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 +7 -0
- data/ext/bioseqalign/Makefile +128 -65
- data/ext/bioseqalign/extconf.rb +1 -0
- data/lib/bioseqalign/version.rb +6 -0
- metadata +28 -31
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
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---
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SHA1:
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metadata.gz: 0b96dd84832f04c18f665123a094d288a91c3030
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data.tar.gz: 96d9c502f30a612eec662baeec5f0a275714e912
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SHA512:
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metadata.gz: 792e24c7020440b3377f9c4f9218b21bdf5c986d582d2ffcf76f0292547d938353544fafe20b02fc2e0a9fe65e622736782e13ca8903807e2a5977c25e407206
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data.tar.gz: fb8c79b054f34495d921307902e0554841e2771742065243912c4a8ff0bf332ede46b8ccbbdcd1cab60884a3575b61b8aa4df3bdf22242dc8a8fc2c027caf678
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data/ext/bioseqalign/Makefile
CHANGED
@@ -5,37 +5,68 @@ SHELL = /bin/sh
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V = 0
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Q1 = $(V:1=)
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Q = $(Q1:0=@)
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-
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ECHO1 = $(V:1=@$n)
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ECHO1 = $(V:1=@:)
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ECHO = $(ECHO1:0=@echo)
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NULLCMD = :
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#### Start of system configuration section. ####
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srcdir = .
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topdir = /
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hdrdir =
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arch_hdrdir = /
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topdir = /home/stef/.rvm/rubies/ruby-2.2.0/include/ruby-2.2.0
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hdrdir = $(topdir)
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arch_hdrdir = /home/stef/.rvm/rubies/ruby-2.2.0/include/ruby-2.2.0/x86_64-linux
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PATH_SEPARATOR = :
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VPATH = $(srcdir):$(arch_hdrdir)/ruby:$(hdrdir)/ruby
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prefix = $(DESTDIR)/
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prefix = $(DESTDIR)/home/stef/.rvm/rubies/ruby-2.2.0
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rubysitearchprefix = $(rubylibprefix)/$(sitearch)
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rubyarchprefix = $(rubylibprefix)/$(arch)
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rubylibprefix = $(libdir)/$(RUBY_BASE_NAME)
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exec_prefix = $(prefix)
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vendorarchhdrdir = $(vendorhdrdir)/$(sitearch)
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sitearchhdrdir = $(sitehdrdir)/$(sitearch)
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rubyarchhdrdir = $(rubyhdrdir)/$(arch)
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vendorhdrdir = $(rubyhdrdir)/vendor_ruby
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sitehdrdir = $(rubyhdrdir)/site_ruby
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rubyhdrdir = $(includedir)/$(
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rubyhdrdir = $(includedir)/$(RUBY_VERSION_NAME)
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vendorarchdir = $(vendorlibdir)/$(sitearch)
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vendorlibdir = $(vendordir)/$(ruby_version)
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vendordir = $(rubylibprefix)/vendor_ruby
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sitearchdir = $(sitelibdir)/$(sitearch)
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sitelibdir = $(sitedir)/$(ruby_version)
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sitedir = $(rubylibprefix)/site_ruby
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rubyarchdir = $(rubylibdir)/$(arch)
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rubylibdir = $(rubylibprefix)/$(ruby_version)
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sitearchincludedir = $(includedir)/$(sitearch)
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archincludedir = $(includedir)/$(arch)
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-
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sitearchlibdir = $(libdir)/$(sitearch)
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-
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archlibdir = $(libdir)/$(arch)
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ridir = $(datarootdir)/$(RI_BASE_NAME)
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mandir = $(
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mandir = $(datarootdir)/man
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localedir = $(datarootdir)/locale
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@@ -49,7 +80,7 @@ dvidir = $(docdir)
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htmldir = $(docdir)
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infodir = $(
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infodir = $(datarootdir)/info
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docdir = $(datarootdir)/doc/$(PACKAGE)
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@@ -57,7 +88,7 @@ oldincludedir = $(DESTDIR)/usr/include
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includedir = $(prefix)/include
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localstatedir = $(
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localstatedir = $(prefix)/var
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sharedstatedir = $(prefix)/com
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@@ -67,48 +98,39 @@ datadir = $(datarootdir)
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datarootdir = $(prefix)/share
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libexecdir = $(
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libexecdir = $(exec_prefix)/libexec
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sbindir = $(exec_prefix)/sbin
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bindir = $(exec_prefix)/bin
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-
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-
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archdir = $(rubylibdir)/$(arch)
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-
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sitelibdir = $(sitedir)/$(ruby_version)
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-
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sitearchdir = $(sitelibdir)/$(sitearch)
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-
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vendorlibdir = $(vendordir)/$(ruby_version)
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-
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vendorarchdir = $(vendorlibdir)/$(sitearch)
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archdir = $(rubyarchdir)
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NULLCMD = :
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CC = gcc
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CXX = g++
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LIBRUBY = $(LIBRUBY_SO)
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LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
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LIBRUBYARG_SHARED = -l$(RUBY_SO_NAME)
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LIBRUBYARG_STATIC = -lruby-
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LIBRUBYARG_SHARED = -Wl,-rpath,'$${ORIGIN}/../lib' -Wl,-R'$${ORIGIN}/../lib' -l$(RUBY_SO_NAME)
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LIBRUBYARG_STATIC = -Wl,-rpath,'${ORIGIN}/../lib' -Wl,-R'${ORIGIN}/../lib' -lruby-static
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empty =
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OUTFLAG = -o $(empty)
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COUTFLAG = -o $(empty)
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RUBY_EXTCONF_H =
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cflags = $(optflags) $(debugflags) $(warnflags)
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optflags = -O3
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debugflags = -
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warnflags = -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wimplicit-function-declaration
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-
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optflags = -O3 -fno-fast-math
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debugflags = -ggdb3
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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
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CCDLFLAGS = -fPIC
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CFLAGS = $(CCDLFLAGS) $(cflags) -fPIC $(ARCH_FLAG)
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INCFLAGS = -I. -I$(arch_hdrdir) -I$(hdrdir)/ruby/backward -I$(hdrdir) -I$(srcdir)
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DEFS =
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CPPFLAGS = -
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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
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CXXFLAGS = $(CFLAGS) -Wall -g
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ldflags = -L. -
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dldflags =
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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
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dldflags =
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ARCH_FLAG =
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DLDFLAGS = $(ldflags) $(dldflags) $(ARCH_FLAG)
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LDSHARED = g++ -shared
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@@ -116,22 +138,36 @@ LDSHAREDXX = $(CXX) -shared
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AR = ar
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EXEEXT =
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RUBY_INSTALL_NAME = $(RUBY_BASE_NAME)
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RUBY_SO_NAME = ruby
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RUBYW_INSTALL_NAME =
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RUBY_VERSION_NAME = $(RUBY_BASE_NAME)-$(ruby_version)
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RUBYW_BASE_NAME = rubyw
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RUBY_BASE_NAME = ruby
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arch = x86_64-linux
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sitearch = $(arch)
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ruby_version =
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ruby =
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ruby_version = 2.2.0
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ruby = $(bindir)/$(RUBY_BASE_NAME)
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RUBY = $(ruby)
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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
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RM = rm -f
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RM_RF = $(RUBY) -run -e rm -- -rf
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RMDIRS = rmdir --ignore-fail-on-non-empty -p
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MAKEDIRS = /bin/mkdir -p
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INSTALL = /usr/bin/install
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INSTALL = /usr/bin/install
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INSTALL_PROG = $(INSTALL) -m 0755
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INSTALL_DATA = $(INSTALL) -m 644
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COPY = cp
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TOUCH = exit >
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#### End of system configuration section. ####
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CXX = g++
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libpath = . $(libdir)
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LIBPATH = -L. -L$(libdir)
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LIBPATH = -L. -L$(libdir) -Wl,-R$(libdir)
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DEFFILE =
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CLEANFILES = mkmf.log
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extout_prefix =
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target_prefix =
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LOCAL_LIBS =
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LIBS = -
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LIBS = -Wl,-rpath,'${ORIGIN}/../lib' -Wl,-R'${ORIGIN}/../lib' -lruby -lpthread -ldl -lcrypt -lm -lc
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ORIG_SRCS = PrefixSuffixAlign.cpp PairwiseAlign.cpp LocalAlign.cpp fitalgntest.cpp GlobalAlign.cpp FitAlign.cpp
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SRCS = $(ORIG_SRCS)
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OBJS = PrefixSuffixAlign.o PairwiseAlign.o LocalAlign.o fitalgntest.o GlobalAlign.o FitAlign.o
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HDRS = $(srcdir)/FitAlign.hpp $(srcdir)/GlobalAlign.hpp $(srcdir)/PrefixSuffixAlign.hpp $(srcdir)/LocalAlign.hpp $(srcdir)/PairwiseAlign.hpp
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TARGET = SeqAlign
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TARGET_NAME = SeqAlign
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TARGET_ENTRY = Init_$(TARGET_NAME)
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DLLIB = $(TARGET).so
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EXTSTATIC =
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STATIC_LIB =
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TIMESTAMP_DIR = .
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BINDIR = $(bindir)
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RUBYCOMMONDIR = $(sitedir)$(target_prefix)
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RUBYLIBDIR = $(sitelibdir)$(target_prefix)
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all: $(DLLIB)
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static: $(STATIC_LIB)
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.PHONY: all install static install-so install-rb
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.PHONY: clean clean-so clean-rb
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.PHONY: clean clean-so clean-static clean-rb
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clean-static::
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clean-rb-default::
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clean-rb::
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clean-so::
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clean: clean-so clean-rb-default clean-rb
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clean: clean-so clean-static clean-rb-default clean-rb
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-$(Q)$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES) .*.time
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distclean-rb-default::
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distclean-rb::
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distclean-so::
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distclean
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distclean-static::
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distclean: clean distclean-so distclean-static distclean-rb-default distclean-rb
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-$(Q)$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
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-$(Q)$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
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-$(Q)$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
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realclean: distclean
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install: install-so install-rb
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install-so: $(RUBYARCHDIR
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-
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$(INSTALL_PROG) $(DLLIB) $(@D)
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install-so: $(DLLIB) $(TIMESTAMP_DIR)/.RUBYARCHDIR.time
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$(INSTALL_PROG) $(DLLIB) $(RUBYARCHDIR)
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clean-static::
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-$(Q)$(RM) $(STATIC_LIB)
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install-rb: pre-install-rb install-rb-default
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install-rb-default: pre-install-rb-default
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pre-install-rb: Makefile
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pre-install-rb-default: Makefile
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pre-install-rb-default:
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-
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$(RUBYARCHDIR
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$(Q) $(MAKEDIRS)
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@$(NULLCMD)
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$(TIMESTAMP_DIR)/.RUBYARCHDIR.time:
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$(Q) $(MAKEDIRS) $(@D) $(RUBYARCHDIR)
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$(Q) $(TOUCH) $@
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site-install: site-install-so site-install-rb
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site-install-so: install-so
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site-install-rb: install-rb
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.SUFFIXES: .c .m .cc .mm .cxx .cpp .
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.SUFFIXES: .c .m .cc .mm .cxx .cpp .o .S
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.cc.o:
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$(ECHO) compiling $(<)
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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.cc.S:
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$(ECHO) translating $(<)
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
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.mm.o:
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$(ECHO) compiling $(<)
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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.mm.S:
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$(ECHO) translating $(<)
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
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.cxx.o:
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$(ECHO) compiling $(<)
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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.cxx.S:
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$(ECHO) translating $(<)
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
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.cpp.o:
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$(ECHO) compiling $(<)
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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.
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$(ECHO)
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -
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.cpp.S:
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$(ECHO) translating $(<)
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$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
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.c.o:
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$(ECHO) compiling $(<)
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$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
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.c.S:
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$(ECHO) translating $(<)
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|
+
$(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 $(DLLIB)
|
246
|
-
|
309
|
+
-$(Q)$(RM) $(@)
|
247
310
|
$(Q) $(LDSHAREDXX) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
|
248
311
|
|
249
312
|
|
250
313
|
|
251
|
-
$(OBJS): $(
|
314
|
+
$(OBJS): $(HDRS) $(ruby_headers)
|
data/ext/bioseqalign/extconf.rb
CHANGED
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.
|
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
|
-
-
|
34
|
+
- ext/bioseqalign/FitAlign.cpp
|
35
|
+
- ext/bioseqalign/FitAlign.cpp~
|
38
36
|
- ext/bioseqalign/FitAlign.hpp
|
39
|
-
- ext/bioseqalign/
|
40
|
-
- ext/bioseqalign/
|
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/
|
55
|
-
- ext/bioseqalign/PairwiseAlign.hpp
|
47
|
+
- ext/bioseqalign/PairwiseAlign.cpp
|
56
48
|
- ext/bioseqalign/PairwiseAlign.cpp~
|
57
|
-
- ext/bioseqalign/
|
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/
|
64
|
-
- ext/bioseqalign/
|
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:
|
84
|
+
rubygems_version: 2.4.3
|
88
85
|
signing_key:
|
89
|
-
specification_version:
|
86
|
+
specification_version: 4
|
90
87
|
summary: Pairwise sequence alignment using seqan
|
91
88
|
test_files: []
|