minimap2 0.2.23.0 → 0.2.23.1

data/ext/minimap2/tex/ngmlr.eval

@@ -0,0 +1,38 @@
+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

@@ -0,0 +1,60 @@
+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

@@ -0,0 +1,62 @@
+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

@@ -0,0 +1,19 @@
+--- Makefile.org	2021-05-27 15:45:11.993128205 +0900
++++ Makefile	2021-05-27 15:46:02.320569154 +0900
+@@ -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 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
+@@ -130,3 +130,4 @@ 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/functions.rb

@@ -2,6 +2,11 @@
 
 module Minimap2
   module FFI
+    attach_function \
+      :main,
+      %i[int pointer],
+      :int
+
     attach_function \
       :mm_set_opt_raw, :mm_set_opt,
       [:pointer, IdxOpt.by_ref, MapOpt.by_ref],

data/lib/minimap2/version.rb

@@ -2,5 +2,5 @@
 
 module Minimap2
   # Minimap2-2.23 (r1111)
-  VERSION = '0.2.23.0'
+  VERSION = '0.2.23.1'
 end

data/lib/minimap2.rb

@@ -31,6 +31,33 @@ module Minimap2
 
   # methods from mappy
   class << self
+
+    # Execute minimap2 comannd with given options.
+    # @overload  execute(arg0,arg1,...)
+    # @param [String] arg minimap2 command option.
+    # @example Get minimap2 version
+    #   Minimap2.execute('--version')
+
+    def Minimap2.execute(*rb_argv)
+      str_ptrs = []
+      # First argument is the program name.
+      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
+
+      # Load all the pointers into a native memory block
+      argv = ::FFI::MemoryPointer.new(:pointer, strptrs.length)
+      strptrs.each_with_index do |p, i|
+        argv[i].put_pointer(0,  p)
+      end
+
+      FFI.main(strptrs.length - 1, argv)
+    end
+
     # Set verbosity level.
     # @param [Integer] level
 
@@ -47,7 +74,12 @@ module Minimap2
 
     def fastx_read(file_path, comment: false, &block)
       path = File.expand_path(file_path)
+
+      # raise error in Ruby because ks.null? is false even if file not exist.
+      raise ArgumentError, "File not found: #{path}" unless File.exist?(path)
+
       ks = FFI.mm_fastx_open(path)
+
       if block_given?
         fastx_each(ks, comment, &block)
       else

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.23.0
+  version: 0.2.23.1
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-11-19 00:00:00.000000000 Z
+date: 2021-12-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -42,11 +42,102 @@ description: Ruby bindings to the Minimap2 aligner.
 email:
 - 2xijok@gmail.com
 executables: []
-extensions: []
+extensions:
+- ext/Rakefile
 extra_rdoc_files: []
 files:
 - LICENSE.txt
 - README.md
+- ext/Rakefile
+- ext/cmappy/cmappy.c
+- ext/cmappy/cmappy.h
+- ext/minimap2.patch
+- ext/minimap2/FAQ.md
+- ext/minimap2/LICENSE.txt
+- ext/minimap2/MANIFEST.in
+- ext/minimap2/Makefile
+- ext/minimap2/Makefile.simde
+- ext/minimap2/NEWS.md
+- ext/minimap2/README.md
+- ext/minimap2/align.c
+- ext/minimap2/bseq.c
+- ext/minimap2/bseq.h
+- ext/minimap2/code_of_conduct.md
+- ext/minimap2/cookbook.md
+- ext/minimap2/esterr.c
+- ext/minimap2/example.c
+- ext/minimap2/format.c
+- ext/minimap2/hit.c
+- ext/minimap2/index.c
+- ext/minimap2/kalloc.c
+- ext/minimap2/kalloc.h
+- ext/minimap2/kdq.h
+- ext/minimap2/ketopt.h
+- ext/minimap2/khash.h
+- ext/minimap2/krmq.h
+- ext/minimap2/kseq.h
+- ext/minimap2/ksort.h
+- ext/minimap2/ksw2.h
+- ext/minimap2/ksw2_dispatch.c
+- ext/minimap2/ksw2_extd2_sse.c
+- ext/minimap2/ksw2_exts2_sse.c
+- ext/minimap2/ksw2_extz2_sse.c
+- ext/minimap2/ksw2_ll_sse.c
+- ext/minimap2/kthread.c
+- ext/minimap2/kthread.h
+- ext/minimap2/kvec.h
+- ext/minimap2/lchain.c
+- ext/minimap2/main.c
+- ext/minimap2/map.c
+- ext/minimap2/minimap.h
+- ext/minimap2/minimap2.1
+- ext/minimap2/misc.c
+- ext/minimap2/misc/README.md
+- ext/minimap2/misc/mmphase.js
+- ext/minimap2/misc/paftools.js
+- ext/minimap2/mmpriv.h
+- ext/minimap2/options.c
+- ext/minimap2/pe.c
+- ext/minimap2/python/README.rst
+- ext/minimap2/python/cmappy.h
+- ext/minimap2/python/cmappy.pxd
+- ext/minimap2/python/mappy.pyx
+- ext/minimap2/python/minimap2.py
+- ext/minimap2/sdust.c
+- ext/minimap2/sdust.h
+- ext/minimap2/seed.c
+- ext/minimap2/setup.py
+- ext/minimap2/sketch.c
+- ext/minimap2/splitidx.c
+- ext/minimap2/sse2neon/emmintrin.h
+- ext/minimap2/test/MT-human.fa
+- ext/minimap2/test/MT-orang.fa
+- ext/minimap2/test/q-inv.fa
+- ext/minimap2/test/q2.fa
+- ext/minimap2/test/t-inv.fa
+- ext/minimap2/test/t2.fa
+- ext/minimap2/tex/Makefile
+- ext/minimap2/tex/bioinfo.cls
+- ext/minimap2/tex/blasr-mc.eval
+- ext/minimap2/tex/bowtie2-s3.sam.eval
+- ext/minimap2/tex/bwa-s3.sam.eval
+- ext/minimap2/tex/bwa.eval
+- ext/minimap2/tex/eval2roc.pl
+- ext/minimap2/tex/graphmap.eval
+- ext/minimap2/tex/hs38-simu.sh
+- ext/minimap2/tex/minialign.eval
+- ext/minimap2/tex/minimap2.bib
+- ext/minimap2/tex/minimap2.tex
+- ext/minimap2/tex/mm2-s3.sam.eval
+- ext/minimap2/tex/mm2-update.tex
+- ext/minimap2/tex/mm2.approx.eval
+- ext/minimap2/tex/mm2.eval
+- ext/minimap2/tex/natbib.bst
+- ext/minimap2/tex/natbib.sty
+- 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
@@ -55,7 +146,6 @@ files:
 - lib/minimap2/ffi/functions.rb
 - lib/minimap2/ffi/mappy.rb
 - lib/minimap2/version.rb
-- vendor/libminimap2.so
 homepage: https://github.com/kojix2/ruby-minimap2
 licenses:
 - MIT