bioseqalign 0.0.1

data/ext/bioseqalign/FitAlign.cpp

@@ -0,0 +1,48 @@
+#include "FitAlign.hpp"
+
+FitAlign::FitAlign() {}
+
+FitAlign::FitAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
+
+// unable to figure out how to properly overload constructor using RICE
+//FitAlign::FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS) : PairwiseAlign(s1, s2, matchS, mismatchS, indelS) {}
+
+//std::string FitAlign::getAlignment() {
+Rice::Array FitAlign::getAlignment() {
+  TSequence tseq1 = seq1;
+  TSequence tseq2 = seq2;
+
+  TStringSet sequences;
+  appendValue(sequences,tseq1);
+  appendValue(sequences,tseq2);
+
+  TAlignGraph alignG(sequences);
+  
+  // don't penalize gaps on begin/end of seq2
+  globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
+
+  /*
+  std::stringstream ss;
+  ss<<alignG;
+  return ss.str();
+  */
+  std::string mat;
+  convertAlignment(alignG, mat);
+  return getArrayFromAlignStr(mat);
+}
+
+
+void FitAlign::run() {
+  TSequence tseq1 = seq1;
+  TSequence tseq2 = seq2;
+
+  TStringSet sequences;
+  appendValue(sequences,tseq1);
+  appendValue(sequences,tseq2);
+
+  TAlignGraph alignG(sequences);
+  
+  // don't penalize gaps on begin/end of seq2
+  score = globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
+  
+}

data/ext/bioseqalign/FitAlign.cpp~

@@ -0,0 +1,42 @@
+#include "FitAlign.hpp"
+
+FitAlign::FitAlign() {}
+
+FitAlign::FitAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
+
+// unable to figure out how to properly overload constructor using RICE
+//FitAlign::FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS) : PairwiseAlign(s1, s2, matchS, mismatchS, indelS) {}
+
+std::string FitAlign::getAlignment() {
+  TSequence tseq1 = seq1;
+  TSequence tseq2 = seq2;
+
+  TStringSet sequences;
+  appendValue(sequences,tseq1);
+  appendValue(sequences,tseq2);
+
+  TAlignGraph alignG(sequences);
+  
+  // don't penalize gaps on begin/end of seq2
+  globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
+
+  std::stringstream ss;
+  ss<<alignG;
+  return ss.str();
+}
+
+
+void FitAlign::run() {
+  TSequence tseq1 = seq1;
+  TSequence tseq2 = seq2;
+
+  TStringSet sequences;
+  appendValue(sequences,tseq1);
+  appendValue(sequences,tseq2);
+
+  TAlignGraph alignG(sequences);
+  
+  // don't penalize gaps on begin/end of seq2
+  score = globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
+  
+}

data/ext/bioseqalign/FitAlign.hpp

@@ -0,0 +1,22 @@
+
+#include <iostream>
+#include <string>
+#include <seqan/align.h>
+
+#include "PairwiseAlign.hpp"
+
+using namespace seqan;
+
+class FitAlign : public PairwiseAlign {
+public:
+  FitAlign();
+  FitAlign(std::string s1, std::string s2);
+  //FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS);
+  virtual ~FitAlign() {}
+  
+  virtual void run();
+  //virtual std::string getAlignment();
+  virtual Rice::Array getAlignment();
+  
+};
+

data/ext/bioseqalign/FitAlign.hpp~

@@ -0,0 +1,20 @@
+#include <iostream>
+#include <string>
+#include <seqan/align.h>
+
+#include "PairwiseAlign.hpp"
+
+using namespace seqan;
+
+class FitAlign : public PairwiseAlign {
+public:
+  FitAlign();
+  FitAlign(std::string s1, std::string s2);
+  //FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS);
+  virtual ~FitAlign() {}
+  
+  virtual void run();
+  virtual std::string getAlignment();
+  
+};
+

data/ext/bioseqalign/GlobalAlign.cpp

@@ -0,0 +1,45 @@
+// global alignment
+
+#include "GlobalAlign.hpp"
+
+GlobalAlign::GlobalAlign() {}
+
+GlobalAlign::GlobalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
+
+Rice::Array GlobalAlign::getAlignment() {
+  TAlign ali;
+  resize(rows(ali), 2);
+  assignSource(row(ali, 0), seq1);
+  assignSource(row(ali, 1), seq2);
+  
+  globalAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore));
+  
+  typedef Iterator<TRow>::Type TRowIterator;
+  TRowIterator it = begin(row(ali, 0));
+  TRowIterator itEnd = end(row(ali, 0));
+  std::string s_row1 = "";
+  for(; it != itEnd; ++it) {
+    if(isGap(it)) s_row1 += "-";
+    else s_row1 += (*it);
+  }
+  TRowIterator it2 = begin(row(ali, 1));
+  TRowIterator itEnd2 = end(row(ali, 1));
+  std::string s_row2 = "";
+  for(; it2 != itEnd2; ++it2) {
+    if(isGap(it2)) s_row2 += "-";
+    else s_row2 += (*it2);
+  }
+
+  return getArrayFromAlignStr(s_row1+s_row2);
+}
+
+
+void GlobalAlign::run() {
+  TAlign ali;
+  resize(rows(ali), 2);
+  assignSource(row(ali, 0), seq1);
+  assignSource(row(ali, 1), seq2);
+  
+  score = globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore));
+}
+

data/ext/bioseqalign/GlobalAlign.cpp~

@@ -0,0 +1,53 @@
+// global alignment
+
+#include "GlobalAlign.hpp"
+
+GlobalAlign::GlobalAlign() {}
+
+GlobalAlign::GlobalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
+
+Rice::Array GlobalAlign::getAlignment() {
+  TAlign ali;
+  resize(rows(ali), 2);
+  assignSource(row(ali, 0), seq1);
+  assignSource(row(ali, 1), seq2);
+  
+  //globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
+  globalAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
+
+  //std::cout<<row(ali, 0)<<std::endl;
+  //std::cout<<row(ali, 1)<<std::endl;
+
+  typedef Iterator<TRow>::Type TRowIterator;
+  TRowIterator it = begin(row(ali, 0));
+  TRowIterator itEnd = end(row(ali, 0));
+  std::string s_row1 = "";
+  for(; it != itEnd; ++it) {
+    if(isGap(it)) s_row1 += "-";
+    else s_row1 += (*it);
+  }
+  TRowIterator it2 = begin(row(ali, 1));
+  TRowIterator itEnd2 = end(row(ali, 1));
+  std::string s_row2 = "";
+  for(; it2 != itEnd2; ++it2) {
+    if(isGap(it2)) s_row2 += "-";
+    else s_row2 += (*it2);
+  }
+
+  // std::cout<<s_row1<<std::endl;
+  // std::cout<<s_row2<<std::endl;
+  // std::cout<<ali<<std::endl;
+  
+  return getArrayFromAlignStr(s_row1+s_row2);
+}
+
+
+void GlobalAlign::run() {
+  TAlign ali;
+  resize(rows(ali), 2);
+  assignSource(row(ali, 0), seq1);
+  assignSource(row(ali, 1), seq2);
+  
+  score = globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
+}
+

data/ext/bioseqalign/GlobalAlign.hpp

@@ -0,0 +1,20 @@
+// global alignment
+
+#include <iostream>
+#include <string>
+#include <seqan/align.h>
+
+#include "PairwiseAlign.hpp"
+
+using namespace seqan;
+
+class GlobalAlign : public PairwiseAlign {
+public:
+  GlobalAlign();
+  GlobalAlign(std::string s1, std::string s2);
+  virtual ~GlobalAlign() {}
+  
+  virtual void run();
+  virtual Rice::Array getAlignment();
+  
+};

data/ext/bioseqalign/GlobalAlign.hpp~

@@ -0,0 +1,53 @@
+// local alignment
+
+#include "LocalAlign.hpp"
+
+LocalAlign::LocalAlign() {}
+
+LocalAlign::LocalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
+
+Rice::Array LocalAlign::getAlignment() {
+  TAlign ali;
+  resize(rows(ali), 2);
+  assignSource(row(ali, 0), seq1);
+  assignSource(row(ali, 1), seq2);
+  
+  //localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
+  localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
+
+  //std::cout<<row(ali, 0)<<std::endl;
+  //std::cout<<row(ali, 1)<<std::endl;
+
+  typedef Iterator<TRow>::Type TRowIterator;
+  TRowIterator it = begin(row(ali, 0));
+  TRowIterator itEnd = end(row(ali, 0));
+  std::string s_row1 = "";
+  for(; it != itEnd; ++it) {
+    if(isGap(it)) s_row1 += "-";
+    else s_row1 += (*it);
+  }
+  TRowIterator it2 = begin(row(ali, 1));
+  TRowIterator itEnd2 = end(row(ali, 1));
+  std::string s_row2 = "";
+  for(; it2 != itEnd2; ++it2) {
+    if(isGap(it2)) s_row2 += "-";
+    else s_row2 += (*it2);
+  }
+
+  // std::cout<<s_row1<<std::endl;
+  // std::cout<<s_row2<<std::endl;
+  // std::cout<<ali<<std::endl;
+  
+  return getArrayFromAlignStr(s_row1+s_row2);
+}
+
+
+void LocalAlign::run() {
+  TAlign ali;
+  resize(rows(ali), 2);
+  assignSource(row(ali, 0), seq1);
+  assignSource(row(ali, 1), seq2);
+  
+  score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
+}
+

data/ext/bioseqalign/LocalAlign.cpp

@@ -0,0 +1,53 @@
+// local alignment
+
+#include "LocalAlign.hpp"
+
+LocalAlign::LocalAlign() {}
+
+LocalAlign::LocalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
+
+Rice::Array LocalAlign::getAlignment() {
+  TAlign ali;
+  resize(rows(ali), 2);
+  assignSource(row(ali, 0), seq1);
+  assignSource(row(ali, 1), seq2);
+  
+  //localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
+  localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
+
+  //std::cout<<row(ali, 0)<<std::endl;
+  //std::cout<<row(ali, 1)<<std::endl;
+
+  typedef Iterator<TRow>::Type TRowIterator;
+  TRowIterator it = begin(row(ali, 0));
+  TRowIterator itEnd = end(row(ali, 0));
+  std::string s_row1 = "";
+  for(; it != itEnd; ++it) {
+    if(isGap(it)) s_row1 += "-";
+    else s_row1 += (*it);
+  }
+  TRowIterator it2 = begin(row(ali, 1));
+  TRowIterator itEnd2 = end(row(ali, 1));
+  std::string s_row2 = "";
+  for(; it2 != itEnd2; ++it2) {
+    if(isGap(it2)) s_row2 += "-";
+    else s_row2 += (*it2);
+  }
+
+  // std::cout<<s_row1<<std::endl;
+  // std::cout<<s_row2<<std::endl;
+  // std::cout<<ali<<std::endl;
+  
+  return getArrayFromAlignStr(s_row1+s_row2);
+}
+
+
+void LocalAlign::run() {
+  TAlign ali;
+  resize(rows(ali), 2);
+  assignSource(row(ali, 0), seq1);
+  assignSource(row(ali, 1), seq2);
+  
+  score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
+}
+

data/ext/bioseqalign/LocalAlign.cpp~

@@ -0,0 +1 @@
+// local alignment

data/ext/bioseqalign/LocalAlign.hpp

@@ -0,0 +1,21 @@
+// local alignment
+
+#include <iostream>
+#include <string>
+#include <seqan/align.h>
+
+#include "PairwiseAlign.hpp"
+
+using namespace seqan;
+
+class LocalAlign : public PairwiseAlign {
+public:
+  LocalAlign();
+  LocalAlign(std::string s1, std::string s2);
+  virtual ~LocalAlign() {}
+  
+  virtual void run();
+  virtual Rice::Array getAlignment();
+  
+};
+

data/ext/bioseqalign/LocalAlign.hpp~

@@ -0,0 +1 @@
+// local alignment

data/ext/bioseqalign/Makefile

@@ -0,0 +1,251 @@
+
+SHELL = /bin/sh
+
+# V=0 quiet, V=1 verbose.  other values don't work.
+V = 0
+Q1 = $(V:1=)
+Q = $(Q1:0=@)
+n=$(NULLCMD)
+ECHO1 = $(V:1=@$n)
+ECHO = $(ECHO1:0=@echo)
+
+#### Start of system configuration section. ####
+
+srcdir = .
+topdir = /usr/include/ruby-1.9.1
+hdrdir = /usr/include/ruby-1.9.1
+arch_hdrdir = /usr/include/ruby-1.9.1/$(arch)
+VPATH = $(srcdir):$(arch_hdrdir)/ruby:$(hdrdir)/ruby
+
+prefix = $(DESTDIR)/usr
+
+rubylibprefix = $(libdir)/$(RUBY_BASE_NAME)
+
+exec_prefix = $(prefix)
+
+vendorhdrdir = $(rubyhdrdir)/vendor_ruby
+
+sitehdrdir = $(rubyhdrdir)/site_ruby
+
+rubyhdrdir = $(includedir)/$(RUBY_BASE_NAME)-$(ruby_version)
+
+vendordir = $(DESTDIR)/usr/lib/ruby/vendor_ruby
+
+sitedir = $(DESTDIR)/usr/local/lib/site_ruby
+
+ridir = $(datarootdir)/$(RI_BASE_NAME)
+
+mandir = $(prefix)/share/man
+
+localedir = $(datarootdir)/locale
+
+libdir = $(exec_prefix)/lib
+
+psdir = $(docdir)
+
+pdfdir = $(docdir)
+
+dvidir = $(docdir)
+
+htmldir = $(docdir)
+
+infodir = $(prefix)/share/info
+
+docdir = $(datarootdir)/doc/$(PACKAGE)
+
+oldincludedir = $(DESTDIR)/usr/include
+
+includedir = $(prefix)/include
+
+localstatedir = $(DESTDIR)/var
+
+sharedstatedir = $(prefix)/com
+
+sysconfdir = $(DESTDIR)/etc
+
+datadir = $(datarootdir)
+
+datarootdir = $(prefix)/share
+
+libexecdir = $(prefix)/lib/ruby1.9.1
+
+sbindir = $(exec_prefix)/sbin
+
+bindir = $(exec_prefix)/bin
+
+rubylibdir = $(rubylibprefix)/$(ruby_version)
+
+archdir = $(rubylibdir)/$(arch)
+
+sitelibdir = $(sitedir)/$(ruby_version)
+
+sitearchdir = $(sitelibdir)/$(sitearch)
+
+vendorlibdir = $(vendordir)/$(ruby_version)
+
+vendorarchdir = $(vendorlibdir)/$(sitearch)
+
+
+NULLCMD = :
+
+CC = gcc
+CXX = g++
+LIBRUBY = $(LIBRUBY_SO)
+LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
+LIBRUBYARG_SHARED = -l$(RUBY_SO_NAME)
+LIBRUBYARG_STATIC = -lruby-1.9.1-static
+OUTFLAG = -o 
+COUTFLAG = -o 
+
+RUBY_EXTCONF_H = 
+cflags   =  $(optflags) $(debugflags) $(warnflags)
+optflags = -O3
+debugflags = -ggdb
+warnflags = -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wimplicit-function-declaration
+CFLAGS   = -fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fno-strict-aliasing -fPIC $(ARCH_FLAG)
+INCFLAGS = -I. -I$(arch_hdrdir) -I$(hdrdir)/ruby/backward -I$(hdrdir) -I$(srcdir)
+DEFS     = 
+CPPFLAGS =  -D_FORTIFY_SOURCE=2 $(DEFS) $(cppflags)  -I/home/stef/ruby_gems/gems/rice-1.6.2/ruby/lib/include
+CXXFLAGS = $(CFLAGS)  -Wall -g
+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
+dldflags = 
+ARCH_FLAG = 
+DLDFLAGS = $(ldflags) $(dldflags) $(ARCH_FLAG)
+LDSHARED = g++ -shared
+LDSHAREDXX = $(CXX) -shared
+AR = ar
+EXEEXT = 
+
+RUBY_BASE_NAME = ruby
+RUBY_INSTALL_NAME = ruby1.9.1
+RUBY_SO_NAME = ruby-1.9.1
+arch = x86_64-linux
+sitearch = $(arch)
+ruby_version = 1.9.1
+ruby = /usr/bin/ruby1.9.1
+RUBY = $(ruby)
+RM = rm -f
+RM_RF = $(RUBY) -run -e rm -- -rf
+RMDIRS = rmdir --ignore-fail-on-non-empty -p
+MAKEDIRS = /bin/mkdir -p
+INSTALL = /usr/bin/install -c
+INSTALL_PROG = $(INSTALL) -m 0755
+INSTALL_DATA = $(INSTALL) -m 644
+COPY = cp
+
+#### End of system configuration section. ####
+
+preload = 
+
+
+CXX = g++
+
+libpath = . $(libdir)
+LIBPATH =  -L. -L$(libdir)
+DEFFILE = 
+
+CLEANFILES = mkmf.log
+DISTCLEANFILES = 
+DISTCLEANDIRS = 
+
+extout = 
+extout_prefix = 
+target_prefix = 
+LOCAL_LIBS = 
+LIBS = -lruby-1.9.1 -lpthread -lrt -ldl -lcrypt -lm   -lc
+SRCS = PrefixSuffixAlign.cpp PairwiseAlign.cpp LocalAlign.cpp fitalgntest.cpp GlobalAlign.cpp FitAlign.cpp
+OBJS = PrefixSuffixAlign.o PairwiseAlign.o LocalAlign.o fitalgntest.o GlobalAlign.o FitAlign.o
+TARGET = SeqAlign
+DLLIB = $(TARGET).so
+EXTSTATIC = 
+STATIC_LIB = 
+
+BINDIR        = $(bindir)
+RUBYCOMMONDIR = $(sitedir)$(target_prefix)
+RUBYLIBDIR    = $(sitelibdir)$(target_prefix)
+RUBYARCHDIR   = $(sitearchdir)$(target_prefix)
+HDRDIR        = $(rubyhdrdir)/ruby$(target_prefix)
+ARCHHDRDIR    = $(rubyhdrdir)/$(arch)/ruby$(target_prefix)
+
+TARGET_SO     = $(DLLIB)
+CLEANLIBS     = $(TARGET).so 
+CLEANOBJS     = *.o  *.bak
+
+all:    $(DLLIB)
+static: $(STATIC_LIB)
+.PHONY: all install static install-so install-rb
+.PHONY: clean clean-so clean-rb
+
+clean-rb-default::
+clean-rb::
+clean-so::
+clean: clean-so clean-rb-default clean-rb
+		@-$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES)
+
+distclean-rb-default::
+distclean-rb::
+distclean-so::
+distclean: clean distclean-so distclean-rb-default distclean-rb
+		@-$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
+		@-$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
+		@-$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
+
+realclean: distclean
+install: install-so install-rb
+
+install-so: $(RUBYARCHDIR)
+install-so: $(RUBYARCHDIR)/$(DLLIB)
+$(RUBYARCHDIR)/$(DLLIB): $(DLLIB)
+	@-$(MAKEDIRS) $(@D)
+	$(INSTALL_PROG) $(DLLIB) $(@D)
+install-rb: pre-install-rb install-rb-default
+install-rb-default: pre-install-rb-default
+pre-install-rb: Makefile
+pre-install-rb-default: Makefile
+pre-install-rb-default:
+	$(ECHO) installing default SeqAlign libraries
+$(RUBYARCHDIR):
+	$(Q) $(MAKEDIRS) $@
+
+site-install: site-install-so site-install-rb
+site-install-so: install-so
+site-install-rb: install-rb
+
+.SUFFIXES: .c .m .cc .mm .cxx .cpp .C .o
+
+.cc.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.mm.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.cxx.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.cpp.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.C.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.c.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
+
+.m.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
+
+$(DLLIB): $(OBJS) Makefile
+	$(ECHO) linking shared-object $(DLLIB)
+	@-$(RM) $(@)
+	$(Q) $(LDSHAREDXX) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
+
+
+
+$(OBJS): $(hdrdir)/ruby.h $(hdrdir)/ruby/defines.h $(arch_hdrdir)/ruby/config.h