bioseqalign 0.0.2 → 0.0.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml ADDED
@@ -0,0 +1,7 @@
1
+ ---
2
+ SHA1:
3
+ metadata.gz: 0b96dd84832f04c18f665123a094d288a91c3030
4
+ data.tar.gz: 96d9c502f30a612eec662baeec5f0a275714e912
5
+ SHA512:
6
+ metadata.gz: 792e24c7020440b3377f9c4f9218b21bdf5c986d582d2ffcf76f0292547d938353544fafe20b02fc2e0a9fe65e622736782e13ca8903807e2a5977c25e407206
7
+ data.tar.gz: fb8c79b054f34495d921307902e0554841e2771742065243912c4a8ff0bf332ede46b8ccbbdcd1cab60884a3575b61b8aa4df3bdf22242dc8a8fc2c027caf678
@@ -5,37 +5,68 @@ SHELL = /bin/sh
5
5
  V = 0
6
6
  Q1 = $(V:1=)
7
7
  Q = $(Q1:0=@)
8
- n=$(NULLCMD)
9
- ECHO1 = $(V:1=@$n)
8
+ ECHO1 = $(V:1=@:)
10
9
  ECHO = $(ECHO1:0=@echo)
10
+ NULLCMD = :
11
11
 
12
12
  #### Start of system configuration section. ####
13
13
 
14
14
  srcdir = .
15
- topdir = /usr/include/ruby-1.9.1
16
- hdrdir = /usr/include/ruby-1.9.1
17
- arch_hdrdir = /usr/include/ruby-1.9.1/$(arch)
15
+ topdir = /home/stef/.rvm/rubies/ruby-2.2.0/include/ruby-2.2.0
16
+ hdrdir = $(topdir)
17
+ arch_hdrdir = /home/stef/.rvm/rubies/ruby-2.2.0/include/ruby-2.2.0/x86_64-linux
18
+ PATH_SEPARATOR = :
18
19
  VPATH = $(srcdir):$(arch_hdrdir)/ruby:$(hdrdir)/ruby
19
20
 
20
- prefix = $(DESTDIR)/usr
21
+ prefix = $(DESTDIR)/home/stef/.rvm/rubies/ruby-2.2.0
22
+
23
+ rubysitearchprefix = $(rubylibprefix)/$(sitearch)
24
+
25
+ rubyarchprefix = $(rubylibprefix)/$(arch)
21
26
 
22
27
  rubylibprefix = $(libdir)/$(RUBY_BASE_NAME)
23
28
 
24
29
  exec_prefix = $(prefix)
25
30
 
31
+ vendorarchhdrdir = $(vendorhdrdir)/$(sitearch)
32
+
33
+ sitearchhdrdir = $(sitehdrdir)/$(sitearch)
34
+
35
+ rubyarchhdrdir = $(rubyhdrdir)/$(arch)
36
+
26
37
  vendorhdrdir = $(rubyhdrdir)/vendor_ruby
27
38
 
28
39
  sitehdrdir = $(rubyhdrdir)/site_ruby
29
40
 
30
- rubyhdrdir = $(includedir)/$(RUBY_BASE_NAME)-$(ruby_version)
41
+ rubyhdrdir = $(includedir)/$(RUBY_VERSION_NAME)
42
+
43
+ vendorarchdir = $(vendorlibdir)/$(sitearch)
44
+
45
+ vendorlibdir = $(vendordir)/$(ruby_version)
46
+
47
+ vendordir = $(rubylibprefix)/vendor_ruby
48
+
49
+ sitearchdir = $(sitelibdir)/$(sitearch)
50
+
51
+ sitelibdir = $(sitedir)/$(ruby_version)
52
+
53
+ sitedir = $(rubylibprefix)/site_ruby
54
+
55
+ rubyarchdir = $(rubylibdir)/$(arch)
56
+
57
+ rubylibdir = $(rubylibprefix)/$(ruby_version)
58
+
59
+ sitearchincludedir = $(includedir)/$(sitearch)
60
+
61
+ archincludedir = $(includedir)/$(arch)
31
62
 
32
- vendordir = $(DESTDIR)/usr/lib/ruby/vendor_ruby
63
+ sitearchlibdir = $(libdir)/$(sitearch)
33
64
 
34
- sitedir = $(DESTDIR)/usr/local/lib/site_ruby
65
+ archlibdir = $(libdir)/$(arch)
35
66
 
36
67
  ridir = $(datarootdir)/$(RI_BASE_NAME)
37
68
 
38
- mandir = $(prefix)/share/man
69
+ mandir = $(datarootdir)/man
39
70
 
40
71
  localedir = $(datarootdir)/locale
41
72
 
@@ -49,7 +80,7 @@ dvidir = $(docdir)
49
80
 
50
81
  htmldir = $(docdir)
51
82
 
52
- infodir = $(prefix)/share/info
83
+ infodir = $(datarootdir)/info
53
84
 
54
85
  docdir = $(datarootdir)/doc/$(PACKAGE)
55
86
 
@@ -57,7 +88,7 @@ oldincludedir = $(DESTDIR)/usr/include
57
88
 
58
89
  includedir = $(prefix)/include
59
90
 
60
- localstatedir = $(DESTDIR)/var
91
+ localstatedir = $(prefix)/var
61
92
 
62
93
  sharedstatedir = $(prefix)/com
63
94
 
@@ -67,48 +98,39 @@ datadir = $(datarootdir)
67
98
 
68
99
  datarootdir = $(prefix)/share
69
100
 
70
- libexecdir = $(prefix)/lib/ruby1.9.1
101
+ libexecdir = $(exec_prefix)/libexec
71
102
 
72
103
  sbindir = $(exec_prefix)/sbin
73
104
 
74
105
  bindir = $(exec_prefix)/bin
75
106
 
76
- rubylibdir = $(rubylibprefix)/$(ruby_version)
77
-
78
- archdir = $(rubylibdir)/$(arch)
79
-
80
- sitelibdir = $(sitedir)/$(ruby_version)
81
-
82
- sitearchdir = $(sitelibdir)/$(sitearch)
83
-
84
- vendorlibdir = $(vendordir)/$(ruby_version)
85
-
86
- vendorarchdir = $(vendorlibdir)/$(sitearch)
107
+ archdir = $(rubyarchdir)
87
108
 
88
109
 
89
- NULLCMD = :
90
110
 
91
111
  CC = gcc
92
112
  CXX = g++
93
113
  LIBRUBY = $(LIBRUBY_SO)
94
114
  LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
95
- LIBRUBYARG_SHARED = -l$(RUBY_SO_NAME)
96
- LIBRUBYARG_STATIC = -lruby-1.9.1-static
97
- OUTFLAG = -o
98
- COUTFLAG = -o
115
+ LIBRUBYARG_SHARED = -Wl,-rpath,'$${ORIGIN}/../lib' -Wl,-R'$${ORIGIN}/../lib' -l$(RUBY_SO_NAME)
116
+ LIBRUBYARG_STATIC = -Wl,-rpath,'${ORIGIN}/../lib' -Wl,-R'${ORIGIN}/../lib' -lruby-static
117
+ empty =
118
+ OUTFLAG = -o $(empty)
119
+ COUTFLAG = -o $(empty)
99
120
 
100
121
  RUBY_EXTCONF_H =
101
122
  cflags = $(optflags) $(debugflags) $(warnflags)
102
- optflags = -O3
103
- debugflags = -ggdb
104
- warnflags = -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wimplicit-function-declaration
105
- CFLAGS = -fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fno-strict-aliasing -fPIC $(ARCH_FLAG)
123
+ optflags = -O3 -fno-fast-math
124
+ debugflags = -ggdb3
125
+ warnflags = -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wimplicit-function-declaration -Wdeprecated-declarations -Wno-packed-bitfield-compat
126
+ CCDLFLAGS = -fPIC
127
+ CFLAGS = $(CCDLFLAGS) $(cflags) -fPIC $(ARCH_FLAG)
106
128
  INCFLAGS = -I. -I$(arch_hdrdir) -I$(hdrdir)/ruby/backward -I$(hdrdir) -I$(srcdir)
107
129
  DEFS =
108
- CPPFLAGS = -D_FORTIFY_SOURCE=2 $(DEFS) $(cppflags) -I/home/stef/ruby_gems/gems/rice-1.6.2/ruby/lib/include
130
+ CPPFLAGS = -I/home/stef/git_repos/tilapia/ext/seqan-1.3.1/ $(DEFS) $(cppflags) -I/home/stef/.rvm/gems/ruby-2.2.0/gems/rice-1.7.0/ruby/lib/include -std=c++11 -Wno-deprecated -Wno-unused-local-typedefs -Wimplicit-function-declaration -Wdeclaration-after-statement
109
131
  CXXFLAGS = $(CFLAGS) -Wall -g
110
- ldflags = -L. -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic -Wl,-export-dynamic -L/home/stef/ruby_gems/gems/rice-1.6.2/ruby/lib/lib -lrice
111
- dldflags =
132
+ ldflags = -L. -fstack-protector -rdynamic -Wl,-export-dynamic -L/home/stef/.rvm/gems/ruby-2.2.0/gems/rice-1.7.0/ruby/lib/lib -lrice
133
+ dldflags =
112
134
  ARCH_FLAG =
113
135
  DLDFLAGS = $(ldflags) $(dldflags) $(ARCH_FLAG)
114
136
  LDSHARED = g++ -shared
@@ -116,22 +138,36 @@ LDSHAREDXX = $(CXX) -shared
116
138
  AR = ar
117
139
  EXEEXT =
118
140
 
141
+
142
+ RUBY_INSTALL_NAME = $(RUBY_BASE_NAME)
143
+
144
+ RUBY_SO_NAME = ruby
145
+
146
+ RUBYW_INSTALL_NAME =
147
+
148
+ RUBY_VERSION_NAME = $(RUBY_BASE_NAME)-$(ruby_version)
149
+
150
+ RUBYW_BASE_NAME = rubyw
151
+
119
152
  RUBY_BASE_NAME = ruby
120
- RUBY_INSTALL_NAME = ruby1.9.1
121
- RUBY_SO_NAME = ruby-1.9.1
153
+
154
+
122
155
  arch = x86_64-linux
123
156
  sitearch = $(arch)
124
- ruby_version = 1.9.1
125
- ruby = /usr/bin/ruby1.9.1
157
+ ruby_version = 2.2.0
158
+ ruby = $(bindir)/$(RUBY_BASE_NAME)
126
159
  RUBY = $(ruby)
160
+ ruby_headers = $(hdrdir)/ruby.h $(hdrdir)/ruby/ruby.h $(hdrdir)/ruby/defines.h $(hdrdir)/ruby/missing.h $(hdrdir)/ruby/intern.h $(hdrdir)/ruby/st.h $(hdrdir)/ruby/subst.h $(arch_hdrdir)/ruby/config.h
161
+
127
162
  RM = rm -f
128
163
  RM_RF = $(RUBY) -run -e rm -- -rf
129
164
  RMDIRS = rmdir --ignore-fail-on-non-empty -p
130
165
  MAKEDIRS = /bin/mkdir -p
131
- INSTALL = /usr/bin/install -c
166
+ INSTALL = /usr/bin/install
132
167
  INSTALL_PROG = $(INSTALL) -m 0755
133
168
  INSTALL_DATA = $(INSTALL) -m 644
134
169
  COPY = cp
170
+ TOUCH = exit >
135
171
 
136
172
  #### End of system configuration section. ####
137
173
 
@@ -141,7 +177,7 @@ preload =
141
177
  CXX = g++
142
178
 
143
179
  libpath = . $(libdir)
144
- LIBPATH = -L. -L$(libdir)
180
+ LIBPATH = -L. -L$(libdir) -Wl,-R$(libdir)
145
181
  DEFFILE =
146
182
 
147
183
  CLEANFILES = mkmf.log
@@ -152,14 +188,19 @@ extout =
152
188
  extout_prefix =
153
189
  target_prefix =
154
190
  LOCAL_LIBS =
155
- LIBS = -lruby-1.9.1 -lpthread -lrt -ldl -lcrypt -lm -lc
156
- SRCS = PrefixSuffixAlign.cpp PairwiseAlign.cpp LocalAlign.cpp fitalgntest.cpp GlobalAlign.cpp FitAlign.cpp
191
+ LIBS = -Wl,-rpath,'${ORIGIN}/../lib' -Wl,-R'${ORIGIN}/../lib' -lruby -lpthread -ldl -lcrypt -lm -lc
192
+ ORIG_SRCS = PrefixSuffixAlign.cpp PairwiseAlign.cpp LocalAlign.cpp fitalgntest.cpp GlobalAlign.cpp FitAlign.cpp
193
+ SRCS = $(ORIG_SRCS)
157
194
  OBJS = PrefixSuffixAlign.o PairwiseAlign.o LocalAlign.o fitalgntest.o GlobalAlign.o FitAlign.o
195
+ HDRS = $(srcdir)/FitAlign.hpp $(srcdir)/GlobalAlign.hpp $(srcdir)/PrefixSuffixAlign.hpp $(srcdir)/LocalAlign.hpp $(srcdir)/PairwiseAlign.hpp
158
196
  TARGET = SeqAlign
197
+ TARGET_NAME = SeqAlign
198
+ TARGET_ENTRY = Init_$(TARGET_NAME)
159
199
  DLLIB = $(TARGET).so
160
200
  EXTSTATIC =
161
201
  STATIC_LIB =
162
202
 
203
+ TIMESTAMP_DIR = .
163
204
  BINDIR = $(bindir)
164
205
  RUBYCOMMONDIR = $(sitedir)$(target_prefix)
165
206
  RUBYLIBDIR = $(sitelibdir)$(target_prefix)
@@ -174,78 +215,100 @@ CLEANOBJS = *.o *.bak
174
215
  all: $(DLLIB)
175
216
  static: $(STATIC_LIB)
176
217
  .PHONY: all install static install-so install-rb
177
- .PHONY: clean clean-so clean-rb
218
+ .PHONY: clean clean-so clean-static clean-rb
178
219
 
220
+ clean-static::
179
221
  clean-rb-default::
180
222
  clean-rb::
181
223
  clean-so::
182
- clean: clean-so clean-rb-default clean-rb
183
- @-$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES)
224
+ clean: clean-so clean-static clean-rb-default clean-rb
225
+ -$(Q)$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES) .*.time
184
226
 
185
227
  distclean-rb-default::
186
228
  distclean-rb::
187
229
  distclean-so::
188
- distclean: clean distclean-so distclean-rb-default distclean-rb
189
- @-$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
190
- @-$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
191
- @-$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
230
+ distclean-static::
231
+ distclean: clean distclean-so distclean-static distclean-rb-default distclean-rb
232
+ -$(Q)$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
233
+ -$(Q)$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
234
+ -$(Q)$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
192
235
 
193
236
  realclean: distclean
194
237
  install: install-so install-rb
195
238
 
196
- install-so: $(RUBYARCHDIR)
197
- install-so: $(RUBYARCHDIR)/$(DLLIB)
198
- $(RUBYARCHDIR)/$(DLLIB): $(DLLIB)
199
- @-$(MAKEDIRS) $(@D)
200
- $(INSTALL_PROG) $(DLLIB) $(@D)
239
+ install-so: $(DLLIB) $(TIMESTAMP_DIR)/.RUBYARCHDIR.time
240
+ $(INSTALL_PROG) $(DLLIB) $(RUBYARCHDIR)
241
+ clean-static::
242
+ -$(Q)$(RM) $(STATIC_LIB)
201
243
  install-rb: pre-install-rb install-rb-default
202
244
  install-rb-default: pre-install-rb-default
203
245
  pre-install-rb: Makefile
204
246
  pre-install-rb-default: Makefile
205
247
  pre-install-rb-default:
206
- $(ECHO) installing default SeqAlign libraries
207
- $(RUBYARCHDIR):
208
- $(Q) $(MAKEDIRS) $@
248
+ @$(NULLCMD)
249
+ $(TIMESTAMP_DIR)/.RUBYARCHDIR.time:
250
+ $(Q) $(MAKEDIRS) $(@D) $(RUBYARCHDIR)
251
+ $(Q) $(TOUCH) $@
209
252
 
210
253
  site-install: site-install-so site-install-rb
211
254
  site-install-so: install-so
212
255
  site-install-rb: install-rb
213
256
 
214
- .SUFFIXES: .c .m .cc .mm .cxx .cpp .C .o
257
+ .SUFFIXES: .c .m .cc .mm .cxx .cpp .o .S
215
258
 
216
259
  .cc.o:
217
260
  $(ECHO) compiling $(<)
218
261
  $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
219
262
 
263
+ .cc.S:
264
+ $(ECHO) translating $(<)
265
+ $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
266
+
220
267
  .mm.o:
221
268
  $(ECHO) compiling $(<)
222
269
  $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
223
270
 
271
+ .mm.S:
272
+ $(ECHO) translating $(<)
273
+ $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
274
+
224
275
  .cxx.o:
225
276
  $(ECHO) compiling $(<)
226
277
  $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
227
278
 
279
+ .cxx.S:
280
+ $(ECHO) translating $(<)
281
+ $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
282
+
228
283
  .cpp.o:
229
284
  $(ECHO) compiling $(<)
230
285
  $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
231
286
 
232
- .C.o:
233
- $(ECHO) compiling $(<)
234
- $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
287
+ .cpp.S:
288
+ $(ECHO) translating $(<)
289
+ $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
235
290
 
236
291
  .c.o:
237
292
  $(ECHO) compiling $(<)
238
293
  $(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
239
294
 
295
+ .c.S:
296
+ $(ECHO) translating $(<)
297
+ $(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -S $<
298
+
240
299
  .m.o:
241
300
  $(ECHO) compiling $(<)
242
301
  $(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
243
302
 
303
+ .m.S:
304
+ $(ECHO) translating $(<)
305
+ $(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -S $<
306
+
244
307
  $(DLLIB): $(OBJS) Makefile
245
308
  $(ECHO) linking shared-object $(DLLIB)
246
- @-$(RM) $(@)
309
+ -$(Q)$(RM) $(@)
247
310
  $(Q) $(LDSHAREDXX) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
248
311
 
249
312
 
250
313
 
251
- $(OBJS): $(hdrdir)/ruby.h $(hdrdir)/ruby/defines.h $(arch_hdrdir)/ruby/config.h
314
+ $(OBJS): $(HDRS) $(ruby_headers)
@@ -1,2 +1,3 @@
1
1
  require 'mkmf-rice'
2
+ dir_config('seqan')
2
3
  create_makefile('SeqAlign')
@@ -0,0 +1,6 @@
1
+
2
+ module BioSeqAlign
3
+
4
+ VERSION='0.0.3'
5
+
6
+ end
metadata CHANGED
@@ -1,8 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bioseqalign
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.0.2
5
- prerelease:
4
+ version: 0.0.3
6
5
  platform: ruby
7
6
  authors:
8
7
  - Stefano R.B.
@@ -14,17 +13,15 @@ dependencies:
14
13
  - !ruby/object:Gem::Dependency
15
14
  name: rice
16
15
  requirement: !ruby/object:Gem::Requirement
17
- none: false
18
16
  requirements:
19
- - - ! '>='
17
+ - - '>='
20
18
  - !ruby/object:Gem::Version
21
19
  version: '0'
22
20
  type: :runtime
23
21
  prerelease: false
24
22
  version_requirements: !ruby/object:Gem::Requirement
25
- none: false
26
23
  requirements:
27
- - - ! '>='
24
+ - - '>='
28
25
  - !ruby/object:Gem::Version
29
26
  version: '0'
30
27
  description: A simple gem to perform fast pairwise sequence alignment using seqan
@@ -34,58 +31,58 @@ extensions:
34
31
  - ext/bioseqalign/extconf.rb
35
32
  extra_rdoc_files: []
36
33
  files:
37
- - lib/bioseqalign.rb
34
+ - ext/bioseqalign/FitAlign.cpp
35
+ - ext/bioseqalign/FitAlign.cpp~
38
36
  - ext/bioseqalign/FitAlign.hpp
39
- - ext/bioseqalign/extconf.rb
40
- - ext/bioseqalign/PrefixSuffixAlign.hpp~
37
+ - ext/bioseqalign/FitAlign.hpp~
38
+ - ext/bioseqalign/GlobalAlign.cpp
39
+ - ext/bioseqalign/GlobalAlign.cpp~
41
40
  - ext/bioseqalign/GlobalAlign.hpp
42
- - ext/bioseqalign/PrefixSuffixAlign.hpp
43
- - ext/bioseqalign/LocalAlign.cpp~
44
- - ext/bioseqalign/PrefixSuffixAlign.cpp~
45
- - ext/bioseqalign/runTest.rb
46
- - ext/bioseqalign/PrefixSuffixAlign.cpp
47
- - ext/bioseqalign/LocalAlign.hpp
48
41
  - ext/bioseqalign/GlobalAlign.hpp~
49
- - ext/bioseqalign/PairwiseAlign.cpp
50
- - ext/bioseqalign/runTest.rb~
51
- - ext/bioseqalign/FitAlign.cpp~
52
42
  - ext/bioseqalign/LocalAlign.cpp
43
+ - ext/bioseqalign/LocalAlign.cpp~
44
+ - ext/bioseqalign/LocalAlign.hpp
45
+ - ext/bioseqalign/LocalAlign.hpp~
53
46
  - ext/bioseqalign/Makefile
54
- - ext/bioseqalign/fitalgntest.cpp~
55
- - ext/bioseqalign/PairwiseAlign.hpp
47
+ - ext/bioseqalign/PairwiseAlign.cpp
56
48
  - ext/bioseqalign/PairwiseAlign.cpp~
57
- - ext/bioseqalign/LocalAlign.hpp~
58
- - ext/bioseqalign/GlobalAlign.cpp~
49
+ - ext/bioseqalign/PairwiseAlign.hpp
59
50
  - ext/bioseqalign/PairwiseAlign.hpp~
51
+ - ext/bioseqalign/PrefixSuffixAlign.cpp
52
+ - ext/bioseqalign/PrefixSuffixAlign.cpp~
53
+ - ext/bioseqalign/PrefixSuffixAlign.hpp
54
+ - ext/bioseqalign/PrefixSuffixAlign.hpp~
55
+ - ext/bioseqalign/extconf.rb
60
56
  - ext/bioseqalign/extconf.rb~
61
- - ext/bioseqalign/FitAlign.hpp~
62
57
  - ext/bioseqalign/fitalgntest.cpp
63
- - ext/bioseqalign/GlobalAlign.cpp
64
- - ext/bioseqalign/FitAlign.cpp
58
+ - ext/bioseqalign/fitalgntest.cpp~
59
+ - ext/bioseqalign/runTest.rb
60
+ - ext/bioseqalign/runTest.rb~
61
+ - lib/bioseqalign.rb
62
+ - lib/bioseqalign/version.rb
65
63
  homepage: https://github.com/stefrb/bioseqalign
66
64
  licenses:
67
65
  - MIT
66
+ metadata: {}
68
67
  post_install_message:
69
68
  rdoc_options: []
70
69
  require_paths:
71
70
  - lib
72
71
  - ext
73
72
  required_ruby_version: !ruby/object:Gem::Requirement
74
- none: false
75
73
  requirements:
76
- - - ! '>='
74
+ - - '>='
77
75
  - !ruby/object:Gem::Version
78
76
  version: '0'
79
77
  required_rubygems_version: !ruby/object:Gem::Requirement
80
- none: false
81
78
  requirements:
82
- - - ! '>='
79
+ - - '>='
83
80
  - !ruby/object:Gem::Version
84
81
  version: '0'
85
82
  requirements: []
86
83
  rubyforge_project:
87
- rubygems_version: 1.8.23
84
+ rubygems_version: 2.4.3
88
85
  signing_key:
89
- specification_version: 3
86
+ specification_version: 4
90
87
  summary: Pairwise sequence alignment using seqan
91
88
  test_files: []