moved ext directory and created mkrf_conf

ext/mkrf_conf.rb

@@ -0,0 +1,49 @@
+# create Rakefile for shared library compilation
+
+require File.join("..",File.dirname(__FILE__),"lib/bio/bwa/library")
+
+path = File.expand_path(File.dirname(__FILE__))
+
+ext = Bio::BWA::Library.lib_extension
+
+flags = ""
+case ext
+  when "so" then flags = "-shared -Wl,-soname,libbwa.so"
+  when "dylib" then flags = "-bundle -undefined dynamic_lookup -flat_namespace"
+end
+
+
+File.open(File.join(path,"Rakefile"),"w") do |rakefile|
+rakefile.write <<-RAKE
+require 'rake/clean'
+    
+source = %w(utils.c bwt.c bwtio.c bwtaln.c bwtgap.c is.c bntseq.c bwtmisc.c bwtindex.c stdaln.c simple_dp.c bwaseqio.c bwase.c bwape.c kstring.c cs2nt.c bwtsw2_core.c bwtsw2_main.c bwtsw2_aux.c bwt_lite.c bwtsw2_chain.c bamlite.c main.c)
+    
+CLEAN.include('*.o')
+CLEAN.include('bwt_gen/*.o')
+
+GEN = FileList['bwt_gen/*.c']
+OBJ_GEN = GEN.ext('o')
+SRC = FileList.new(source)
+OBJ_SRC = SRC.ext('o')    
+
+rule '.o' => '.c' do |t|
+  sh "gcc -c -g -Wall -O2 -DHAVE_PTHREAD "+t.source+" -o "+t.name
+end
+    
+task :compile_gen => OBJ_GEN do
+  sh "ar -cru bwt_gen/libbwtgen.a "+OBJ_GEN.join(" ")
+end
+    
+task :compile_lib => OBJ_SRC do
+  sh "gcc #{flags} "+OBJ_SRC.join(" ")+" -o libbwa.#{ext} -lm -lz -lpthread -Lbwt_gen -lbwtgen"
+end
+  
+task :default => [:compile_gen, :compile_lib, :clean]
+  
+RAKE
+
+end
+
+
+