diff --git a/.deps/LDBlockShow.Po b/.deps/LDBlockShow.Po new file mode 100644 index 0000000..9ae2398 --- /dev/null +++ b/.deps/LDBlockShow.Po @@ -0,0 +1,452 @@ +LDBlockShow.o: src/LDBlockShow.cpp src/HeadIN.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/stdc-predef.h \ + /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h \ + /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/include/bits/byteswap-16.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/timex.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/setjmp.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/map \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tree.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_map.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_multimap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/bits/stdlib-float.h \ + /usr/local/include/zlib.h /usr/local/include/zconf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \ + /usr/include/limits.h /usr/include/bits/posix1_lim.h \ + /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ + /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ + src/./include/gzstream/gzstream.c src/./include/gzstream/gzstream.h \ + /usr/include/string.h src/./DataClass.h src/./CommFun.h src/FileDeal.h \ + src/./FilterGenotype.h src/Calculate.h src/PairWiseRR.h src/PairWiseDD.h \ + src/GetFig.h + +src/HeadIN.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: + +/usr/include/bits/wordsize.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: + +/usr/include/features.h: + +/usr/include/stdc-predef.h: + +/usr/include/sys/cdefs.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: + +/usr/include/bits/wchar.h: + +/usr/include/xlocale.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: + +/usr/include/ctype.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/include/bits/byteswap-16.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/time.h: + +/usr/include/bits/sched.h: + +/usr/include/bits/time.h: + +/usr/include/bits/timex.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/setjmp.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: + +/usr/include/wctype.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/map: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tree.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_map.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_multimap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/huge_valf.h: + +/usr/include/bits/huge_vall.h: + +/usr/include/bits/inf.h: + +/usr/include/bits/nan.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/alloca.h: + +/usr/include/bits/stdlib-float.h: + +/usr/local/include/zlib.h: + +/usr/local/include/zconf.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h: + +/usr/include/limits.h: + +/usr/include/bits/posix1_lim.h: + +/usr/include/bits/local_lim.h: + +/usr/include/linux/limits.h: + +/usr/include/bits/posix2_lim.h: + +/usr/include/bits/xopen_lim.h: + +src/./include/gzstream/gzstream.c: + +src/./include/gzstream/gzstream.h: + +/usr/include/string.h: + +src/./DataClass.h: + +src/./CommFun.h: + +src/FileDeal.h: + +src/./FilterGenotype.h: + +src/Calculate.h: + +src/PairWiseRR.h: + +src/PairWiseDD.h: + +src/GetFig.h: diff --git a/INSTALL.txt b/INSTALL.txt new file mode 100644 index 0000000..e8c5629 --- /dev/null +++ b/INSTALL.txt @@ -0,0 +1,90 @@ + +LDBlockShow: A new simple and efficient software for Linkage Disequilibrium Decay analysis based Variant Call Format + +1) Introduction +----------------------------------------------------------------------------------------------------------------- +################################################################################################################# + +This software relies on the zlib library packages [zlib] + +----------------------- zlib infomation ---------------------- +if Lib [zlib] do not work +you can download form this website and install it +http://www.zlib.net/ + +2) INSTALL Method1 +---------------------------------------------------------------------------------------------------------------- +################################################################################################################ + +Just execute as follows : + git clone https://github.com/BGI-shenzhen/LDBlockShow.git + chmod 755 configure ; ./configure ; + make; + mv LDBlockShow bin/ ; + + +**Note:** If fail to link,try to re-install the libraries [**_zlib_**](https://zlib.net/) + + +3) INSTALL Method2 +---------------------------------------------------------------------------------------------------------------- +################################################################################################################ +A) Method2 For linux/Unix + For linux/Unix , execute as follows : + tar -zxvf LDBlockShowXXX.tar.gz + cd LDBlockShowXXX; + cd src; + make ; make clean + ../bin/LDBlockShow + + #I had compiled and installed these gz library packages [zlib] on the linux X64 platform + if Link do not work ,try Re-install the gz library and copy them to the library Dir + + LDBlockShowXX/src/include/zlib + + +B) Method2 For macOS platform INSTALL + you should must pre-install the library [zlib] and copy them to the corresponding library directory + + #step1 :Should must re-install the gz library [zlib] + see [zlib] website + + #step2 : # Copy these gz library file into the corresponding library directory + + cp libz.a libz.so* LDBlockShowXX/src/include/zlib + + #step3 : + sh make.sh # or [make && make clean] + + + +C) Other Method +Note if it can't work . follow below B1-B6 or use the static Compiled [BamDeal_Linux ] +############################################ + #autoscan ./ + #cp configure.scan configure.ac + +# if can't work, follow below 6 commands + B1: aclocal #// src/automake-1.9/aclocal + B2: autoconf #// src/automake-1.9/autoconf + B3: autoheader #// src/automake-1.9/autoheader + B4: automake --add-missing #// src/automake-1.9/automake --add-missing + B5: ./configure + B6: make +############################################# +#swimming in the sky & flying in the sea# + + + +4) Contact +---------------------------------------------------------------------------------------------------------------- +################################################################################################################ +email: hewm2008@gmail.com / hewm2008@qq.com +join the QQ Group : 125293663 + + + +######################swimming in the sky and flying in the sea ########################### ## + + + diff --git a/LDBlockShow_Manual_Chinese.pdf b/LDBlockShow_Manual_Chinese.pdf new file mode 100644 index 0000000..3e2c1f7 Binary files /dev/null and b/LDBlockShow_Manual_Chinese.pdf differ diff --git a/LDBlockShow_Manual_English.pdf b/LDBlockShow_Manual_English.pdf new file mode 100644 index 0000000..e222965 Binary files /dev/null and b/LDBlockShow_Manual_English.pdf differ diff --git a/LICENSE b/LICENSE index b7028d2..8527ff4 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2020 BGI-shenzhen +Copyright (c) 2018 BGI-shenzhen Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..351fc73 --- /dev/null +++ b/Makefile @@ -0,0 +1,634 @@ +# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile. Generated from Makefile.in by configure. + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, +# Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + + + + +pkgdatadir = $(datadir)/bin/LDBlockShow +pkgincludedir = $(includedir)/bin/LDBlockShow +pkglibdir = $(libdir)/bin/LDBlockShow +pkglibexecdir = $(libexecdir)/bin/LDBlockShow +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +bin_PROGRAMS = LDBlockShow$(EXEEXT) +subdir = . +DIST_COMMON = $(am__configure_deps) $(srcdir)/Makefile.am \ + $(srcdir)/Makefile.in $(srcdir)/config.h.in \ + $(top_srcdir)/configure depcomp install-sh missing +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.ac +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \ + configure.lineno config.status.lineno +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = config.h +CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = +am__installdirs = "$(DESTDIR)$(bindir)" +PROGRAMS = $(bin_PROGRAMS) +am_LDBlockShow_OBJECTS = LDBlockShow.$(OBJEXT) +LDBlockShow_OBJECTS = $(am_LDBlockShow_OBJECTS) +LDBlockShow_DEPENDENCIES = +LDBlockShow_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) \ + $(LDBlockShow_LDFLAGS) $(LDFLAGS) -o $@ +DEFAULT_INCLUDES = -I. +depcomp = $(SHELL) $(top_srcdir)/depcomp +am__depfiles_maybe = depfiles +am__mv = mv -f +CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ + $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) +CXXLD = $(CXX) +CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \ + -o $@ +SOURCES = $(LDBlockShow_SOURCES) +DIST_SOURCES = $(LDBlockShow_SOURCES) +ETAGS = etags +CTAGS = ctags +DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) +distdir = $(PACKAGE)-$(VERSION) +top_distdir = $(distdir) +am__remove_distdir = \ + { test ! -d "$(distdir)" \ + || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \ + && rm -fr "$(distdir)"; }; } +DIST_ARCHIVES = $(distdir).tar.gz +GZIP_ENV = --best +distuninstallcheck_listfiles = find . -type f -print +distcleancheck_listfiles = find . -type f -print +ACLOCAL = ${SHELL} /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32/missing --run aclocal-1.11 +AMTAR = ${SHELL} /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32/missing --run tar +AUTOCONF = ${SHELL} /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32/missing --run autoconf +AUTOHEADER = ${SHELL} /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32/missing --run autoheader +AUTOMAKE = ${SHELL} /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32/missing --run automake-1.11 +AWK = gawk +CC = gcc +CCDEPMODE = depmode=gcc3 +CFLAGS = -g -O2 +CPP = gcc -E +CPPFLAGS = +CXX = g++ +CXXDEPMODE = depmode=gcc3 +CXXFLAGS = -g -O2 +CYGPATH_W = echo +DEFS = -DHAVE_CONFIG_H +DEPDIR = .deps +ECHO_C = +ECHO_N = -n +ECHO_T = +EGREP = /bin/grep -E +EXEEXT = +GREP = /bin/grep +INSTALL = /usr/bin/install -c +INSTALL_DATA = ${INSTALL} -m 644 +INSTALL_PROGRAM = ${INSTALL} +INSTALL_SCRIPT = ${INSTALL} +INSTALL_STRIP_PROGRAM = $(install_sh) -c -s +LDFLAGS = +LIBOBJS = +LIBS = -lz +LN_S = ln -s +LTLIBOBJS = +MAKEINFO = ${SHELL} /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32/missing --run makeinfo +MKDIR_P = /bin/mkdir -p +OBJEXT = o +PACKAGE = bin/LDBlockShow +PACKAGE_BUGREPORT = hewm2008@gmail.com +PACKAGE_NAME = bin/LDBlockShow +PACKAGE_STRING = bin/LDBlockShow 1.32 +PACKAGE_TARNAME = bin-ldblockshow +PACKAGE_VERSION = 1.32 +PATH_SEPARATOR = : +RANLIB = ranlib +SET_MAKE = +SHELL = /bin/sh +STRIP = +VERSION = 1.32 +abs_builddir = /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32 +abs_srcdir = /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32 +abs_top_builddir = /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32 +abs_top_srcdir = /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32 +ac_ct_CC = gcc +ac_ct_CXX = g++ +am__include = include +am__leading_dot = . +am__quote = +am__tar = ${AMTAR} chof - "$$tardir" +am__untar = ${AMTAR} xf - +bindir = ${exec_prefix}/bin +build_alias = +builddir = . +datadir = ${datarootdir} +datarootdir = ${prefix}/share +docdir = ${datarootdir}/doc/${PACKAGE_TARNAME} +dvidir = ${docdir} +exec_prefix = ${prefix} +host_alias = +htmldir = ${docdir} +includedir = ${prefix}/include +infodir = ${datarootdir}/info +install_sh = ${SHELL} /hwfssz4/BC_PUB/Pipeline/Install/LDBlockShow-1.32/install-sh +libdir = ${exec_prefix}/lib +libexecdir = ${exec_prefix}/libexec +localedir = ${datarootdir}/locale +localstatedir = ${prefix}/var +mandir = ${datarootdir}/man +mkdir_p = /bin/mkdir -p +oldincludedir = /usr/include +pdfdir = ${docdir} +prefix = /usr/local +program_transform_name = s,x,x, +psdir = ${docdir} +sbindir = ${exec_prefix}/sbin +sharedstatedir = ${prefix}/com +srcdir = . +sysconfdir = ${prefix}/etc +target_alias = +top_build_prefix = +top_builddir = . +top_srcdir = . +AUTOMAKE_OPTIONS = foreign +LDBlockShow_SOURCES = src/LDBlockShow.cpp +LDBlockShow_LDFLAGS = -g -O2 +LDBlockShow_LDADD = -lz +all: config.h + $(MAKE) $(AM_MAKEFLAGS) all-am + +.SUFFIXES: +.SUFFIXES: .cpp .o .obj +am--refresh: + @: +$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) + @for dep in $?; do \ + case '$(am__configure_deps)' in \ + *$$dep*) \ + echo ' cd $(srcdir) && $(AUTOMAKE) --foreign'; \ + $(am__cd) $(srcdir) && $(AUTOMAKE) --foreign \ + && exit 0; \ + exit 1;; \ + esac; \ + done; \ + echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \ + $(am__cd) $(top_srcdir) && \ + $(AUTOMAKE) --foreign Makefile +.PRECIOUS: Makefile +Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status + @case '$?' in \ + *config.status*) \ + echo ' $(SHELL) ./config.status'; \ + $(SHELL) ./config.status;; \ + *) \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \ + esac; + +$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) + $(SHELL) ./config.status --recheck + +$(top_srcdir)/configure: $(am__configure_deps) + $(am__cd) $(srcdir) && $(AUTOCONF) && echo chmod 755 bin/\* >> $(top_srcdir)/configure +$(ACLOCAL_M4): $(am__aclocal_m4_deps) + $(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS) +$(am__aclocal_m4_deps): + +config.h: stamp-h1 + @if test ! -f $@; then \ + rm -f stamp-h1; \ + $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \ + else :; fi + +stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status + @rm -f stamp-h1 + cd $(top_builddir) && $(SHELL) ./config.status config.h +$(srcdir)/config.h.in: $(am__configure_deps) + ($(am__cd) $(top_srcdir) && $(AUTOHEADER)) + rm -f stamp-h1 + touch $@ + +distclean-hdr: + -rm -f config.h stamp-h1 +install-binPROGRAMS: $(bin_PROGRAMS) + @$(NORMAL_INSTALL) + test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)" + @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ + for p in $$list; do echo "$$p $$p"; done | \ + sed 's/$(EXEEXT)$$//' | \ + while read p p1; do if test -f $$p; \ + then echo "$$p"; echo "$$p"; else :; fi; \ + done | \ + sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \ + -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \ + sed 'N;N;N;s,\n, ,g' | \ + $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \ + { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \ + if ($$2 == $$4) files[d] = files[d] " " $$1; \ + else { print "f", $$3 "/" $$4, $$1; } } \ + END { for (d in files) print "f", d, files[d] }' | \ + while read type dir files; do \ + if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \ + test -z "$$files" || { \ + echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ + $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \ + } \ + ; done + +uninstall-binPROGRAMS: + @$(NORMAL_UNINSTALL) + @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ + files=`for p in $$list; do echo "$$p"; done | \ + sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \ + -e 's/$$/$(EXEEXT)/' `; \ + test -n "$$list" || exit 0; \ + echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \ + cd "$(DESTDIR)$(bindir)" && rm -f $$files + +clean-binPROGRAMS: + -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS) +LDBlockShow$(EXEEXT): $(LDBlockShow_OBJECTS) $(LDBlockShow_DEPENDENCIES) + @rm -f LDBlockShow$(EXEEXT) + $(LDBlockShow_LINK) $(LDBlockShow_OBJECTS) $(LDBlockShow_LDADD) $(LIBS) + +mostlyclean-compile: + -rm -f *.$(OBJEXT) + +distclean-compile: + -rm -f *.tab.c + +include ./$(DEPDIR)/LDBlockShow.Po + +.cpp.o: + $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< + $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po +# source='$<' object='$@' libtool=no \ +# DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ +# $(CXXCOMPILE) -c -o $@ $< + +.cpp.obj: + $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'` + $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po +# source='$<' object='$@' libtool=no \ +# DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ +# $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'` + +LDBlockShow.o: src/LDBlockShow.cpp + $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT LDBlockShow.o -MD -MP -MF $(DEPDIR)/LDBlockShow.Tpo -c -o LDBlockShow.o `test -f 'src/LDBlockShow.cpp' || echo '$(srcdir)/'`src/LDBlockShow.cpp + $(am__mv) $(DEPDIR)/LDBlockShow.Tpo $(DEPDIR)/LDBlockShow.Po +# source='src/LDBlockShow.cpp' object='LDBlockShow.o' libtool=no \ +# DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ +# $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o LDBlockShow.o `test -f 'src/LDBlockShow.cpp' || echo '$(srcdir)/'`src/LDBlockShow.cpp + +LDBlockShow.obj: src/LDBlockShow.cpp + $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT LDBlockShow.obj -MD -MP -MF $(DEPDIR)/LDBlockShow.Tpo -c -o LDBlockShow.obj `if test -f 'src/LDBlockShow.cpp'; then $(CYGPATH_W) 'src/LDBlockShow.cpp'; else $(CYGPATH_W) '$(srcdir)/src/LDBlockShow.cpp'; fi` + $(am__mv) $(DEPDIR)/LDBlockShow.Tpo $(DEPDIR)/LDBlockShow.Po +# source='src/LDBlockShow.cpp' object='LDBlockShow.obj' libtool=no \ +# DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ +# $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o LDBlockShow.obj `if test -f 'src/LDBlockShow.cpp'; then $(CYGPATH_W) 'src/LDBlockShow.cpp'; else $(CYGPATH_W) '$(srcdir)/src/LDBlockShow.cpp'; fi` + +ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) + list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ + unique=`for i in $$list; do \ + if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ + done | \ + $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ + END { if (nonempty) { for (i in files) print i; }; }'`; \ + mkid -fID $$unique +tags: TAGS + +TAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ + $(TAGS_FILES) $(LISP) + set x; \ + here=`pwd`; \ + list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \ + unique=`for i in $$list; do \ + if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ + done | \ + $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ + END { if (nonempty) { for (i in files) print i; }; }'`; \ + shift; \ + if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \ + test -n "$$unique" || unique=$$empty_fix; \ + if test $$# -gt 0; then \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + "$$@" $$unique; \ + else \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + $$unique; \ + fi; \ + fi +ctags: CTAGS +CTAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ + $(TAGS_FILES) $(LISP) + list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \ + unique=`for i in $$list; do \ + if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ + done | \ + $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ + END { if (nonempty) { for (i in files) print i; }; }'`; \ + test -z "$(CTAGS_ARGS)$$unique" \ + || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \ + $$unique + +GTAGS: + here=`$(am__cd) $(top_builddir) && pwd` \ + && $(am__cd) $(top_srcdir) \ + && gtags -i $(GTAGS_ARGS) "$$here" + +distclean-tags: + -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags + +distdir: $(DISTFILES) + $(am__remove_distdir) + test -d "$(distdir)" || mkdir "$(distdir)" + @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ + topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ + list='$(DISTFILES)'; \ + dist_files=`for file in $$list; do echo $$file; done | \ + sed -e "s|^$$srcdirstrip/||;t" \ + -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \ + case $$dist_files in \ + */*) $(MKDIR_P) `echo "$$dist_files" | \ + sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \ + sort -u` ;; \ + esac; \ + for file in $$dist_files; do \ + if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \ + if test -d $$d/$$file; then \ + dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \ + if test -d "$(distdir)/$$file"; then \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ + if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \ + cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ + cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \ + else \ + test -f "$(distdir)/$$file" \ + || cp -p $$d/$$file "$(distdir)/$$file" \ + || exit 1; \ + fi; \ + done + -test -n "$(am__skip_mode_fix)" \ + || find "$(distdir)" -type d ! -perm -755 \ + -exec chmod u+rwx,go+rx {} \; -o \ + ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \ + ! -type d ! -perm -400 -exec chmod a+r {} \; -o \ + ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \ + || chmod -R a+r "$(distdir)" +dist-gzip: distdir + tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz + $(am__remove_distdir) + +dist-bzip2: distdir + tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2 + $(am__remove_distdir) + +dist-lzma: distdir + tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma + $(am__remove_distdir) + +dist-xz: distdir + tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz + $(am__remove_distdir) + +dist-tarZ: distdir + tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z + $(am__remove_distdir) + +dist-shar: distdir + shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz + $(am__remove_distdir) + +dist-zip: distdir + -rm -f $(distdir).zip + zip -rq $(distdir).zip $(distdir) + $(am__remove_distdir) + +dist dist-all: distdir + tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz + $(am__remove_distdir) + +# This target untars the dist file and tries a VPATH configuration. Then +# it guarantees that the distribution is self-contained by making another +# tarfile. +distcheck: dist + case '$(DIST_ARCHIVES)' in \ + *.tar.gz*) \ + GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\ + *.tar.bz2*) \ + bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\ + *.tar.lzma*) \ + lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\ + *.tar.xz*) \ + xz -dc $(distdir).tar.xz | $(am__untar) ;;\ + *.tar.Z*) \ + uncompress -c $(distdir).tar.Z | $(am__untar) ;;\ + *.shar.gz*) \ + GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\ + *.zip*) \ + unzip $(distdir).zip ;;\ + esac + chmod -R a-w $(distdir); chmod u+w $(distdir) + mkdir $(distdir)/_build + mkdir $(distdir)/_inst + chmod a-w $(distdir) + test -d $(distdir)/_build || exit 0; \ + dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \ + && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \ + && am__cwd=`pwd` \ + && $(am__cd) $(distdir)/_build \ + && ../configure --srcdir=.. --prefix="$$dc_install_base" \ + $(DISTCHECK_CONFIGURE_FLAGS) \ + && $(MAKE) $(AM_MAKEFLAGS) \ + && $(MAKE) $(AM_MAKEFLAGS) dvi \ + && $(MAKE) $(AM_MAKEFLAGS) check \ + && $(MAKE) $(AM_MAKEFLAGS) install \ + && $(MAKE) $(AM_MAKEFLAGS) installcheck \ + && $(MAKE) $(AM_MAKEFLAGS) uninstall \ + && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \ + distuninstallcheck \ + && chmod -R a-w "$$dc_install_base" \ + && ({ \ + (cd ../.. && umask 077 && mkdir "$$dc_destdir") \ + && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \ + && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \ + && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \ + distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \ + } || { rm -rf "$$dc_destdir"; exit 1; }) \ + && rm -rf "$$dc_destdir" \ + && $(MAKE) $(AM_MAKEFLAGS) dist \ + && rm -rf $(DIST_ARCHIVES) \ + && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \ + && cd "$$am__cwd" \ + || exit 1 + $(am__remove_distdir) + @(echo "$(distdir) archives ready for distribution: "; \ + list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \ + sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x' +distuninstallcheck: + @$(am__cd) '$(distuninstallcheck_dir)' \ + && test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \ + || { echo "ERROR: files left after uninstall:" ; \ + if test -n "$(DESTDIR)"; then \ + echo " (check DESTDIR support)"; \ + fi ; \ + $(distuninstallcheck_listfiles) ; \ + exit 1; } >&2 +distcleancheck: distclean + @if test '$(srcdir)' = . ; then \ + echo "ERROR: distcleancheck can only run from a VPATH build" ; \ + exit 1 ; \ + fi + @test `$(distcleancheck_listfiles) | wc -l` -eq 0 \ + || { echo "ERROR: files left in build directory after distclean:" ; \ + $(distcleancheck_listfiles) ; \ + exit 1; } >&2 +check-am: all-am +check: check-am +all-am: Makefile $(PROGRAMS) config.h +installdirs: + for dir in "$(DESTDIR)$(bindir)"; do \ + test -z "$$dir" || $(MKDIR_P) "$$dir"; \ + done +install: install-am +install-exec: install-exec-am +install-data: install-data-am +uninstall: uninstall-am + +install-am: all-am + @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am + +installcheck: installcheck-am +install-strip: + $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \ + install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \ + `test -z '$(STRIP)' || \ + echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install +mostlyclean-generic: + +clean-generic: + +distclean-generic: + -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES) + -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES) + +maintainer-clean-generic: + @echo "This command is intended for maintainers to use" + @echo "it deletes files that may require special tools to rebuild." +clean: clean-am + +clean-am: clean-binPROGRAMS clean-generic mostlyclean-am + +distclean: distclean-am + -rm -f $(am__CONFIG_DISTCLEAN_FILES) + -rm -rf ./$(DEPDIR) + -rm -f Makefile +distclean-am: clean-am distclean-compile distclean-generic \ + distclean-hdr distclean-tags + +dvi: dvi-am + +dvi-am: + +html: html-am + +html-am: + +info: info-am + +info-am: + +install-data-am: + +install-dvi: install-dvi-am + +install-dvi-am: + +install-exec-am: install-binPROGRAMS + +install-html: install-html-am + +install-html-am: + +install-info: install-info-am + +install-info-am: + +install-man: + +install-pdf: install-pdf-am + +install-pdf-am: + +install-ps: install-ps-am + +install-ps-am: + +installcheck-am: + +maintainer-clean: maintainer-clean-am + -rm -f $(am__CONFIG_DISTCLEAN_FILES) + -rm -rf $(top_srcdir)/autom4te.cache + -rm -rf ./$(DEPDIR) + -rm -f Makefile +maintainer-clean-am: distclean-am maintainer-clean-generic + +mostlyclean: mostlyclean-am + +mostlyclean-am: mostlyclean-compile mostlyclean-generic + +pdf: pdf-am + +pdf-am: + +ps: ps-am + +ps-am: + +uninstall-am: uninstall-binPROGRAMS + +.MAKE: all install-am install-strip + +.PHONY: CTAGS GTAGS all all-am am--refresh check check-am clean \ + clean-binPROGRAMS clean-generic ctags dist dist-all dist-bzip2 \ + dist-gzip dist-lzma dist-shar dist-tarZ dist-xz dist-zip \ + distcheck distclean distclean-compile distclean-generic \ + distclean-hdr distclean-tags distcleancheck distdir \ + distuninstallcheck dvi dvi-am html html-am info info-am \ + install install-am install-binPROGRAMS install-data \ + install-data-am install-dvi install-dvi-am install-exec \ + install-exec-am install-html install-html-am install-info \ + install-info-am install-man install-pdf install-pdf-am \ + install-ps install-ps-am install-strip installcheck \ + installcheck-am installdirs maintainer-clean \ + maintainer-clean-generic mostlyclean mostlyclean-compile \ + mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \ + uninstall-am uninstall-binPROGRAMS + +#CPPFLAGS = --std=c++11 + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/Makefile.am b/Makefile.am new file mode 100644 index 0000000..790ae88 --- /dev/null +++ b/Makefile.am @@ -0,0 +1,6 @@ +AUTOMAKE_OPTIONS = foreign +bin_PROGRAMS = LDBlockShow +LDBlockShow_SOURCES = src/LDBlockShow.cpp +LDBlockShow_LDFLAGS = -g -O2 +LDBlockShow_LDADD = -lz +#CPPFLAGS = --std=c++11 diff --git a/Makefile.in b/Makefile.in new file mode 100644 index 0000000..c67846a --- /dev/null +++ b/Makefile.in @@ -0,0 +1,634 @@ +# Makefile.in generated by automake 1.11.1 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, +# Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +@SET_MAKE@ + +VPATH = @srcdir@ +pkgdatadir = $(datadir)/@PACKAGE@ +pkgincludedir = $(includedir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkglibexecdir = $(libexecdir)/@PACKAGE@ +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +bin_PROGRAMS = LDBlockShow$(EXEEXT) +subdir = . +DIST_COMMON = $(am__configure_deps) $(srcdir)/Makefile.am \ + $(srcdir)/Makefile.in $(srcdir)/config.h.in \ + $(top_srcdir)/configure depcomp install-sh missing +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.ac +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \ + configure.lineno config.status.lineno +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = config.h +CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = +am__installdirs = "$(DESTDIR)$(bindir)" +PROGRAMS = $(bin_PROGRAMS) +am_LDBlockShow_OBJECTS = LDBlockShow.$(OBJEXT) +LDBlockShow_OBJECTS = $(am_LDBlockShow_OBJECTS) +LDBlockShow_DEPENDENCIES = +LDBlockShow_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) \ + $(LDBlockShow_LDFLAGS) $(LDFLAGS) -o $@ +DEFAULT_INCLUDES = -I.@am__isrc@ +depcomp = $(SHELL) $(top_srcdir)/depcomp +am__depfiles_maybe = depfiles +am__mv = mv -f +CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ + $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) +CXXLD = $(CXX) +CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \ + -o $@ +SOURCES = $(LDBlockShow_SOURCES) +DIST_SOURCES = $(LDBlockShow_SOURCES) +ETAGS = etags +CTAGS = ctags +DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) +distdir = $(PACKAGE)-$(VERSION) +top_distdir = $(distdir) +am__remove_distdir = \ + { test ! -d "$(distdir)" \ + || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \ + && rm -fr "$(distdir)"; }; } +DIST_ARCHIVES = $(distdir).tar.gz +GZIP_ENV = --best +distuninstallcheck_listfiles = find . -type f -print +distcleancheck_listfiles = find . -type f -print +ACLOCAL = @ACLOCAL@ +AMTAR = @AMTAR@ +AUTOCONF = @AUTOCONF@ +AUTOHEADER = @AUTOHEADER@ +AUTOMAKE = @AUTOMAKE@ +AWK = @AWK@ +CC = @CC@ +CCDEPMODE = @CCDEPMODE@ +CFLAGS = @CFLAGS@ +CPP = @CPP@ +CPPFLAGS = @CPPFLAGS@ +CXX = @CXX@ +CXXDEPMODE = @CXXDEPMODE@ +CXXFLAGS = @CXXFLAGS@ +CYGPATH_W = @CYGPATH_W@ +DEFS = @DEFS@ +DEPDIR = @DEPDIR@ +ECHO_C = @ECHO_C@ +ECHO_N = @ECHO_N@ +ECHO_T = @ECHO_T@ +EGREP = @EGREP@ +EXEEXT = @EXEEXT@ +GREP = @GREP@ +INSTALL = @INSTALL@ +INSTALL_DATA = @INSTALL_DATA@ +INSTALL_PROGRAM = @INSTALL_PROGRAM@ +INSTALL_SCRIPT = @INSTALL_SCRIPT@ +INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@ +LDFLAGS = @LDFLAGS@ +LIBOBJS = @LIBOBJS@ +LIBS = @LIBS@ +LN_S = @LN_S@ +LTLIBOBJS = @LTLIBOBJS@ +MAKEINFO = @MAKEINFO@ +MKDIR_P = @MKDIR_P@ +OBJEXT = @OBJEXT@ +PACKAGE = @PACKAGE@ +PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ +PACKAGE_NAME = @PACKAGE_NAME@ +PACKAGE_STRING = @PACKAGE_STRING@ +PACKAGE_TARNAME = @PACKAGE_TARNAME@ +PACKAGE_VERSION = @PACKAGE_VERSION@ +PATH_SEPARATOR = @PATH_SEPARATOR@ +RANLIB = @RANLIB@ +SET_MAKE = @SET_MAKE@ +SHELL = @SHELL@ +STRIP = @STRIP@ +VERSION = @VERSION@ +abs_builddir = @abs_builddir@ +abs_srcdir = @abs_srcdir@ +abs_top_builddir = @abs_top_builddir@ +abs_top_srcdir = @abs_top_srcdir@ +ac_ct_CC = @ac_ct_CC@ +ac_ct_CXX = @ac_ct_CXX@ +am__include = @am__include@ +am__leading_dot = @am__leading_dot@ +am__quote = @am__quote@ +am__tar = @am__tar@ +am__untar = @am__untar@ +bindir = @bindir@ +build_alias = @build_alias@ +builddir = @builddir@ +datadir = @datadir@ +datarootdir = @datarootdir@ +docdir = @docdir@ +dvidir = @dvidir@ +exec_prefix = @exec_prefix@ +host_alias = @host_alias@ +htmldir = @htmldir@ +includedir = @includedir@ +infodir = @infodir@ +install_sh = @install_sh@ +libdir = @libdir@ +libexecdir = @libexecdir@ +localedir = @localedir@ +localstatedir = @localstatedir@ +mandir = @mandir@ +mkdir_p = @mkdir_p@ +oldincludedir = @oldincludedir@ +pdfdir = @pdfdir@ +prefix = @prefix@ +program_transform_name = @program_transform_name@ +psdir = @psdir@ +sbindir = @sbindir@ +sharedstatedir = @sharedstatedir@ +srcdir = @srcdir@ +sysconfdir = @sysconfdir@ +target_alias = @target_alias@ +top_build_prefix = @top_build_prefix@ +top_builddir = @top_builddir@ +top_srcdir = @top_srcdir@ +AUTOMAKE_OPTIONS = foreign +LDBlockShow_SOURCES = src/LDBlockShow.cpp +LDBlockShow_LDFLAGS = -g -O2 +LDBlockShow_LDADD = -lz +all: config.h + $(MAKE) $(AM_MAKEFLAGS) all-am + +.SUFFIXES: +.SUFFIXES: .cpp .o .obj +am--refresh: + @: +$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) + @for dep in $?; do \ + case '$(am__configure_deps)' in \ + *$$dep*) \ + echo ' cd $(srcdir) && $(AUTOMAKE) --foreign'; \ + $(am__cd) $(srcdir) && $(AUTOMAKE) --foreign \ + && exit 0; \ + exit 1;; \ + esac; \ + done; \ + echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \ + $(am__cd) $(top_srcdir) && \ + $(AUTOMAKE) --foreign Makefile +.PRECIOUS: Makefile +Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status + @case '$?' in \ + *config.status*) \ + echo ' $(SHELL) ./config.status'; \ + $(SHELL) ./config.status;; \ + *) \ + echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \ + cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \ + esac; + +$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES) + $(SHELL) ./config.status --recheck + +$(top_srcdir)/configure: $(am__configure_deps) + $(am__cd) $(srcdir) && $(AUTOCONF) +$(ACLOCAL_M4): $(am__aclocal_m4_deps) + $(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS) +$(am__aclocal_m4_deps): + +config.h: stamp-h1 + @if test ! -f $@; then \ + rm -f stamp-h1; \ + $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \ + else :; fi + +stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status + @rm -f stamp-h1 + cd $(top_builddir) && $(SHELL) ./config.status config.h +$(srcdir)/config.h.in: $(am__configure_deps) + ($(am__cd) $(top_srcdir) && $(AUTOHEADER)) + rm -f stamp-h1 + touch $@ + +distclean-hdr: + -rm -f config.h stamp-h1 +install-binPROGRAMS: $(bin_PROGRAMS) + @$(NORMAL_INSTALL) + test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)" + @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ + for p in $$list; do echo "$$p $$p"; done | \ + sed 's/$(EXEEXT)$$//' | \ + while read p p1; do if test -f $$p; \ + then echo "$$p"; echo "$$p"; else :; fi; \ + done | \ + sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \ + -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \ + sed 'N;N;N;s,\n, ,g' | \ + $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \ + { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \ + if ($$2 == $$4) files[d] = files[d] " " $$1; \ + else { print "f", $$3 "/" $$4, $$1; } } \ + END { for (d in files) print "f", d, files[d] }' | \ + while read type dir files; do \ + if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \ + test -z "$$files" || { \ + echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ + $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \ + } \ + ; done + +uninstall-binPROGRAMS: + @$(NORMAL_UNINSTALL) + @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ + files=`for p in $$list; do echo "$$p"; done | \ + sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \ + -e 's/$$/$(EXEEXT)/' `; \ + test -n "$$list" || exit 0; \ + echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \ + cd "$(DESTDIR)$(bindir)" && rm -f $$files + +clean-binPROGRAMS: + -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS) +LDBlockShow$(EXEEXT): $(LDBlockShow_OBJECTS) $(LDBlockShow_DEPENDENCIES) + @rm -f LDBlockShow$(EXEEXT) + $(LDBlockShow_LINK) $(LDBlockShow_OBJECTS) $(LDBlockShow_LDADD) $(LIBS) + +mostlyclean-compile: + -rm -f *.$(OBJEXT) + +distclean-compile: + -rm -f *.tab.c + +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/LDBlockShow.Po@am__quote@ + +.cpp.o: +@am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< +@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@ +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ +@am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $< + +.cpp.obj: +@am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'` +@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@ +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ +@am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'` + +LDBlockShow.o: src/LDBlockShow.cpp +@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT LDBlockShow.o -MD -MP -MF $(DEPDIR)/LDBlockShow.Tpo -c -o LDBlockShow.o `test -f 'src/LDBlockShow.cpp' || echo '$(srcdir)/'`src/LDBlockShow.cpp +@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/LDBlockShow.Tpo $(DEPDIR)/LDBlockShow.Po +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='src/LDBlockShow.cpp' object='LDBlockShow.o' libtool=no @AMDEPBACKSLASH@ +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ +@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o LDBlockShow.o `test -f 'src/LDBlockShow.cpp' || echo '$(srcdir)/'`src/LDBlockShow.cpp + +LDBlockShow.obj: src/LDBlockShow.cpp +@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT LDBlockShow.obj -MD -MP -MF $(DEPDIR)/LDBlockShow.Tpo -c -o LDBlockShow.obj `if test -f 'src/LDBlockShow.cpp'; then $(CYGPATH_W) 'src/LDBlockShow.cpp'; else $(CYGPATH_W) '$(srcdir)/src/LDBlockShow.cpp'; fi` +@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/LDBlockShow.Tpo $(DEPDIR)/LDBlockShow.Po +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='src/LDBlockShow.cpp' object='LDBlockShow.obj' libtool=no @AMDEPBACKSLASH@ +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ +@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o LDBlockShow.obj `if test -f 'src/LDBlockShow.cpp'; then $(CYGPATH_W) 'src/LDBlockShow.cpp'; else $(CYGPATH_W) '$(srcdir)/src/LDBlockShow.cpp'; fi` + +ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) + list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ + unique=`for i in $$list; do \ + if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ + done | \ + $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ + END { if (nonempty) { for (i in files) print i; }; }'`; \ + mkid -fID $$unique +tags: TAGS + +TAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ + $(TAGS_FILES) $(LISP) + set x; \ + here=`pwd`; \ + list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \ + unique=`for i in $$list; do \ + if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ + done | \ + $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ + END { if (nonempty) { for (i in files) print i; }; }'`; \ + shift; \ + if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \ + test -n "$$unique" || unique=$$empty_fix; \ + if test $$# -gt 0; then \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + "$$@" $$unique; \ + else \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + $$unique; \ + fi; \ + fi +ctags: CTAGS +CTAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ + $(TAGS_FILES) $(LISP) + list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \ + unique=`for i in $$list; do \ + if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ + done | \ + $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ + END { if (nonempty) { for (i in files) print i; }; }'`; \ + test -z "$(CTAGS_ARGS)$$unique" \ + || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \ + $$unique + +GTAGS: + here=`$(am__cd) $(top_builddir) && pwd` \ + && $(am__cd) $(top_srcdir) \ + && gtags -i $(GTAGS_ARGS) "$$here" + +distclean-tags: + -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags + +distdir: $(DISTFILES) + $(am__remove_distdir) + test -d "$(distdir)" || mkdir "$(distdir)" + @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ + topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ + list='$(DISTFILES)'; \ + dist_files=`for file in $$list; do echo $$file; done | \ + sed -e "s|^$$srcdirstrip/||;t" \ + -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \ + case $$dist_files in \ + */*) $(MKDIR_P) `echo "$$dist_files" | \ + sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \ + sort -u` ;; \ + esac; \ + for file in $$dist_files; do \ + if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \ + if test -d $$d/$$file; then \ + dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \ + if test -d "$(distdir)/$$file"; then \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ + if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \ + cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ + cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \ + else \ + test -f "$(distdir)/$$file" \ + || cp -p $$d/$$file "$(distdir)/$$file" \ + || exit 1; \ + fi; \ + done + -test -n "$(am__skip_mode_fix)" \ + || find "$(distdir)" -type d ! -perm -755 \ + -exec chmod u+rwx,go+rx {} \; -o \ + ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \ + ! -type d ! -perm -400 -exec chmod a+r {} \; -o \ + ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \ + || chmod -R a+r "$(distdir)" +dist-gzip: distdir + tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz + $(am__remove_distdir) + +dist-bzip2: distdir + tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2 + $(am__remove_distdir) + +dist-lzma: distdir + tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma + $(am__remove_distdir) + +dist-xz: distdir + tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz + $(am__remove_distdir) + +dist-tarZ: distdir + tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z + $(am__remove_distdir) + +dist-shar: distdir + shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz + $(am__remove_distdir) + +dist-zip: distdir + -rm -f $(distdir).zip + zip -rq $(distdir).zip $(distdir) + $(am__remove_distdir) + +dist dist-all: distdir + tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz + $(am__remove_distdir) + +# This target untars the dist file and tries a VPATH configuration. Then +# it guarantees that the distribution is self-contained by making another +# tarfile. +distcheck: dist + case '$(DIST_ARCHIVES)' in \ + *.tar.gz*) \ + GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\ + *.tar.bz2*) \ + bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\ + *.tar.lzma*) \ + lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\ + *.tar.xz*) \ + xz -dc $(distdir).tar.xz | $(am__untar) ;;\ + *.tar.Z*) \ + uncompress -c $(distdir).tar.Z | $(am__untar) ;;\ + *.shar.gz*) \ + GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\ + *.zip*) \ + unzip $(distdir).zip ;;\ + esac + chmod -R a-w $(distdir); chmod u+w $(distdir) + mkdir $(distdir)/_build + mkdir $(distdir)/_inst + chmod a-w $(distdir) + test -d $(distdir)/_build || exit 0; \ + dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \ + && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \ + && am__cwd=`pwd` \ + && $(am__cd) $(distdir)/_build \ + && ../configure --srcdir=.. --prefix="$$dc_install_base" \ + $(DISTCHECK_CONFIGURE_FLAGS) \ + && $(MAKE) $(AM_MAKEFLAGS) \ + && $(MAKE) $(AM_MAKEFLAGS) dvi \ + && $(MAKE) $(AM_MAKEFLAGS) check \ + && $(MAKE) $(AM_MAKEFLAGS) install \ + && $(MAKE) $(AM_MAKEFLAGS) installcheck \ + && $(MAKE) $(AM_MAKEFLAGS) uninstall \ + && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \ + distuninstallcheck \ + && chmod -R a-w "$$dc_install_base" \ + && ({ \ + (cd ../.. && umask 077 && mkdir "$$dc_destdir") \ + && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \ + && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \ + && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \ + distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \ + } || { rm -rf "$$dc_destdir"; exit 1; }) \ + && rm -rf "$$dc_destdir" \ + && $(MAKE) $(AM_MAKEFLAGS) dist \ + && rm -rf $(DIST_ARCHIVES) \ + && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \ + && cd "$$am__cwd" \ + || exit 1 + $(am__remove_distdir) + @(echo "$(distdir) archives ready for distribution: "; \ + list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \ + sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x' +distuninstallcheck: + @$(am__cd) '$(distuninstallcheck_dir)' \ + && test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \ + || { echo "ERROR: files left after uninstall:" ; \ + if test -n "$(DESTDIR)"; then \ + echo " (check DESTDIR support)"; \ + fi ; \ + $(distuninstallcheck_listfiles) ; \ + exit 1; } >&2 +distcleancheck: distclean + @if test '$(srcdir)' = . ; then \ + echo "ERROR: distcleancheck can only run from a VPATH build" ; \ + exit 1 ; \ + fi + @test `$(distcleancheck_listfiles) | wc -l` -eq 0 \ + || { echo "ERROR: files left in build directory after distclean:" ; \ + $(distcleancheck_listfiles) ; \ + exit 1; } >&2 +check-am: all-am +check: check-am +all-am: Makefile $(PROGRAMS) config.h +installdirs: + for dir in "$(DESTDIR)$(bindir)"; do \ + test -z "$$dir" || $(MKDIR_P) "$$dir"; \ + done +install: install-am +install-exec: install-exec-am +install-data: install-data-am +uninstall: uninstall-am + +install-am: all-am + @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am + +installcheck: installcheck-am +install-strip: + $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \ + install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \ + `test -z '$(STRIP)' || \ + echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install +mostlyclean-generic: + +clean-generic: + +distclean-generic: + -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES) + -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES) + +maintainer-clean-generic: + @echo "This command is intended for maintainers to use" + @echo "it deletes files that may require special tools to rebuild." +clean: clean-am + +clean-am: clean-binPROGRAMS clean-generic mostlyclean-am + +distclean: distclean-am + -rm -f $(am__CONFIG_DISTCLEAN_FILES) + -rm -rf ./$(DEPDIR) + -rm -f Makefile +distclean-am: clean-am distclean-compile distclean-generic \ + distclean-hdr distclean-tags + +dvi: dvi-am + +dvi-am: + +html: html-am + +html-am: + +info: info-am + +info-am: + +install-data-am: + +install-dvi: install-dvi-am + +install-dvi-am: + +install-exec-am: install-binPROGRAMS + +install-html: install-html-am + +install-html-am: + +install-info: install-info-am + +install-info-am: + +install-man: + +install-pdf: install-pdf-am + +install-pdf-am: + +install-ps: install-ps-am + +install-ps-am: + +installcheck-am: + +maintainer-clean: maintainer-clean-am + -rm -f $(am__CONFIG_DISTCLEAN_FILES) + -rm -rf $(top_srcdir)/autom4te.cache + -rm -rf ./$(DEPDIR) + -rm -f Makefile +maintainer-clean-am: distclean-am maintainer-clean-generic + +mostlyclean: mostlyclean-am + +mostlyclean-am: mostlyclean-compile mostlyclean-generic + +pdf: pdf-am + +pdf-am: + +ps: ps-am + +ps-am: + +uninstall-am: uninstall-binPROGRAMS + +.MAKE: all install-am install-strip + +.PHONY: CTAGS GTAGS all all-am am--refresh check check-am clean \ + clean-binPROGRAMS clean-generic ctags dist dist-all dist-bzip2 \ + dist-gzip dist-lzma dist-shar dist-tarZ dist-xz dist-zip \ + distcheck distclean distclean-compile distclean-generic \ + distclean-hdr distclean-tags distcleancheck distdir \ + distuninstallcheck dvi dvi-am html html-am info info-am \ + install install-am install-binPROGRAMS install-data \ + install-data-am install-dvi install-dvi-am install-exec \ + install-exec-am install-html install-html-am install-info \ + install-info-am install-man install-pdf install-pdf-am \ + install-ps install-ps-am install-strip installcheck \ + installcheck-am installdirs maintainer-clean \ + maintainer-clean-generic mostlyclean mostlyclean-compile \ + mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \ + uninstall-am uninstall-binPROGRAMS + +#CPPFLAGS = --std=c++11 + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/README.md b/README.md index 2696def..08902e4 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,291 @@ -# LDBlocksShow ->LDBlockShow: a fast and effective tool for Show Region Linkage disequilibrium heatmap Figure analysis based on variant call format files +# LDBlockShow +### 1 Introduction +LDBlockShow is a fast and effective tool to generate linkage disequilibrium (LD) heatmap from VCF files. It is more time and memory saving than other current tools. LDBlockShow can generate the plots of LD heatmap and interested statistics or annotation results simultaneously. In addition, it also supports subgroup analysis. + +### 2 Download and Install +------------ + + 2.1. linux/MaxOS [Download](https://github.com/BGI-shenzhen/LDBlockShow/archive/v1.32.tar.gz) + + 2.2 Pre-install + LDblockshow is for Linux/Unix/macOS only. Before installing, please make sure the following pre-requirements are ready to use. + 1) g++ : g++ with [--std=c++11](https://gcc.gnu.org/) > 4.8+ is recommended + 2) zlib : [zlib](https://zlib.net/) > 1.2.3 is recommended + 3) Perl : The [SVG.pm](https://metacpan.org/release/SVG) in Perl should be installed. LDBlockShow uses this module to plot figures. We have provided a built-in SVG module in the package. + + + 2.3 Install + Users can install it with the following options: + Option 1: +
+ git clone https://github.com/BGI-shenzhen/LDBlockShow.git + chmod 755 configure ; ./configure; + make; + mv LDBlockShow bin/; # [rm *.o] ++ +**Note:** If failed to link,try to re-install the libraries [**_zlib_**](https://zlib.net/) + +Option 2: +
+ tar -zxvf LDBlockShowXXX.tar.gz + cd LDBlockShowXXX; cd src; + sh make.sh ## Linux : [ make ; make clean ] + ../bin/LDBlockShow ++**Note:** For macOS, if plink doesn't work, please re-download [**mac _plinks_**](https://www.cog-genomics.org/plink2/) and put it into the directory [LDBlockShowXXX/bin] +**Note:** If failed to link,try to re-install the libraries [**_zlib_**](https://zlib.net/) + +### 3 Parameter description +------------ +3.1 LDBlockShow +3.1.1 Main parameter + +```php + ./bin/LDBlockShow + + Usage: LDBlockShow -InVCF
+-InVCF The input file in VCF format +-OutPut The output file directory and output file name prefix (e.g., /path/pop1) +-Region The defined region to show the LD heatmap (format: chr:start:end) + +-SeleVar The LD measurement (1: D' 2: R^2), the default is 1. +-SubPop A sample list for subgroup analysis +-BlockType The definition of blocks. The default 1 is called by PLINK1 to generate the block defined by Gabriel et al.2. Solid spine of LD3 is also supported [2]. Users can also define their own cutoff of r2 and D’ for blocks [3] combined with the option of “-BlockCut” or supply their own block region definition [4] combined with the option of “-FixBlock”. 5 can be used as input if users prefer to not show the block region. + +-InGWAS The statistics file (e.g., association statistics, but other values such as Tajima’s D can also be accepted) for generate plot together with the LD plot. File formatted as: [chr position Pvalue] +-InGFF Input GFF3 format file for genomic region annotation + +-BlockCut For block type 3, the defined cutoff for strong LD, and the ratio of strong LD SNP in one block. Default is 0.85:0.9. That’s, if the user chose D’ in the -SeleVar option, then in one block, the ratio of SNP pairs with D’ over 0.85 is 0.9. +-FixBlock For block type 4, users can use this option to supply a self-defined block region. The file contains three columns, including chromosome, block region start position, and block region end position. +-MerMinSNPNum The minimum SNP number to merge color grids with the same color. Default is 50. Details please see Fig 1 in this manual. + +-help Show more parameters ++ +3.1.2 Other parameters +```php +./bin/LDBlockShow -h + + Para [-i] is show for [-InVCF], Para [-o] is show for [-OutPut], Para [-r] is show for [-Region] + + -InGenotype
+-InGenotype Input file in genotype format. +-InPlink The prefix of input file in PLINK format. +-MAF Filter SNPs with low minor allele frequency (default ≤0.05) +-Het Filter SNPs with high heterozygosis ratio (default ≥0.9) +-Miss Filter SNPs with high missing rate (default ≥0.25) + +-TagSNPCut The LD cutoff for selecting tag SNPs. Default is 0.8. +-OutPng Convert the SVG file to PNG file +-OutPdf Convert SVG file to Pdf file. ++Note: If users failed to open small SVG files, please use the “-Outpdf” option to use the PDF file. For large SVG files, “-OutPng” can be used to get a relatively small figure file. + +3.2 ShowLDSVG +This program is designed for users to optimize the figure (e.g., change colors) generated by LDBlockShow. +3.2.1 Brief parameters +```php +./bin/ShowLDSVG + Options + -InPreFix
+-InPreFix The prefix of input file (i.e., the output file of LDBlockShow) +-OutPut The out file (svg, png and pdf format plot files) +-help More parameters in detail ++ +3.2.2 Detail parameters +```php +./bin/ShowLDSVG -h + -InGWAS
+-InGWAS The statistics file (e.g., association statistics, but other values such as Tajima’s D can also be accepted) for generate plot together with the LD plot. File formatted as: [chr position Pvalue] +-NoLogP By default, the P value from the -InGWAS file will be -log10 transformed, with this option, the P value will not be transformed. +-Cutline The significance cutline of the -InGWAS file. +-PointSize Users can use this option (any number over 0) to set the point size. +-InGFF The GFF file for genomic region annotation. By default, the gene name will be shown in the plot; +-NoGeneName Gene name will not be shown in the plot with this option. +-crGene Define the colors of different genomic regions. By default, CDS, intron, UTR and intergenic regions will be shown in #e7298a, light blue, #7570b3, and #a6cee3, respectively. + +Parameters to optimize the color of the heatmap: +-crBegin Color for no LD (R^2/D’=0) default: white +-crMiddle Color for R^2/D’=0.5, default: yellow +-crEnd Color for complete LD (R^2/D’=1), default: red +-NumGradien The number of gradients from crBegin to crEnd +-crTagSNP Color for the tag SNP. + +Parameters to optimize the grids in the heatmap: +-CrGrid Border color of the grids, default: white +-WidthGrid The width of the border, default = 1 +-NoGrid No border + +-ShowNum Show the LD measurement value in the grids (not recommended when SNP number is over 50). +-NoShowLDist When the distance between SNPs over this number, their pairwise LD will not be showed in the figure. Default is 10,000,000. +-MerMinSNPNum When number of SNPs over the default 50, ShowLDSVG will merge adjacent same color grids. User can change this number to any integer numbers. +-OutPng Convert the SVG file to PNG file +-OutPdf Convert SVG file to Pdf file. +-ResizeH Set the height of the image (default 4096), which can be used to adjust the resolution for PNG file. The width will be adjusted automatically. ++ +Note: When SNP number is large (e.g., over 100), the output SVG file might be very large. ShowLDSVG will merge adjacent same color grids. With smaller number of gradients (set by -NumGradien), the figure will be compressed to be smaller. -MerMinSNPNum is used to set the minimum number of SNPs, that’s, if there is more SNPs than this number (default 50), the output SVG will be compressed. + +3.3 Output files +
+out.site.gz: Remained SNPs after filtering [chr site] +out.blocks.gz: Block file [chr start end block_length SNP_number SNPs] +out.TriangleV.gz: Region Pairwise R^2/D' +out.svg: Output plot in SVG format +out.png: Output plot in png format +out.pdf: Output plot in pdf format ++ + + +### 4 Example +------------ + +See more detailed usage in the [Chinese Documentation](https://github.com/BGI-shenzhen/LDBlockShow/blob/master/LDBlockShow_Manual_Chinese.pdf) +See more detailed usage in the [English Documentation](https://github.com/BGI-shenzhen/LDBlockShow/blob/master/LDBlockShow_Manual_English.pdf) +See the example directory and Manual.pdf for more detail. + + +* Example 1) show Figure with Defaut LD Blocks + +
+#../../bin/LDBlockShow -InVCF Test.vcf.gz -OutPut out -Region chr11:24100000:24200000 -OutPng -SeleVar 1 +../../bin/LDBlockShow -InVCF Test.vcf.gz -OutPut out -Region chr11:24100000:24200000 -OutPng -SeleVar 2 +# [-SeleVar 1] is D' , [-SeleVar 2] is RR . # the default is D' ++ +![out.png](https://github.com/BGI-shenzhen/LDBlockShow/blob/master/example/Example1/out.png) + + +* Example 2) Output LDHeatMap combined with GWAS statistics +``` +#../../bin/LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -Region chr11:24100000:24200000 -InGWAS gwas.pvalue -OutPng +../../bin/LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -Region chr11:24100000:24200000 -InGWAS gwas.pvalue -OutPng -SeleVar 2 +## you can run ShowLDSVG with more parameters to optimize the plot ## +# ../../bin/ShowLDSVG -InPreFix out -OutPut out -InGWAS gwas.pvalue -Cutline 7 -ShowNum -PointSize 3 -OutPng +``` + +![out.png](https://github.com/BGI-shenzhen/LDBlockShow/blob/master/example/Example2/out.png) + + +* Example 3) show Figure with genomic annotation +``` +#../../bin/LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -InGWAS gwas.pvalue -InGFF In.gff -Region chr11:24100000:24200000 -OutPng -SeleVar 1 +../../bin/LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -InGWAS gwas.pvalue -InGFF In.gff -Region chr11:24100000:24200000 -OutPng -SeleVar 2 +## you can run ShowLDSVG with more parameters to optimize the plot ## +#../../bin/ShowLDSVG -InPreFix out -OutPut out.svg -InGWAS gwas.pvalue -Cutline 7 -InGFF In.gff -crGene yellow:lightblue:pink:orange -showNum -OutPng +#../../bin/ShowLDSVG -InPreFix out -OutPut out.svg -InGFF In.gff +``` + +![out.png](https://github.com/BGI-shenzhen/LDBlockShow/blob/master/example/Example3/out.png) + + + +### 5 Advantages +To evaluate the performance of LDBlockShow, we used test VCF files to generate the LD heatmap by using LDBlockShow, Haploview[4], LDheatmap[5] and gpart. The calculated r2 and D’ values of LDBlockShow is the same with other tools. As shown in Figure below, LDBlockShow is more time and memory saving than other tools. + +![Advantages](https://github.com/BGI-shenzhen/LDBlockShow/blob/master/example/Fig/out2.png) + The above figure shows the comparison of computing cost for LDBlockShow, Ldheatmap, Haploview and gpart. CPU time (A) and memory cost (B) for different methods are shown with a fixed SNP number of 100 and sample size ranging from 2,000 to 60,000. CPU time (C) and memory cost (D) for different methods are shown with a fixed sample size of 2,000 and SNP number ranged from 100 to 1,200. When testing datasets in A-D, both LDBlockShow and gpart finished the analyses within reasonable time and memory. We further tested their performance when handling large dataset. CPU time (E) and memory cost (F) for these two methods are shown with a fixed sample size of 100,000 and SNP number ranged from 300 to 2,500. Computation is performed with one thread of an Intel Xeon CPU E5-2630 v4. + As shown in Table below, LDBlockShow can generate the plots of LD heatmap and interested statistics or annotation results simultaneously. In addition, LDBlockShow also supports subgroup analysis. + +| Performance | LDBlockShow | Haploview | LDheatmap | gpart | +|:-----------------------------------------|:-----------------------:|:---------------------:|:---------------------:|:---------------------:| +|Input | | | | | +|Compressed VCF file | √ | × | × | × | +|Uncompressed VCF file | √ | × | × | √ | +|Support subgroup analysis | √ | × | × | × | +|Output | | | | | +|Visualize additional statistics | √ | × | × | × | +|Visualize genomic annotation | √ | × | × | √ | +|Compressed SVG | √ | × | × | × | +|PNG file | √ | √ | × | √ | +|Block region | √ | √ | × | √ | +|LD measurement | R2/D' | R2/D' | R2 | R2/D' | + + +### 6 An example image generated by LDBlockShow. +------------ + +![heatmap](https://github.com/BGI-shenzhen/LDBlockShow/blob/master/example/Fig/out1.png) + +### 7 Discussing +------------ +- [:email:](https://github.com/BGI-shenzhen/LDBlockShow) hewm2008@gmail.com / hewm2008@qq.com +- join the QQ Group : 125293663 + +######################swimming in the sky and flying in the sea ############################# + diff --git a/aclocal.m4 b/aclocal.m4 new file mode 100644 index 0000000..bcc213b --- /dev/null +++ b/aclocal.m4 @@ -0,0 +1,951 @@ +# generated automatically by aclocal 1.11.1 -*- Autoconf -*- + +# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, +# 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc. +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +m4_ifndef([AC_AUTOCONF_VERSION], + [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl +m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.63],, +[m4_warning([this file was generated for autoconf 2.63. +You have another version of autoconf. It may work, but is not guaranteed to. +If you have problems, you may need to regenerate the build system entirely. +To do so, use the procedure documented by the package, typically `autoreconf'.])]) + +# Copyright (C) 2002, 2003, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# AM_AUTOMAKE_VERSION(VERSION) +# ---------------------------- +# Automake X.Y traces this macro to ensure aclocal.m4 has been +# generated from the m4 files accompanying Automake X.Y. +# (This private macro should not be called outside this file.) +AC_DEFUN([AM_AUTOMAKE_VERSION], +[am__api_version='1.11' +dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to +dnl require some minimum version. Point them to the right macro. +m4_if([$1], [1.11.1], [], + [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl +]) + +# _AM_AUTOCONF_VERSION(VERSION) +# ----------------------------- +# aclocal traces this macro to find the Autoconf version. +# This is a private macro too. Using m4_define simplifies +# the logic in aclocal, which can simply ignore this definition. +m4_define([_AM_AUTOCONF_VERSION], []) + +# AM_SET_CURRENT_AUTOMAKE_VERSION +# ------------------------------- +# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced. +# This function is AC_REQUIREd by AM_INIT_AUTOMAKE. +AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], +[AM_AUTOMAKE_VERSION([1.11.1])dnl +m4_ifndef([AC_AUTOCONF_VERSION], + [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl +_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))]) + +# AM_AUX_DIR_EXPAND -*- Autoconf -*- + +# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets +# $ac_aux_dir to `$srcdir/foo'. In other projects, it is set to +# `$srcdir', `$srcdir/..', or `$srcdir/../..'. +# +# Of course, Automake must honor this variable whenever it calls a +# tool from the auxiliary directory. The problem is that $srcdir (and +# therefore $ac_aux_dir as well) can be either absolute or relative, +# depending on how configure is run. This is pretty annoying, since +# it makes $ac_aux_dir quite unusable in subdirectories: in the top +# source directory, any form will work fine, but in subdirectories a +# relative path needs to be adjusted first. +# +# $ac_aux_dir/missing +# fails when called from a subdirectory if $ac_aux_dir is relative +# $top_srcdir/$ac_aux_dir/missing +# fails if $ac_aux_dir is absolute, +# fails when called from a subdirectory in a VPATH build with +# a relative $ac_aux_dir +# +# The reason of the latter failure is that $top_srcdir and $ac_aux_dir +# are both prefixed by $srcdir. In an in-source build this is usually +# harmless because $srcdir is `.', but things will broke when you +# start a VPATH build or use an absolute $srcdir. +# +# So we could use something similar to $top_srcdir/$ac_aux_dir/missing, +# iff we strip the leading $srcdir from $ac_aux_dir. That would be: +# am_aux_dir='\$(top_srcdir)/'`expr "$ac_aux_dir" : "$srcdir//*\(.*\)"` +# and then we would define $MISSING as +# MISSING="\${SHELL} $am_aux_dir/missing" +# This will work as long as MISSING is not called from configure, because +# unfortunately $(top_srcdir) has no meaning in configure. +# However there are other variables, like CC, which are often used in +# configure, and could therefore not use this "fixed" $ac_aux_dir. +# +# Another solution, used here, is to always expand $ac_aux_dir to an +# absolute PATH. The drawback is that using absolute paths prevent a +# configured tree to be moved without reconfiguration. + +AC_DEFUN([AM_AUX_DIR_EXPAND], +[dnl Rely on autoconf to set up CDPATH properly. +AC_PREREQ([2.50])dnl +# expand $ac_aux_dir to an absolute path +am_aux_dir=`cd $ac_aux_dir && pwd` +]) + +# AM_CONDITIONAL -*- Autoconf -*- + +# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006, 2008 +# Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# serial 9 + +# AM_CONDITIONAL(NAME, SHELL-CONDITION) +# ------------------------------------- +# Define a conditional. +AC_DEFUN([AM_CONDITIONAL], +[AC_PREREQ(2.52)dnl + ifelse([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])], + [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl +AC_SUBST([$1_TRUE])dnl +AC_SUBST([$1_FALSE])dnl +_AM_SUBST_NOTMAKE([$1_TRUE])dnl +_AM_SUBST_NOTMAKE([$1_FALSE])dnl +m4_define([_AM_COND_VALUE_$1], [$2])dnl +if $2; then + $1_TRUE= + $1_FALSE='#' +else + $1_TRUE='#' + $1_FALSE= +fi +AC_CONFIG_COMMANDS_PRE( +[if test -z "${$1_TRUE}" && test -z "${$1_FALSE}"; then + AC_MSG_ERROR([[conditional "$1" was never defined. +Usually this means the macro was only invoked conditionally.]]) +fi])]) + +# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009 +# Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# serial 10 + +# There are a few dirty hacks below to avoid letting `AC_PROG_CC' be +# written in clear, in which case automake, when reading aclocal.m4, +# will think it sees a *use*, and therefore will trigger all it's +# C support machinery. Also note that it means that autoscan, seeing +# CC etc. in the Makefile, will ask for an AC_PROG_CC use... + + +# _AM_DEPENDENCIES(NAME) +# ---------------------- +# See how the compiler implements dependency checking. +# NAME is "CC", "CXX", "GCJ", or "OBJC". +# We try a few techniques and use that to set a single cache variable. +# +# We don't AC_REQUIRE the corresponding AC_PROG_CC since the latter was +# modified to invoke _AM_DEPENDENCIES(CC); we would have a circular +# dependency, and given that the user is not expected to run this macro, +# just rely on AC_PROG_CC. +AC_DEFUN([_AM_DEPENDENCIES], +[AC_REQUIRE([AM_SET_DEPDIR])dnl +AC_REQUIRE([AM_OUTPUT_DEPENDENCY_COMMANDS])dnl +AC_REQUIRE([AM_MAKE_INCLUDE])dnl +AC_REQUIRE([AM_DEP_TRACK])dnl + +ifelse([$1], CC, [depcc="$CC" am_compiler_list=], + [$1], CXX, [depcc="$CXX" am_compiler_list=], + [$1], OBJC, [depcc="$OBJC" am_compiler_list='gcc3 gcc'], + [$1], UPC, [depcc="$UPC" am_compiler_list=], + [$1], GCJ, [depcc="$GCJ" am_compiler_list='gcc3 gcc'], + [depcc="$$1" am_compiler_list=]) + +AC_CACHE_CHECK([dependency style of $depcc], + [am_cv_$1_dependencies_compiler_type], +[if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then + # We make a subdir and do the tests there. Otherwise we can end up + # making bogus files that we don't know about and never remove. For + # instance it was reported that on HP-UX the gcc test will end up + # making a dummy file named `D' -- because `-MD' means `put the output + # in D'. + mkdir conftest.dir + # Copy depcomp to subdir because otherwise we won't find it if we're + # using a relative directory. + cp "$am_depcomp" conftest.dir + cd conftest.dir + # We will build objects and dependencies in a subdirectory because + # it helps to detect inapplicable dependency modes. For instance + # both Tru64's cc and ICC support -MD to output dependencies as a + # side effect of compilation, but ICC will put the dependencies in + # the current directory while Tru64 will put them in the object + # directory. + mkdir sub + + am_cv_$1_dependencies_compiler_type=none + if test "$am_compiler_list" = ""; then + am_compiler_list=`sed -n ['s/^#*\([a-zA-Z0-9]*\))$/\1/p'] < ./depcomp` + fi + am__universal=false + m4_case([$1], [CC], + [case " $depcc " in #( + *\ -arch\ *\ -arch\ *) am__universal=true ;; + esac], + [CXX], + [case " $depcc " in #( + *\ -arch\ *\ -arch\ *) am__universal=true ;; + esac]) + + for depmode in $am_compiler_list; do + # Setup a source with many dependencies, because some compilers + # like to wrap large dependency lists on column 80 (with \), and + # we should not choose a depcomp mode which is confused by this. + # + # We need to recreate these files for each test, as the compiler may + # overwrite some of them when testing with obscure command lines. + # This happens at least with the AIX C compiler. + : > sub/conftest.c + for i in 1 2 3 4 5 6; do + echo '#include "conftst'$i'.h"' >> sub/conftest.c + # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with + # Solaris 8's {/usr,}/bin/sh. + touch sub/conftst$i.h + done + echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf + + # We check with `-c' and `-o' for the sake of the "dashmstdout" + # mode. It turns out that the SunPro C++ compiler does not properly + # handle `-M -o', and we need to detect this. Also, some Intel + # versions had trouble with output in subdirs + am__obj=sub/conftest.${OBJEXT-o} + am__minus_obj="-o $am__obj" + case $depmode in + gcc) + # This depmode causes a compiler race in universal mode. + test "$am__universal" = false || continue + ;; + nosideeffect) + # after this tag, mechanisms are not by side-effect, so they'll + # only be used when explicitly requested + if test "x$enable_dependency_tracking" = xyes; then + continue + else + break + fi + ;; + msvisualcpp | msvcmsys) + # This compiler won't grok `-c -o', but also, the minuso test has + # not run yet. These depmodes are late enough in the game, and + # so weak that their functioning should not be impacted. + am__obj=conftest.${OBJEXT-o} + am__minus_obj= + ;; + none) break ;; + esac + if depmode=$depmode \ + source=sub/conftest.c object=$am__obj \ + depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \ + $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \ + >/dev/null 2>conftest.err && + grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 && + grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 && + grep $am__obj sub/conftest.Po > /dev/null 2>&1 && + ${MAKE-make} -s -f confmf > /dev/null 2>&1; then + # icc doesn't choke on unknown options, it will just issue warnings + # or remarks (even with -Werror). So we grep stderr for any message + # that says an option was ignored or not supported. + # When given -MP, icc 7.0 and 7.1 complain thusly: + # icc: Command line warning: ignoring option '-M'; no argument required + # The diagnosis changed in icc 8.0: + # icc: Command line remark: option '-MP' not supported + if (grep 'ignoring option' conftest.err || + grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else + am_cv_$1_dependencies_compiler_type=$depmode + break + fi + fi + done + + cd .. + rm -rf conftest.dir +else + am_cv_$1_dependencies_compiler_type=none +fi +]) +AC_SUBST([$1DEPMODE], [depmode=$am_cv_$1_dependencies_compiler_type]) +AM_CONDITIONAL([am__fastdep$1], [ + test "x$enable_dependency_tracking" != xno \ + && test "$am_cv_$1_dependencies_compiler_type" = gcc3]) +]) + + +# AM_SET_DEPDIR +# ------------- +# Choose a directory name for dependency files. +# This macro is AC_REQUIREd in _AM_DEPENDENCIES +AC_DEFUN([AM_SET_DEPDIR], +[AC_REQUIRE([AM_SET_LEADING_DOT])dnl +AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl +]) + + +# AM_DEP_TRACK +# ------------ +AC_DEFUN([AM_DEP_TRACK], +[AC_ARG_ENABLE(dependency-tracking, +[ --disable-dependency-tracking speeds up one-time build + --enable-dependency-tracking do not reject slow dependency extractors]) +if test "x$enable_dependency_tracking" != xno; then + am_depcomp="$ac_aux_dir/depcomp" + AMDEPBACKSLASH='\' +fi +AM_CONDITIONAL([AMDEP], [test "x$enable_dependency_tracking" != xno]) +AC_SUBST([AMDEPBACKSLASH])dnl +_AM_SUBST_NOTMAKE([AMDEPBACKSLASH])dnl +]) + +# Generate code to set up dependency tracking. -*- Autoconf -*- + +# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2008 +# Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +#serial 5 + +# _AM_OUTPUT_DEPENDENCY_COMMANDS +# ------------------------------ +AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS], +[{ + # Autoconf 2.62 quotes --file arguments for eval, but not when files + # are listed without --file. Let's play safe and only enable the eval + # if we detect the quoting. + case $CONFIG_FILES in + *\'*) eval set x "$CONFIG_FILES" ;; + *) set x $CONFIG_FILES ;; + esac + shift + for mf + do + # Strip MF so we end up with the name of the file. + mf=`echo "$mf" | sed -e 's/:.*$//'` + # Check whether this is an Automake generated Makefile or not. + # We used to match only the files named `Makefile.in', but + # some people rename them; so instead we look at the file content. + # Grep'ing the first line is not enough: some people post-process + # each Makefile.in and add a new line on top of each file to say so. + # Grep'ing the whole file is not good either: AIX grep has a line + # limit of 2048, but all sed's we know have understand at least 4000. + if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then + dirpart=`AS_DIRNAME("$mf")` + else + continue + fi + # Extract the definition of DEPDIR, am__include, and am__quote + # from the Makefile without running `make'. + DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"` + test -z "$DEPDIR" && continue + am__include=`sed -n 's/^am__include = //p' < "$mf"` + test -z "am__include" && continue + am__quote=`sed -n 's/^am__quote = //p' < "$mf"` + # When using ansi2knr, U may be empty or an underscore; expand it + U=`sed -n 's/^U = //p' < "$mf"` + # Find all dependency output files, they are included files with + # $(DEPDIR) in their names. We invoke sed twice because it is the + # simplest approach to changing $(DEPDIR) to its actual value in the + # expansion. + for file in `sed -n " + s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \ + sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do + # Make sure the directory exists. + test -f "$dirpart/$file" && continue + fdir=`AS_DIRNAME(["$file"])` + AS_MKDIR_P([$dirpart/$fdir]) + # echo "creating $dirpart/$file" + echo '# dummy' > "$dirpart/$file" + done + done +} +])# _AM_OUTPUT_DEPENDENCY_COMMANDS + + +# AM_OUTPUT_DEPENDENCY_COMMANDS +# ----------------------------- +# This macro should only be invoked once -- use via AC_REQUIRE. +# +# This code is only required when automatic dependency tracking +# is enabled. FIXME. This creates each `.P' file that we will +# need in order to bootstrap the dependency handling code. +AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS], +[AC_CONFIG_COMMANDS([depfiles], + [test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS], + [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"]) +]) + +# Do all the work for Automake. -*- Autoconf -*- + +# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, +# 2005, 2006, 2008, 2009 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# serial 16 + +# This macro actually does too much. Some checks are only needed if +# your package does certain things. But this isn't really a big deal. + +# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE]) +# AM_INIT_AUTOMAKE([OPTIONS]) +# ----------------------------------------------- +# The call with PACKAGE and VERSION arguments is the old style +# call (pre autoconf-2.50), which is being phased out. PACKAGE +# and VERSION should now be passed to AC_INIT and removed from +# the call to AM_INIT_AUTOMAKE. +# We support both call styles for the transition. After +# the next Automake release, Autoconf can make the AC_INIT +# arguments mandatory, and then we can depend on a new Autoconf +# release and drop the old call support. +AC_DEFUN([AM_INIT_AUTOMAKE], +[AC_PREREQ([2.62])dnl +dnl Autoconf wants to disallow AM_ names. We explicitly allow +dnl the ones we care about. +m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl +AC_REQUIRE([AM_SET_CURRENT_AUTOMAKE_VERSION])dnl +AC_REQUIRE([AC_PROG_INSTALL])dnl +if test "`cd $srcdir && pwd`" != "`pwd`"; then + # Use -I$(srcdir) only when $(srcdir) != ., so that make's output + # is not polluted with repeated "-I." + AC_SUBST([am__isrc], [' -I$(srcdir)'])_AM_SUBST_NOTMAKE([am__isrc])dnl + # test to see if srcdir already configured + if test -f $srcdir/config.status; then + AC_MSG_ERROR([source directory already configured; run "make distclean" there first]) + fi +fi + +# test whether we have cygpath +if test -z "$CYGPATH_W"; then + if (cygpath --version) >/dev/null 2>/dev/null; then + CYGPATH_W='cygpath -w' + else + CYGPATH_W=echo + fi +fi +AC_SUBST([CYGPATH_W]) + +# Define the identity of the package. +dnl Distinguish between old-style and new-style calls. +m4_ifval([$2], +[m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl + AC_SUBST([PACKAGE], [$1])dnl + AC_SUBST([VERSION], [$2])], +[_AM_SET_OPTIONS([$1])dnl +dnl Diagnose old-style AC_INIT with new-style AM_AUTOMAKE_INIT. +m4_if(m4_ifdef([AC_PACKAGE_NAME], 1)m4_ifdef([AC_PACKAGE_VERSION], 1), 11,, + [m4_fatal([AC_INIT should be called with package and version arguments])])dnl + AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])dnl + AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])])dnl + +_AM_IF_OPTION([no-define],, +[AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package]) + AC_DEFINE_UNQUOTED(VERSION, "$VERSION", [Version number of package])])dnl + +# Some tools Automake needs. +AC_REQUIRE([AM_SANITY_CHECK])dnl +AC_REQUIRE([AC_ARG_PROGRAM])dnl +AM_MISSING_PROG(ACLOCAL, aclocal-${am__api_version}) +AM_MISSING_PROG(AUTOCONF, autoconf) +AM_MISSING_PROG(AUTOMAKE, automake-${am__api_version}) +AM_MISSING_PROG(AUTOHEADER, autoheader) +AM_MISSING_PROG(MAKEINFO, makeinfo) +AC_REQUIRE([AM_PROG_INSTALL_SH])dnl +AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl +AC_REQUIRE([AM_PROG_MKDIR_P])dnl +# We need awk for the "check" target. The system "awk" is bad on +# some platforms. +AC_REQUIRE([AC_PROG_AWK])dnl +AC_REQUIRE([AC_PROG_MAKE_SET])dnl +AC_REQUIRE([AM_SET_LEADING_DOT])dnl +_AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])], + [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])], + [_AM_PROG_TAR([v7])])]) +_AM_IF_OPTION([no-dependencies],, +[AC_PROVIDE_IFELSE([AC_PROG_CC], + [_AM_DEPENDENCIES(CC)], + [define([AC_PROG_CC], + defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl +AC_PROVIDE_IFELSE([AC_PROG_CXX], + [_AM_DEPENDENCIES(CXX)], + [define([AC_PROG_CXX], + defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl +AC_PROVIDE_IFELSE([AC_PROG_OBJC], + [_AM_DEPENDENCIES(OBJC)], + [define([AC_PROG_OBJC], + defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl +]) +_AM_IF_OPTION([silent-rules], [AC_REQUIRE([AM_SILENT_RULES])])dnl +dnl The `parallel-tests' driver may need to know about EXEEXT, so add the +dnl `am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This macro +dnl is hooked onto _AC_COMPILER_EXEEXT early, see below. +AC_CONFIG_COMMANDS_PRE(dnl +[m4_provide_if([_AM_COMPILER_EXEEXT], + [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl +]) + +dnl Hook into `_AC_COMPILER_EXEEXT' early to learn its expansion. Do not +dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further +dnl mangled by Autoconf and run in a shell conditional statement. +m4_define([_AC_COMPILER_EXEEXT], +m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])]) + + +# When config.status generates a header, we must update the stamp-h file. +# This file resides in the same directory as the config header +# that is generated. The stamp files are numbered to have different names. + +# Autoconf calls _AC_AM_CONFIG_HEADER_HOOK (when defined) in the +# loop where config.status creates the headers, so we can generate +# our stamp files there. +AC_DEFUN([_AC_AM_CONFIG_HEADER_HOOK], +[# Compute $1's index in $config_headers. +_am_arg=$1 +_am_stamp_count=1 +for _am_header in $config_headers :; do + case $_am_header in + $_am_arg | $_am_arg:* ) + break ;; + * ) + _am_stamp_count=`expr $_am_stamp_count + 1` ;; + esac +done +echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count]) + +# Copyright (C) 2001, 2003, 2005, 2008 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# AM_PROG_INSTALL_SH +# ------------------ +# Define $install_sh. +AC_DEFUN([AM_PROG_INSTALL_SH], +[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl +if test x"${install_sh}" != xset; then + case $am_aux_dir in + *\ * | *\ *) + install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;; + *) + install_sh="\${SHELL} $am_aux_dir/install-sh" + esac +fi +AC_SUBST(install_sh)]) + +# Copyright (C) 2003, 2005 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# serial 2 + +# Check whether the underlying file-system supports filenames +# with a leading dot. For instance MS-DOS doesn't. +AC_DEFUN([AM_SET_LEADING_DOT], +[rm -rf .tst 2>/dev/null +mkdir .tst 2>/dev/null +if test -d .tst; then + am__leading_dot=. +else + am__leading_dot=_ +fi +rmdir .tst 2>/dev/null +AC_SUBST([am__leading_dot])]) + +# Check to see how 'make' treats includes. -*- Autoconf -*- + +# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# serial 4 + +# AM_MAKE_INCLUDE() +# ----------------- +# Check to see how make treats includes. +AC_DEFUN([AM_MAKE_INCLUDE], +[am_make=${MAKE-make} +cat > confinc << 'END' +am__doit: + @echo this is the am__doit target +.PHONY: am__doit +END +# If we don't find an include directive, just comment out the code. +AC_MSG_CHECKING([for style of include used by $am_make]) +am__include="#" +am__quote= +_am_result=none +# First try GNU make style include. +echo "include confinc" > confmf +# Ignore all kinds of additional output from `make'. +case `$am_make -s -f confmf 2> /dev/null` in #( +*the\ am__doit\ target*) + am__include=include + am__quote= + _am_result=GNU + ;; +esac +# Now try BSD make style include. +if test "$am__include" = "#"; then + echo '.include "confinc"' > confmf + case `$am_make -s -f confmf 2> /dev/null` in #( + *the\ am__doit\ target*) + am__include=.include + am__quote="\"" + _am_result=BSD + ;; + esac +fi +AC_SUBST([am__include]) +AC_SUBST([am__quote]) +AC_MSG_RESULT([$_am_result]) +rm -f confinc confmf +]) + +# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*- + +# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008 +# Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# serial 6 + +# AM_MISSING_PROG(NAME, PROGRAM) +# ------------------------------ +AC_DEFUN([AM_MISSING_PROG], +[AC_REQUIRE([AM_MISSING_HAS_RUN]) +$1=${$1-"${am_missing_run}$2"} +AC_SUBST($1)]) + + +# AM_MISSING_HAS_RUN +# ------------------ +# Define MISSING if not defined so far and test if it supports --run. +# If it does, set am_missing_run to use it, otherwise, to nothing. +AC_DEFUN([AM_MISSING_HAS_RUN], +[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl +AC_REQUIRE_AUX_FILE([missing])dnl +if test x"${MISSING+set}" != xset; then + case $am_aux_dir in + *\ * | *\ *) + MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;; + *) + MISSING="\${SHELL} $am_aux_dir/missing" ;; + esac +fi +# Use eval to expand $SHELL +if eval "$MISSING --run true"; then + am_missing_run="$MISSING --run " +else + am_missing_run= + AC_MSG_WARN([`missing' script is too old or missing]) +fi +]) + +# Copyright (C) 2003, 2004, 2005, 2006 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# AM_PROG_MKDIR_P +# --------------- +# Check for `mkdir -p'. +AC_DEFUN([AM_PROG_MKDIR_P], +[AC_PREREQ([2.60])dnl +AC_REQUIRE([AC_PROG_MKDIR_P])dnl +dnl Automake 1.8 to 1.9.6 used to define mkdir_p. We now use MKDIR_P, +dnl while keeping a definition of mkdir_p for backward compatibility. +dnl @MKDIR_P@ is magic: AC_OUTPUT adjusts its value for each Makefile. +dnl However we cannot define mkdir_p as $(MKDIR_P) for the sake of +dnl Makefile.ins that do not define MKDIR_P, so we do our own +dnl adjustment using top_builddir (which is defined more often than +dnl MKDIR_P). +AC_SUBST([mkdir_p], ["$MKDIR_P"])dnl +case $mkdir_p in + [[\\/$]]* | ?:[[\\/]]*) ;; + */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;; +esac +]) + +# Helper functions for option handling. -*- Autoconf -*- + +# Copyright (C) 2001, 2002, 2003, 2005, 2008 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# serial 4 + +# _AM_MANGLE_OPTION(NAME) +# ----------------------- +AC_DEFUN([_AM_MANGLE_OPTION], +[[_AM_OPTION_]m4_bpatsubst($1, [[^a-zA-Z0-9_]], [_])]) + +# _AM_SET_OPTION(NAME) +# ------------------------------ +# Set option NAME. Presently that only means defining a flag for this option. +AC_DEFUN([_AM_SET_OPTION], +[m4_define(_AM_MANGLE_OPTION([$1]), 1)]) + +# _AM_SET_OPTIONS(OPTIONS) +# ---------------------------------- +# OPTIONS is a space-separated list of Automake options. +AC_DEFUN([_AM_SET_OPTIONS], +[m4_foreach_w([_AM_Option], [$1], [_AM_SET_OPTION(_AM_Option)])]) + +# _AM_IF_OPTION(OPTION, IF-SET, [IF-NOT-SET]) +# ------------------------------------------- +# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise. +AC_DEFUN([_AM_IF_OPTION], +[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])]) + +# Check to make sure that the build environment is sane. -*- Autoconf -*- + +# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 2008 +# Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# serial 5 + +# AM_SANITY_CHECK +# --------------- +AC_DEFUN([AM_SANITY_CHECK], +[AC_MSG_CHECKING([whether build environment is sane]) +# Just in case +sleep 1 +echo timestamp > conftest.file +# Reject unsafe characters in $srcdir or the absolute working directory +# name. Accept space and tab only in the latter. +am_lf=' +' +case `pwd` in + *[[\\\"\#\$\&\'\`$am_lf]]*) + AC_MSG_ERROR([unsafe absolute working directory name]);; +esac +case $srcdir in + *[[\\\"\#\$\&\'\`$am_lf\ \ ]]*) + AC_MSG_ERROR([unsafe srcdir value: `$srcdir']);; +esac + +# Do `set' in a subshell so we don't clobber the current shell's +# arguments. Must try -L first in case configure is actually a +# symlink; some systems play weird games with the mod time of symlinks +# (eg FreeBSD returns the mod time of the symlink's containing +# directory). +if ( + set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null` + if test "$[*]" = "X"; then + # -L didn't work. + set X `ls -t "$srcdir/configure" conftest.file` + fi + rm -f conftest.file + if test "$[*]" != "X $srcdir/configure conftest.file" \ + && test "$[*]" != "X conftest.file $srcdir/configure"; then + + # If neither matched, then we have a broken ls. This can happen + # if, for instance, CONFIG_SHELL is bash and it inherits a + # broken ls alias from the environment. This has actually + # happened. Such a system could not be considered "sane". + AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken +alias in your environment]) + fi + + test "$[2]" = conftest.file + ) +then + # Ok. + : +else + AC_MSG_ERROR([newly created file is older than distributed files! +Check your system clock]) +fi +AC_MSG_RESULT(yes)]) + +# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# AM_PROG_INSTALL_STRIP +# --------------------- +# One issue with vendor `install' (even GNU) is that you can't +# specify the program used to strip binaries. This is especially +# annoying in cross-compiling environments, where the build's strip +# is unlikely to handle the host's binaries. +# Fortunately install-sh will honor a STRIPPROG variable, so we +# always use install-sh in `make install-strip', and initialize +# STRIPPROG with the value of the STRIP variable (set by the user). +AC_DEFUN([AM_PROG_INSTALL_STRIP], +[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl +# Installed binaries are usually stripped using `strip' when the user +# run `make install-strip'. However `strip' might not be the right +# tool to use in cross-compilation environments, therefore Automake +# will honor the `STRIP' environment variable to overrule this program. +dnl Don't test for $cross_compiling = yes, because it might be `maybe'. +if test "$cross_compiling" != no; then + AC_CHECK_TOOL([STRIP], [strip], :) +fi +INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s" +AC_SUBST([INSTALL_STRIP_PROGRAM])]) + +# Copyright (C) 2006, 2008 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# serial 2 + +# _AM_SUBST_NOTMAKE(VARIABLE) +# --------------------------- +# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in. +# This macro is traced by Automake. +AC_DEFUN([_AM_SUBST_NOTMAKE]) + +# AM_SUBST_NOTMAKE(VARIABLE) +# --------------------------- +# Public sister of _AM_SUBST_NOTMAKE. +AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)]) + +# Check how to create a tarball. -*- Autoconf -*- + +# Copyright (C) 2004, 2005 Free Software Foundation, Inc. +# +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# serial 2 + +# _AM_PROG_TAR(FORMAT) +# -------------------- +# Check how to create a tarball in format FORMAT. +# FORMAT should be one of `v7', `ustar', or `pax'. +# +# Substitute a variable $(am__tar) that is a command +# writing to stdout a FORMAT-tarball containing the directory +# $tardir. +# tardir=directory && $(am__tar) > result.tar +# +# Substitute a variable $(am__untar) that extract such +# a tarball read from stdin. +# $(am__untar) < result.tar +AC_DEFUN([_AM_PROG_TAR], +[# Always define AMTAR for backward compatibility. +AM_MISSING_PROG([AMTAR], [tar]) +m4_if([$1], [v7], + [am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'], + [m4_case([$1], [ustar],, [pax],, + [m4_fatal([Unknown tar format])]) +AC_MSG_CHECKING([how to create a $1 tar archive]) +# Loop over all known methods to create a tar archive until one works. +_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none' +_am_tools=${am_cv_prog_tar_$1-$_am_tools} +# Do not fold the above two line into one, because Tru64 sh and +# Solaris sh will not grok spaces in the rhs of `-'. +for _am_tool in $_am_tools +do + case $_am_tool in + gnutar) + for _am_tar in tar gnutar gtar; + do + AM_RUN_LOG([$_am_tar --version]) && break + done + am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"' + am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"' + am__untar="$_am_tar -xf -" + ;; + plaintar) + # Must skip GNU tar: if it does not support --format= it doesn't create + # ustar tarball either. + (tar --version) >/dev/null 2>&1 && continue + am__tar='tar chf - "$$tardir"' + am__tar_='tar chf - "$tardir"' + am__untar='tar xf -' + ;; + pax) + am__tar='pax -L -x $1 -w "$$tardir"' + am__tar_='pax -L -x $1 -w "$tardir"' + am__untar='pax -r' + ;; + cpio) + am__tar='find "$$tardir" -print | cpio -o -H $1 -L' + am__tar_='find "$tardir" -print | cpio -o -H $1 -L' + am__untar='cpio -i -H $1 -d' + ;; + none) + am__tar=false + am__tar_=false + am__untar=false + ;; + esac + + # If the value was cached, stop now. We just wanted to have am__tar + # and am__untar set. + test -n "${am_cv_prog_tar_$1}" && break + + # tar/untar a dummy directory, and stop if the command works + rm -rf conftest.dir + mkdir conftest.dir + echo GrepMe > conftest.dir/file + AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar]) + rm -rf conftest.dir + if test -s conftest.tar; then + AM_RUN_LOG([$am__untar