/NEWS.md

@@ -1,3 +1,17 @@
+Release 2.24-r1122 (26 December 2021)
+-------------------------------------
+
+This release improves alignment around long poorly aligned regions. Older
+minimap2 may chain through such regions in rare cases which may result in
+missing alignments later. The issue has become worse since the the change of
+the chaining algorithm in v2.19. v2.23 implements an incomplete remedy. This
+release provides a better solution with a X-drop-like heuristic and by enabling
+two-bandwidth chaining in the assembly mode.
+
+(2.24: 26 December 2021, r1122)
+
+
+
 Release 2.23-r1111 (18 November 2021)
 -------------------------------------
 

data/ext/minimap2/README.md

@@ -74,8 +74,8 @@ Detailed evaluations are available from the [minimap2 paper][doi] or the
 Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
 the [release page][release] with:
 ```sh
-curl -L https://github.com/lh3/minimap2/releases/download/v2.23/minimap2-2.23_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.23_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.24_x64-linux/minimap2
 ```
 If you want to compile from the source, you need to have a C compiler, GNU make
 and zlib development files installed. Then type `make` in the source code

data/ext/minimap2/cookbook.md

@@ -31,8 +31,8 @@ To acquire the data used in this cookbook and to install minimap2 and paftools,
 please follow the command lines below:
 ```sh
 # install minimap2 executables
-curl -L https://github.com/lh3/minimap2/releases/download/v2.23/minimap2-2.23_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.23_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.24_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
 export PATH="$PATH:"`pwd`                               # put the current directory on PATH
 # download example datasets
 curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -

data/ext/minimap2/hit.c

@@ -279,7 +279,7 @@ int mm_filter_strand_retained(int n_regs, mm_reg1_t *r)
 	int i, k;
 	for (i = k = 0; i < n_regs; ++i) {
 		int p = r[i].parent;
-		if (!r[i].strand_retained || r[i].div < r[p].div * 5.0f) {
+		if (!r[i].strand_retained || r[i].div < r[p].div * 5.0f || r[i].div < 0.01f) {
 			if (k < i) r[k++] = r[i];
 			else ++k;
 		}

data/ext/minimap2/lchain.c

@@ -6,7 +6,25 @@
 #include "kalloc.h"
 #include "krmq.h"
 
-uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_t *p, int32_t *v, int32_t *t, int32_t min_cnt, int32_t min_sc, int32_t *n_u_, int32_t *n_v_)
+static int64_t mg_chain_bk_end(int32_t max_drop, const mm128_t *z, const int32_t *f, const int64_t *p, int32_t *t, int64_t k)
+{
+	int64_t i = z[k].y, end_i = -1, max_i = i;
+	int32_t max_s = 0;
+	if (i < 0 || t[i] != 0) return i;
+	do {
+		int32_t s;
+		t[i] = 2;
+		end_i = i = p[i];
+		s = i < 0? z[k].x : (int32_t)z[k].x - f[i];
+		if (s > max_s) max_s = s, max_i = i;
+		else if (max_s - s > max_drop) break;
+	} while (i >= 0 && t[i] == 0);
+	for (i = z[k].y; i >= 0 && i != end_i; i = p[i]) // reset modified t[]
+		t[i] = 0;
+	return max_i;
+}
+
+uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_t *p, int32_t *v, int32_t *t, int32_t min_cnt, int32_t min_sc, int32_t max_drop, int32_t *n_u_, int32_t *n_v_)
 {
 	mm128_t *z;
 	uint64_t *u;
@@ -24,26 +42,32 @@ uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_
 
 	memset(t, 0, n * 4);
 	for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // precompute n_u
-		int64_t n_v0 = n_v;
-		int32_t sc;
-		for (i = z[k].y; i >= 0 && t[i] == 0; i = p[i])
-			++n_v, t[i] = 1;
-		sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
-		if (sc >= min_sc && n_v > n_v0 && n_v - n_v0 >= min_cnt)
-			++n_u;
-		else n_v = n_v0;
+		if (t[z[k].y] == 0) {
+			int64_t n_v0 = n_v, end_i;
+			int32_t sc;
+			end_i = mg_chain_bk_end(max_drop, z, f, p, t, k);
+			for (i = z[k].y; i != end_i; i = p[i])
+				++n_v, t[i] = 1;
+			sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
+			if (sc >= min_sc && n_v > n_v0 && n_v - n_v0 >= min_cnt)
+				++n_u;
+			else n_v = n_v0;
+		}
 	}
 	KMALLOC(km, u, n_u);
 	memset(t, 0, n * 4);
 	for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // populate u[]
-		int64_t n_v0 = n_v;
-		int32_t sc;
-		for (i = z[k].y; i >= 0 && t[i] == 0; i = p[i])
-			v[n_v++] = i, t[i] = 1;
-		sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
-		if (sc >= min_sc && n_v > n_v0 && n_v - n_v0 >= min_cnt)
-			u[n_u++] = (uint64_t)sc << 32 | (n_v - n_v0);
-		else n_v = n_v0;
+		if (t[z[k].y] == 0) {
+			int64_t n_v0 = n_v, end_i;
+			int32_t sc;
+			end_i = mg_chain_bk_end(max_drop, z, f, p, t, k);
+			for (i = z[k].y; i != end_i; i = p[i])
+				v[n_v++] = i, t[i] = 1;
+			sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
+			if (sc >= min_sc && n_v > n_v0 && n_v - n_v0 >= min_cnt)
+				u[n_u++] = (uint64_t)sc << 32 | (n_v - n_v0);
+			else n_v = n_v0;
+		}
 	}
 	kfree(km, z);
 	assert(n_v < INT32_MAX);
@@ -124,7 +148,7 @@ static inline int32_t comput_sc(const mm128_t *ai, const mm128_t *aj, int32_t ma
 mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
 					  int is_cdna, int n_seg, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
 { // TODO: make sure this works when n has more than 32 bits
-	int32_t *f, *t, *v, n_u, n_v, mmax_f = 0;
+	int32_t *f, *t, *v, n_u, n_v, mmax_f = 0, max_drop = bw;
 	int64_t *p, i, j, max_ii, st = 0, n_iter = 0;
 	uint64_t *u;
 
@@ -135,6 +159,7 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
 	}
 	if (max_dist_x < bw) max_dist_x = bw;
 	if (max_dist_y < bw && !is_cdna) max_dist_y = bw;
+	if (is_cdna) max_drop = INT32_MAX;
 	KMALLOC(km, p, n);
 	KMALLOC(km, f, n);
 	KMALLOC(km, v, n);
@@ -181,7 +206,7 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
 		if (mmax_f < max_f) mmax_f = max_f;
 	}
 
-	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, &n_u, &n_v);
+	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
 	*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
 	kfree(km, p); kfree(km, f); kfree(km, t);
 	if (n_u == 0) {
@@ -225,7 +250,7 @@ static inline int32_t comput_sc_simple(const mm128_t *ai, const mm128_t *aj, flo
 mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_skip, int cap_rmq_size, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
 					   int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
 {
-	int32_t *f,*t, *v, n_u, n_v, mmax_f = 0, max_rmq_size = 0;
+	int32_t *f,*t, *v, n_u, n_v, mmax_f = 0, max_rmq_size = 0, max_drop = bw;
 	int64_t *p, i, i0, st = 0, st_inner = 0, n_iter = 0;
 	uint64_t *u;
 	lc_elem_t *root = 0, *root_inner = 0;
@@ -333,7 +358,7 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
 	}
 	km_destroy(mem_mp);
 
-	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, &n_u, &n_v);
+	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
 	*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
 	kfree(km, p); kfree(km, f); kfree(km, t);
 	if (n_u == 0) {

data/ext/minimap2/main.c

@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.23-r1111"
+#define MM_VERSION "2.24-r1122"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -76,6 +76,8 @@ static ko_longopt_t long_options[] = {
 	{ "cap-kalloc",     ko_required_argument, 349 },
 	{ "q-occ-frac",     ko_required_argument, 350 },
 	{ "chain-skip-scale",ko_required_argument,351 },
+	{ "print-chains",   ko_no_argument,       352 },
+	{ "no-hash-name",   ko_no_argument,       353 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
 	{ "version",        ko_no_argument,       'V' },
@@ -233,6 +235,8 @@ int main(int argc, char *argv[])
 		else if (c == 348) opt.flag |= MM_F_QSTRAND | MM_F_NO_INV; // --qstrand
 		else if (c == 349) opt.cap_kalloc = mm_parse_num(o.arg); // --cap-kalloc
 		else if (c == 350) opt.q_occ_frac = atof(o.arg); // --q-occ-frac
+		else if (c == 352) mm_dbg_flag |= MM_DBG_PRINT_CHAIN; // --print-chains
+		else if (c == 353) opt.flag |= MM_F_NO_HASH_NAME; // --no-hash-name
 		else if (c == 330) {
 			fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
 		} else if (c == 314) { // --frag

data/ext/minimap2/map.c

@@ -248,7 +248,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 	if (qlen_sum == 0 || n_segs <= 0 || n_segs > MM_MAX_SEG) return;
 	if (opt->max_qlen > 0 && qlen_sum > opt->max_qlen) return;
 
-	hash  = qname? __ac_X31_hash_string(qname) : 0;
+	hash  = qname && !(opt->flag & MM_F_NO_HASH_NAME)? __ac_X31_hash_string(qname) : 0;
 	hash ^= __ac_Wang_hash(qlen_sum) + __ac_Wang_hash(opt->seed);
 	hash  = __ac_Wang_hash(hash);
 
@@ -328,7 +328,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 		mm_hit_sort(b->km, &n_regs0, regs0, opt->alt_drop); // this step can be merged into mm_gen_regs(); will do if this shows up in profile
 	}
 
-	if (mm_dbg_flag & MM_DBG_PRINT_SEED)
+	if (mm_dbg_flag & (MM_DBG_PRINT_SEED|MM_DBG_PRINT_CHAIN))
 		for (j = 0; j < n_regs0; ++j)
 			for (i = regs0[j].as; i < regs0[j].as + regs0[j].cnt; ++i)
 				fprintf(stderr, "CN\t%d\t%s\t%d\t%c\t%d\t%d\t%d\n", j, mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),

data/ext/minimap2/minimap.h

@@ -39,6 +39,7 @@
 #define MM_F_RMQ           (0x80000000LL)
 #define MM_F_QSTRAND       (0x100000000LL)
 #define MM_F_NO_INV        (0x200000000LL)
+#define MM_F_NO_HASH_NAME  (0x400000000LL)
 
 #define MM_I_HPC          0x1
 #define MM_I_NO_SEQ       0x2

data/ext/minimap2/minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "18 November 2021" "minimap2-2.23 (r1111)" "Bioinformatics tools"
+.TH minimap2 1 "18 December 2021" "minimap2-2.24 (r1122)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -77,7 +77,7 @@ SAM format.
 Minimizer k-mer length [15]
 .TP
 .BI -w \ INT
-Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer
+Minimizer window size [10]. A minimizer is the smallest k-mer
 in a window of w consecutive k-mers.
 .TP
 .B -H
@@ -318,6 +318,9 @@ faster for short reads, but slower for long reads. [no]
 .B --no-pairing
 Treat two reads in a pair as independent reads. The mate related fields in SAM
 are still properly populated.
+.TP
+.B --no-hash-name
+Produce the same alignment for identical sequences regardless of their sequence names.
 .SS Alignment options
 .TP 10
 .BI -A \ INT
@@ -562,7 +565,7 @@ Align older PacBio continuous long (CLR) reads to a reference genome
 .B asm5
 Long assembly to reference mapping
 .RB ( -k19
-.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
+.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
 .BR -N50 ).
 Typically, the alignment will not extend to regions with 5% or higher sequence
 divergence. Only use this preset if the average divergence is far below 5%.
@@ -570,14 +573,14 @@ divergence. Only use this preset if the average divergence is far below 5%.
 .B asm10
 Long assembly to reference mapping
 .RB ( -k19
-.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
+.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
 .BR -N50 ).
 Up to 10% sequence divergence.
 .TP
 .B asm20
 Long assembly to reference mapping
 .RB ( -k19
-.B -w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
+.B -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
 .BR -N50 ).
 Up to 20% sequence divergence.
 .TP
@@ -603,7 +606,7 @@ Long-read splice alignment for PacBio CCS reads
 .B sr
 Short single-end reads without splicing
 .RB ( -k21
-.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m20
+.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m25
 .B -s40 -g100 -2K50m --heap-sort=yes
 .BR --secondary=no ).
 .TP

data/ext/minimap2/misc/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.23-r1111';
+var paftools_version = '2.24-r1122';
 
 /*****************************
  ***** Library functions *****

data/ext/minimap2/mmpriv.h

@@ -13,6 +13,7 @@
 #define MM_DBG_PRINT_QNAME   0x2
 #define MM_DBG_PRINT_SEED    0x4
 #define MM_DBG_PRINT_ALN_SEQ 0x8
+#define MM_DBG_PRINT_CHAIN   0x10
 
 #define MM_SEED_LONG_JOIN  (1ULL<<40)
 #define MM_SEED_IGNORE     (1ULL<<41)

data/ext/minimap2/options.c

@@ -74,6 +74,7 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
 		if (opt->max_mid_occ > opt->min_mid_occ && opt->mid_occ > opt->max_mid_occ)
 			opt->mid_occ = opt->max_mid_occ;
 	}
+	if (opt->bw_long < opt->bw) opt->bw_long = opt->bw;
 	if (mm_verbose >= 3)
 		fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), opt->mid_occ);
 }
@@ -113,7 +114,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		mo->min_dp_max = 200;
 	} else if (strncmp(preset, "asm", 3) == 0) {
 		io->flag = 0, io->k = 19, io->w = 19;
-		mo->bw = mo->bw_long = 100000;
+		mo->bw = 1000, mo->bw_long = 100000;
 		mo->max_gap = 10000;
 		mo->flag |= MM_F_RMQ;
 		mo->min_mid_occ = 50, mo->max_mid_occ = 500;

data/ext/minimap2/python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.23'
+__version__ = '2.24'
 
 cmappy.mm_reset_timer()
 

data/ext/minimap2/setup.py

@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.23',
+	version = '2.24',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),

data/lib/minimap2/aligner.rb

@@ -90,7 +90,7 @@ module Minimap2
       end
 
       if fn_idx_in
-        warn 'Since fn_idx_in is specified, the seq argument will be ignored.' if seq
+        warn "Since fn_idx_in is specified, the seq argument will be ignored." if seq
         reader = FFI.mm_idx_reader_open(fn_idx_in, idx_opt, fn_idx_out)
 
         # The Ruby version raises an error here
@@ -169,13 +169,13 @@ module Minimap2
           c = hit[:cigar32].read_array_of_uint32(hit[:n_cigar32])
           cigar = c.map { |x| [x >> 4, x & 0xf] } # 32-bit CIGAR encoding -> Ruby array
 
-          _cs = ''
+          _cs = ""
           if cs
             l_cs_str = FFI.mm_gen_cs(km, cs_str, m_cs_str, @index, regs[i], seq, 1)
             _cs = cs_str.read_pointer.read_string(l_cs_str)
           end
 
-          _md = ''
+          _md = ""
           if md
             l_cs_str = FFI.mm_gen_md(km, cs_str, m_cs_str, @index, regs[i], seq)
             _md = cs_str.read_pointer.read_string(l_cs_str)
@@ -204,7 +204,7 @@ module Minimap2
       lp = ::FFI::MemoryPointer.new(:int)
       s = FFI.mappy_fetch_seq(index, name, start, stop, lp)
       l = lp.read_int
-      return nil if l.zero?
+      return nil if l == 0
 
       s.read_string(l)
     end

data/lib/minimap2/alignment.rb

@@ -89,20 +89,20 @@ module Minimap2
     # Convert to the PAF format without the QueryName and QueryLength columns.
 
     def to_s
-      strand = if @strand.positive?
-                 '+'
-               elsif @strand.negative?
-                 '-'
+      strand = if @strand > 0
+                 "+"
+               elsif @strand < 0
+                 "-"
                else
-                 '?'
+                 "?"
                end
-      tp = @primary != 0 ? 'tp:A:P' : 'tp:A:S'
-      ts = if @trans_strand.positive?
-             'ts:A:+'
-           elsif @trans_strand.negative?
-             'ts:A:-'
+      tp = @primary != 0 ? "tp:A:P" : "tp:A:S"
+      ts = if @trans_strand > 0
+             "ts:A:+"
+           elsif @trans_strand < 0
+             "ts:A:-"
            else
-             'ts:A:.'
+             "ts:A:."
            end
       a = [@q_st, @q_en, strand, @ctg, @ctg_len, @r_st, @r_en,
            @mlen, @blen, @mapq, tp, ts, "cg:Z:#{@cigar_str}"]

data/lib/minimap2/ffi/constants.rb

@@ -36,7 +36,8 @@ module Minimap2
     SAM_HIT_ONLY     = 0x40000000
     RMQ              = 0x80000000  # LL
     QSTRAND          = 0x100000000 # LL
-    NO_INV           = 0x200000000
+    NO_INV           = 0x200000000 # LL
+    NO_HASH_NAME     = 0x400000000 # LL
 
     HPC              = 0x1
     NO_SEQ           = 0x2
@@ -56,7 +57,7 @@ module Minimap2
     CIGAR_EQ_MATCH   = 7
     CIGAR_X_MISMATCH = 8
 
-    CIGAR_STR        = 'MIDNSHP=XB'
+    CIGAR_STR        = "MIDNSHP=XB"
 
     # emulate 128-bit integers
     class MM128 < ::FFI::Struct

data/lib/minimap2/ffi.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 # bit fields
-require 'ffi/bit_struct'
+require "ffi/bit_struct"
 module Minimap2
   # Native APIs
   module FFI
@@ -21,6 +21,6 @@ module Minimap2
   end
 end
 
-require_relative 'ffi/constants'
-require_relative 'ffi/functions'
-require_relative 'ffi/mappy'
+require_relative "ffi/constants"
+require_relative "ffi/functions"
+require_relative "ffi/mappy"

data/lib/minimap2/version.rb

@@ -2,5 +2,5 @@
 
 module Minimap2
   # Minimap2-2.23 (r1111)
-  VERSION = '0.2.23.1'
+  VERSION = "0.2.24.0"
 end

data/lib/minimap2.rb

@@ -1,12 +1,12 @@
 # frozen_string_literal: true
 
 # dependencies
-require 'ffi'
+require "ffi"
 
 # modules
-require_relative 'minimap2/aligner'
-require_relative 'minimap2/alignment'
-require_relative 'minimap2/version'
+require_relative "minimap2/aligner"
+require_relative "minimap2/alignment"
+require_relative "minimap2/version"
 
 # Minimap2 mapper for long read sequences
 # https://github.com/lh3/minimap2
@@ -19,19 +19,18 @@ module Minimap2
     attr_accessor :ffi_lib
   end
 
-  lib_name = ::FFI.map_library_name('minimap2')
-  self.ffi_lib = if ENV['MINIMAPDIR']
-                   File.expand_path(lib_name, ENV['MINIMAPDIR'])
+  lib_name = ::FFI.map_library_name("minimap2")
+  self.ffi_lib = if ENV["MINIMAPDIR"]
+                   File.expand_path(lib_name, ENV["MINIMAPDIR"])
                  else
                    File.expand_path("../vendor/#{lib_name}", __dir__)
                  end
 
   # friendlier error message
-  autoload :FFI, 'minimap2/ffi'
+  autoload :FFI, "minimap2/ffi"
 
   # methods from mappy
   class << self
-
     # Execute minimap2 comannd with given options.
     # @overload  execute(arg0,arg1,...)
     # @param [String] arg minimap2 command option.
@@ -41,27 +40,35 @@ module Minimap2
     def Minimap2.execute(*rb_argv)
       str_ptrs = []
       # First argument is the program name.
-      str_ptrs << ::FFI::MemoryPointer.from_string('minimap2')
+      str_ptrs << ::FFI::MemoryPointer.from_string("minimap2")
       rb_argv.each do |arg|
         arg.to_s.split(/\s+/).each do |s|
           str_ptrs << ::FFI::MemoryPointer.from_string(s)
         end
       end
-      strptrs << nil
+      str_ptrs << nil
 
       # Load all the pointers into a native memory block
-      argv = ::FFI::MemoryPointer.new(:pointer, strptrs.length)
-      strptrs.each_with_index do |p, i|
+      argv = ::FFI::MemoryPointer.new(:pointer, str_ptrs.length)
+      str_ptrs.each_with_index do |p, i|
         argv[i].put_pointer(0,  p)
       end
 
-      FFI.main(strptrs.length - 1, argv)
+      FFI.main(str_ptrs.length - 1, argv)
+    end
+
+    # Get verbosity level.
+    # @return [Integer] verbosity level.
+
+    def verbose
+      FFI.mm_verbose_level(-1)
     end
 
     # Set verbosity level.
-    # @param [Integer] level
+    # @param [Integer] verbosity level
+    # @return [Integer] verbosity level.
 
-    def verbose(level = -1)
+    def verbose=(level)
       FFI.mm_verbose_level(level)
     end
 
@@ -109,11 +116,11 @@ module Minimap2
     end
 
     def fastx_next(ks, read_comment)
-      qual = ks[:qual][:s] if (ks[:qual][:l]).positive?
+      qual = ks[:qual][:s] if (ks[:qual][:l]) > 0
       name = ks[:name][:s]
       seq  = ks[:seq][:s]
       if read_comment
-        comment = ks[:comment][:s] if (ks[:comment][:l]).positive?
+        comment = ks[:comment][:s] if (ks[:comment][:l]) > 0
         [name, seq, qual, comment]
       else
         [name, seq, qual]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.23.1
+  version: 0.2.24.0
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-12-16 00:00:00.000000000 Z
+date: 2021-12-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -137,7 +137,6 @@ files:
 - ext/minimap2/tex/ngmlr.eval
 - ext/minimap2/tex/roc.gp
 - ext/minimap2/tex/snap-s3.sam.eval
-- ext/vendor/libminimap2.so
 - lib/minimap2.rb
 - lib/minimap2/aligner.rb
 - lib/minimap2/alignment.rb
@@ -165,7 +164,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.26
+rubygems_version: 3.3.3
 signing_key: 
 specification_version: 4
 summary: minimap2