From 16f1ab3fd51731ec19fd3744f319d89c432e0270 Mon Sep 17 00:00:00 2001 From: Jeremiah Wala Date: Thu, 18 Jun 2015 14:03:03 -0400 Subject: [PATCH] fixed build --- src/GenomicRegionCollection.cpp | 13 +- src/Makefile | 57 ++-- src/Makefile.in | 53 ++-- src/autogen.sh | 7 + src/config.h | 59 +++++ src/config.h.in | 58 +++++ src/config.status | 221 +++++++++++++++- src/configure | 445 +++++++++++++++++++++++++++++--- src/configure.ac | 5 +- 9 files changed, 839 insertions(+), 79 deletions(-) create mode 100755 src/autogen.sh create mode 100644 src/config.h create mode 100644 src/config.h.in diff --git a/src/GenomicRegionCollection.cpp b/src/GenomicRegionCollection.cpp index 59b01d435..9938e8f95 100644 --- a/src/GenomicRegionCollection.cpp +++ b/src/GenomicRegionCollection.cpp @@ -1,12 +1,14 @@ -//#include "SnowTools/GenomicRegionCollection.h" +#include "SnowTools/GenomicRegionCollection.h" #include #include #include #include "SnowTools/gzstream.h" #include - + +#ifdef HAVE_BOOST_ICL_INTERVAL_SET_HPP #include +#endif //#define DEBUG_OVERLAPS 1 @@ -414,12 +416,11 @@ GRC GenomicRegionCollection::intersection(GRC& subject, bool ignore_strand /* template GRC GenomicRegionCollection::complement(GRC& subject, bool ignore_strand) { - -#ifdef BOOST_CONFIG_HPP GRC out; // get this - that +#ifdef BOOST_CONFIG_HPP using namespace boost::icl; typedef interval_set TIntervalSet; @@ -462,8 +463,8 @@ GRC GenomicRegionCollection::complement(GRC& subject, bool ignore_strand) return out; #else - std::cerr << "No Boost library detected. GenomicRegionCollection::complement will not function. Returning Empty GRC" - return GRC(); + std::cerr << "No Boost library detected. GenomicRegionCollection::complement will not function. Returning Empty GRC" << std::endl; + return out; #endif } diff --git a/src/Makefile b/src/Makefile index fb99bc31d..5694da0c8 100644 --- a/src/Makefile +++ b/src/Makefile @@ -38,8 +38,8 @@ POST_UNINSTALL = : bin_PROGRAMS = snowtools$(EXEEXT) subdir = . DIST_COMMON = $(am__configure_deps) $(srcdir)/Makefile.am \ - $(srcdir)/Makefile.in $(top_srcdir)/configure compile depcomp \ - install-sh missing + $(srcdir)/Makefile.in $(srcdir)/config.h.in \ + $(top_srcdir)/configure compile 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) \ @@ -47,6 +47,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \ configure.lineno configure.status.lineno mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = config.h CONFIG_CLEAN_FILES = LIBRARIES = $(noinst_LIBRARIES) AR = ar @@ -85,7 +86,7 @@ am_snowtools_OBJECTS = snowtools-SnowTools.$(OBJEXT) \ snowtools_OBJECTS = $(am_snowtools_OBJECTS) snowtools_DEPENDENCIES = $(top_builddir)/libsnowtools.a \ $(top_builddir)/bwa/libbwa.a $(top_builddir)/htslib/libhts.a -DEFAULT_INCLUDES = -I. -I$(srcdir) +DEFAULT_INCLUDES = -I. -I$(srcdir) -I. depcomp = $(SHELL) $(top_srcdir)/depcomp am__depfiles_maybe = depfiles CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ @@ -131,13 +132,13 @@ AWK = gawk CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -O3 -CPPFLAGS = -I/xchip/gistic/Jeremiah/boost_1_58_0 +CPPFLAGS = -I/xchip/gistic/Jeremiah/boost_1_58_0DUMY CXX = g++ CXXCPP = g++ -E CXXDEPMODE = depmode=gcc3 CXXFLAGS = -O3 CYGPATH_W = echo -DEFS = -DPACKAGE_NAME=\"snowtools\" -DPACKAGE_TARNAME=\"snowtools\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"snowtools\ 1.0\" -DPACKAGE_BUGREPORT=\"jwala@broadinstitute.org\" -DPACKAGE=\"snowtools\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_CLOCK_GETTIME=1 +DEFS = -DHAVE_CONFIG_H DEPDIR = .deps ECHO_C = ECHO_N = -n @@ -224,7 +225,8 @@ snowtools_CPPFLAGS = \ snowtools_LDADD = $(top_builddir)/libsnowtools.a $(top_builddir)/bwa/libbwa.a $(top_builddir)/htslib/libhts.a snowtools_LDFLAGS = -pthread -std=c++11 snowtools_SOURCES = SnowTools.cpp CoverageTool.cpp RealignTool.cpp -all: all-recursive +all: config.h + $(MAKE) $(AM_MAKEFLAGS) all-recursive .SUFFIXES: .SUFFIXES: .C .c .cpp .o .obj @@ -262,6 +264,23 @@ $(top_srcdir)/configure: $(am__configure_deps) $(ACLOCAL_M4): $(am__aclocal_m4_deps) cd $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS) +config.h: stamp-h1 + @if test ! -f $@; then \ + rm -f stamp-h1; \ + $(MAKE) 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) + cd $(top_srcdir) && $(AUTOHEADER) + rm -f stamp-h1 + touch $@ + +distclean-hdr: + -rm -f config.h stamp-h1 + clean-noinstLIBRARIES: -test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES) libsnowtools.a: $(libsnowtools_a_OBJECTS) $(libsnowtools_a_DEPENDENCIES) @@ -786,7 +805,7 @@ ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) mkid -fID $$unique tags: TAGS -TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ +TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) tags=; \ here=`pwd`; \ @@ -803,7 +822,7 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \ fi; \ done; \ - list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ + list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \ unique=`for i in $$list; do \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ done | \ @@ -815,11 +834,11 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ $$tags $$unique; \ fi ctags: CTAGS -CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ +CTAGS: ctags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) tags=; \ here=`pwd`; \ - list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ + list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \ unique=`for i in $$list; do \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ done | \ @@ -980,7 +999,7 @@ distcleancheck: distclean exit 1; } >&2 check-am: all-am check: check-recursive -all-am: Makefile $(LIBRARIES) $(PROGRAMS) +all-am: Makefile $(LIBRARIES) $(PROGRAMS) config.h installdirs: installdirs-recursive installdirs-am: for dir in "$(DESTDIR)$(bindir)"; do \ @@ -1020,7 +1039,7 @@ distclean: distclean-recursive -rm -rf ./$(DEPDIR) -rm -f Makefile distclean-am: clean-am distclean-compile distclean-generic \ - distclean-tags + distclean-hdr distclean-tags dvi: dvi-recursive @@ -1070,13 +1089,13 @@ uninstall-info: uninstall-info-recursive clean-noinstLIBRARIES clean-recursive ctags ctags-recursive \ dist dist-all dist-bzip2 dist-gzip dist-shar dist-tarZ \ dist-zip distcheck distclean distclean-compile \ - distclean-generic distclean-recursive 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-exec install-exec-am \ - install-info install-info-am install-man install-strip \ - installcheck installcheck-am installdirs installdirs-am \ - maintainer-clean maintainer-clean-generic \ + distclean-generic distclean-hdr distclean-recursive \ + 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-exec \ + install-exec-am install-info install-info-am install-man \ + install-strip installcheck installcheck-am installdirs \ + installdirs-am maintainer-clean maintainer-clean-generic \ maintainer-clean-recursive mostlyclean mostlyclean-compile \ mostlyclean-generic mostlyclean-recursive pdf pdf-am ps ps-am \ tags tags-recursive uninstall uninstall-am \ diff --git a/src/Makefile.in b/src/Makefile.in index 59dbfc451..34568752e 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -38,8 +38,8 @@ POST_UNINSTALL = : bin_PROGRAMS = snowtools$(EXEEXT) subdir = . DIST_COMMON = $(am__configure_deps) $(srcdir)/Makefile.am \ - $(srcdir)/Makefile.in $(top_srcdir)/configure compile depcomp \ - install-sh missing + $(srcdir)/Makefile.in $(srcdir)/config.h.in \ + $(top_srcdir)/configure compile 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) \ @@ -47,6 +47,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \ configure.lineno configure.status.lineno mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = config.h CONFIG_CLEAN_FILES = LIBRARIES = $(noinst_LIBRARIES) AR = ar @@ -85,7 +86,7 @@ am_snowtools_OBJECTS = snowtools-SnowTools.$(OBJEXT) \ snowtools_OBJECTS = $(am_snowtools_OBJECTS) snowtools_DEPENDENCIES = $(top_builddir)/libsnowtools.a \ $(top_builddir)/bwa/libbwa.a $(top_builddir)/htslib/libhts.a -DEFAULT_INCLUDES = -I. -I$(srcdir) +DEFAULT_INCLUDES = -I. -I$(srcdir) -I. depcomp = $(SHELL) $(top_srcdir)/depcomp am__depfiles_maybe = depfiles CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ @@ -224,7 +225,8 @@ snowtools_CPPFLAGS = \ snowtools_LDADD = $(top_builddir)/libsnowtools.a $(top_builddir)/bwa/libbwa.a $(top_builddir)/htslib/libhts.a snowtools_LDFLAGS = -pthread -std=c++11 snowtools_SOURCES = SnowTools.cpp CoverageTool.cpp RealignTool.cpp -all: all-recursive +all: config.h + $(MAKE) $(AM_MAKEFLAGS) all-recursive .SUFFIXES: .SUFFIXES: .C .c .cpp .o .obj @@ -262,6 +264,23 @@ $(top_srcdir)/configure: $(am__configure_deps) $(ACLOCAL_M4): $(am__aclocal_m4_deps) cd $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS) +config.h: stamp-h1 + @if test ! -f $@; then \ + rm -f stamp-h1; \ + $(MAKE) 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) + cd $(top_srcdir) && $(AUTOHEADER) + rm -f stamp-h1 + touch $@ + +distclean-hdr: + -rm -f config.h stamp-h1 + clean-noinstLIBRARIES: -test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES) libsnowtools.a: $(libsnowtools_a_OBJECTS) $(libsnowtools_a_DEPENDENCIES) @@ -786,7 +805,7 @@ ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) mkid -fID $$unique tags: TAGS -TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ +TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) tags=; \ here=`pwd`; \ @@ -803,7 +822,7 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \ fi; \ done; \ - list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ + list='$(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 | \ @@ -815,11 +834,11 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ $$tags $$unique; \ fi ctags: CTAGS -CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ +CTAGS: ctags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) tags=; \ here=`pwd`; \ - list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ + list='$(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 | \ @@ -980,7 +999,7 @@ distcleancheck: distclean exit 1; } >&2 check-am: all-am check: check-recursive -all-am: Makefile $(LIBRARIES) $(PROGRAMS) +all-am: Makefile $(LIBRARIES) $(PROGRAMS) config.h installdirs: installdirs-recursive installdirs-am: for dir in "$(DESTDIR)$(bindir)"; do \ @@ -1020,7 +1039,7 @@ distclean: distclean-recursive -rm -rf ./$(DEPDIR) -rm -f Makefile distclean-am: clean-am distclean-compile distclean-generic \ - distclean-tags + distclean-hdr distclean-tags dvi: dvi-recursive @@ -1070,13 +1089,13 @@ uninstall-info: uninstall-info-recursive clean-noinstLIBRARIES clean-recursive ctags ctags-recursive \ dist dist-all dist-bzip2 dist-gzip dist-shar dist-tarZ \ dist-zip distcheck distclean distclean-compile \ - distclean-generic distclean-recursive 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-exec install-exec-am \ - install-info install-info-am install-man install-strip \ - installcheck installcheck-am installdirs installdirs-am \ - maintainer-clean maintainer-clean-generic \ + distclean-generic distclean-hdr distclean-recursive \ + 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-exec \ + install-exec-am install-info install-info-am install-man \ + install-strip installcheck installcheck-am installdirs \ + installdirs-am maintainer-clean maintainer-clean-generic \ maintainer-clean-recursive mostlyclean mostlyclean-compile \ mostlyclean-generic mostlyclean-recursive pdf pdf-am ps ps-am \ tags tags-recursive uninstall uninstall-am \ diff --git a/src/autogen.sh b/src/autogen.sh new file mode 100755 index 000000000..11a278c94 --- /dev/null +++ b/src/autogen.sh @@ -0,0 +1,7 @@ +#!/bin/sh + +set -ex +aclocal +autoconf +autoheader +automake -a diff --git a/src/config.h b/src/config.h new file mode 100644 index 000000000..cb77b5a46 --- /dev/null +++ b/src/config.h @@ -0,0 +1,59 @@ +/* config.h. Generated by configure. */ +/* config.h.in. Generated from configure.ac by autoheader. */ + +/* Define to 1 if you have the header file. */ +/* #undef HAVE_BOOST_ICL_INTERVAL_SET_HPP */ + +/* clock_getttime found */ +#define HAVE_CLOCK_GETTIME 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_INTTYPES_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_MEMORY_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STDINT_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STDLIB_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STRINGS_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_STRING_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_SYS_STAT_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_SYS_TYPES_H 1 + +/* Define to 1 if you have the header file. */ +#define HAVE_UNISTD_H 1 + +/* Name of package */ +#define PACKAGE "snowtools" + +/* Define to the address where bug reports for this package should be sent. */ +#define PACKAGE_BUGREPORT "jwala@broadinstitute.org" + +/* Define to the full name of this package. */ +#define PACKAGE_NAME "snowtools" + +/* Define to the full name and version of this package. */ +#define PACKAGE_STRING "snowtools 1.0" + +/* Define to the one symbol short name of this package. */ +#define PACKAGE_TARNAME "snowtools" + +/* Define to the version of this package. */ +#define PACKAGE_VERSION "1.0" + +/* Define to 1 if you have the ANSI C header files. */ +#define STDC_HEADERS 1 + +/* Version number of package */ +#define VERSION "1.0" diff --git a/src/config.h.in b/src/config.h.in new file mode 100644 index 000000000..d02dfba5f --- /dev/null +++ b/src/config.h.in @@ -0,0 +1,58 @@ +/* config.h.in. Generated from configure.ac by autoheader. */ + +/* Define to 1 if you have the header file. */ +#undef HAVE_BOOST_ICL_INTERVAL_SET_HPP + +/* clock_getttime found */ +#undef HAVE_CLOCK_GETTIME + +/* Define to 1 if you have the header file. */ +#undef HAVE_INTTYPES_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_MEMORY_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDINT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDLIB_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STRINGS_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STRING_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_STAT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_TYPES_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_UNISTD_H + +/* Name of package */ +#undef PACKAGE + +/* Define to the address where bug reports for this package should be sent. */ +#undef PACKAGE_BUGREPORT + +/* Define to the full name of this package. */ +#undef PACKAGE_NAME + +/* Define to the full name and version of this package. */ +#undef PACKAGE_STRING + +/* Define to the one symbol short name of this package. */ +#undef PACKAGE_TARNAME + +/* Define to the version of this package. */ +#undef PACKAGE_VERSION + +/* Define to 1 if you have the ANSI C header files. */ +#undef STDC_HEADERS + +/* Version number of package */ +#undef VERSION diff --git a/src/config.status b/src/config.status index f173716db..c7770d47f 100755 --- a/src/config.status +++ b/src/config.status @@ -272,6 +272,7 @@ _CSEOF echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5 echo >&5 config_files=" Makefile" +config_headers=" config.h" config_commands=" depfiles" ac_cs_usage="\ @@ -287,10 +288,15 @@ Usage: $0 [OPTIONS] [FILE]... --recheck update $as_me by reconfiguring in the same conditions --file=FILE[:TEMPLATE] instantiate the configuration file FILE + --header=FILE[:TEMPLATE] + instantiate the configuration header FILE Configuration files: $config_files +Configuration headers: +$config_headers + Configuration commands: $config_commands @@ -393,6 +399,7 @@ do # Handling of arguments. "Makefile" ) CONFIG_FILES="$CONFIG_FILES Makefile" ;; "depfiles" ) CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; + "config.h" ) CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;; *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 echo "$as_me: error: invalid argument: $ac_config_target" >&2;} { (exit 1); exit 1; }; };; @@ -405,6 +412,7 @@ done # bizarre bug on SunOS 4.1.3. if $ac_need_defaults; then test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files + test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands fi @@ -469,7 +477,7 @@ s,@mandir@,${prefix}/man,;t t s,@build_alias@,,;t t s,@host_alias@,,;t t s,@target_alias@,,;t t -s,@DEFS@,-DPACKAGE_NAME=\"snowtools\" -DPACKAGE_TARNAME=\"snowtools\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"snowtools\ 1.0\" -DPACKAGE_BUGREPORT=\"jwala@broadinstitute.org\" -DPACKAGE=\"snowtools\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_CLOCK_GETTIME=1 ,;t t +s,@DEFS@,-DHAVE_CONFIG_H,;t t s,@ECHO_C@,,;t t s,@ECHO_N@,-n,;t t s,@ECHO_T@,,;t t @@ -499,7 +507,7 @@ s,@am__untar@,${AMTAR} xf -,;t t s,@CXX@,g++,;t t s,@CXXFLAGS@,-O3,;t t s,@LDFLAGS@,,;t t -s,@CPPFLAGS@, -I/xchip/gistic/Jeremiah/boost_1_58_0,;t t +s,@CPPFLAGS@, -I/xchip/gistic/Jeremiah/boost_1_58_0DUMY,;t t s,@ac_ct_CXX@,g++,;t t s,@EXEEXT@,,;t t s,@OBJEXT@,o,;t t @@ -761,6 +769,215 @@ s,@INSTALL@,$ac_INSTALL,;t t done +# +# CONFIG_HEADER section. +# + +# These sed commands are passed to sed as "A NAME B NAME C VALUE D", where +# NAME is the cpp macro being defined and VALUE is the value it is being given. +# +# ac_d sets the value in "#define NAME VALUE" lines. +ac_dA='s,^\([ ]*\)#\([ ]*define[ ][ ]*\)' +ac_dB='[ ].*$,\1#\2' +ac_dC=' ' +ac_dD=',;t' +# ac_u turns "#undef NAME" without trailing blanks into "#define NAME VALUE". +ac_uA='s,^\([ ]*\)#\([ ]*\)undef\([ ][ ]*\)' +ac_uB='$,\1#\2define\3' +ac_uC=' ' +ac_uD=',;t' + +for ac_file in : $CONFIG_HEADERS; do test "x$ac_file" = x: && continue + # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in". + case $ac_file in + - | *:- | *:-:* ) # input from stdin + cat >$tmp/stdin + ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'` + ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;; + *:* ) ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'` + ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;; + * ) ac_file_in=$ac_file.in ;; + esac + + test x"$ac_file" != x- && { echo "$as_me:$LINENO: creating $ac_file" >&5 +echo "$as_me: creating $ac_file" >&6;} + + # First look for the input files in the build tree, otherwise in the + # src tree. + ac_file_inputs=`IFS=: + for f in $ac_file_in; do + case $f in + -) echo $tmp/stdin ;; + [\\/$]*) + # Absolute (can't be DOS-style, as IFS=:) + test -f "$f" || { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + # Do quote $f, to prevent DOS paths from being IFS'd. + echo "$f";; + *) # Relative + if test -f "$f"; then + # Build tree + echo "$f" + elif test -f "$srcdir/$f"; then + # Source tree + echo "$srcdir/$f" + else + # /dev/null tree + { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + fi;; + esac + done` || { (exit 1); exit 1; } + # Remove the trailing spaces. + sed 's/[ ]*$//' $ac_file_inputs >$tmp/in + + # Handle all the #define templates only if necessary. + if grep "^[ ]*#[ ]*define" $tmp/in >/dev/null; then + # If there are no defines, we may have an empty if/fi + : + cat >$tmp/defines.sed <$tmp/out + rm -f $tmp/in + mv $tmp/out $tmp/in + + fi # grep + + # Handle all the #undef templates + cat >$tmp/undefs.sed <$tmp/out + rm -f $tmp/in + mv $tmp/out $tmp/in + + # Let's still pretend it is `configure' which instantiates (i.e., don't + # use $as_me), people would be surprised to read: + # /* config.h. Generated by config.status. */ + if test x"$ac_file" = x-; then + echo "/* Generated by configure. */" >$tmp/config.h + else + echo "/* $ac_file. Generated by configure. */" >$tmp/config.h + fi + cat $tmp/in >>$tmp/config.h + rm -f $tmp/in + if test x"$ac_file" != x-; then + if diff $ac_file $tmp/config.h >/dev/null 2>&1; then + { echo "$as_me:$LINENO: $ac_file is unchanged" >&5 +echo "$as_me: $ac_file is unchanged" >&6;} + else + ac_dir=`(dirname "$ac_file") 2>/dev/null || +$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$ac_file" : 'X\(//\)[^/]' \| \ + X"$ac_file" : 'X\(//\)$' \| \ + X"$ac_file" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$ac_file" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + { if $as_mkdir_p; then + mkdir -p "$ac_dir" + else + as_dir="$ac_dir" + as_dirs= + while test ! -d "$as_dir"; do + as_dirs="$as_dir $as_dirs" + as_dir=`(dirname "$as_dir") 2>/dev/null || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + done + test ! -n "$as_dirs" || mkdir $as_dirs + fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5 +echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;} + { (exit 1); exit 1; }; }; } + + rm -f $ac_file + mv $tmp/config.h $ac_file + fi + else + cat $tmp/config.h + rm -f $tmp/config.h + fi +# Compute $ac_file's index in $config_headers. +_am_stamp_count=1 +for _am_header in $config_headers :; do + case $_am_header in + $ac_file | $ac_file:* ) + break ;; + * ) + _am_stamp_count=`expr $_am_stamp_count + 1` ;; + esac +done +echo "timestamp for $ac_file" >`(dirname $ac_file) 2>/dev/null || +$as_expr X$ac_file : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X$ac_file : 'X\(//\)[^/]' \| \ + X$ac_file : 'X\(//\)$' \| \ + X$ac_file : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X$ac_file | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'`/stamp-h$_am_stamp_count +done + # # CONFIG_COMMANDS section. # diff --git a/src/configure b/src/configure index 3cdba5d9e..a3f72edee 100755 --- a/src/configure +++ b/src/configure @@ -1765,7 +1765,8 @@ am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -' -##AC_CONFIG_HEADER([config.h]) + ac_config_headers="$ac_config_headers config.h" + ##m4_include([m4/m4_ax_openmp.m4]) # Checks for programs. @@ -4321,7 +4322,7 @@ fi; if test "$with_boost" -a -d "$with_boost"; then boost_include="-I$with_boost" else - boostr=/xchip/gistic/Jeremiah/boost_1_58_0 + boostr=/xchip/gistic/Jeremiah/boost_1_58_0DUMY boost_include="-I$boostr" fi @@ -4411,6 +4412,161 @@ LIBS="$LIBS" # Make sure the HTSlib headers can be found #AC_CHECK_HEADERS([htslib/hts.h],,[AC_MSG_ERROR([The HTSlib library must be installed. You can specify its path with the --with-htslib=PATH option])]) +# Make sure the bamtools headers can be found + +for ac_header in boost/icl/interval_set.hpp +do +as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 +else + # Is the header compilable? +echo "$as_me:$LINENO: checking $ac_header usability" >&5 +echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6 +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_header_compiler=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_header_compiler=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +echo "${ECHO_T}$ac_header_compiler" >&6 + +# Is the header present? +echo "$as_me:$LINENO: checking $ac_header presence" >&5 +echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6 +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include <$ac_header> +_ACEOF +if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 + (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null; then + if test -s conftest.err; then + ac_cpp_err=$ac_cxx_preproc_warn_flag + ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag + else + ac_cpp_err= + fi +else + ac_cpp_err=yes +fi +if test -z "$ac_cpp_err"; then + ac_header_preproc=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi +rm -f conftest.err conftest.$ac_ext +echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +echo "${ECHO_T}$ac_header_preproc" >&6 + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in + yes:no: ) + { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 +echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 +echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 +echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 +echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 +echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 +echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 +echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} + { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 +echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} + ( + cat <<\_ASBOX +## --------------------------------------- ## +## Report this to jwala@broadinstitute.org ## +## --------------------------------------- ## +_ASBOX + ) | + sed "s/^/$as_me: WARNING: /" >&2 + ;; +esac +echo "$as_me:$LINENO: checking for $ac_header" >&5 +echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 +if eval "test \"\${$as_ac_Header+set}\" = set"; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + eval "$as_ac_Header=\$ac_header_preproc" +fi +echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 +echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 + +fi +if test `eval echo '${'$as_ac_Header'}'` = yes; then + cat >>confdefs.h <<_ACEOF +#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +else + { echo "$as_me:$LINENO: WARNING: The Boost library must be installed for a few of the interval operations. NOT REQUIRED for VariantBam. Specify its path with the --with-boost=PATH option" >&5 +echo "$as_me: WARNING: The Boost library must be installed for a few of the interval operations. NOT REQUIRED for VariantBam. Specify its path with the --with-boost=PATH option" >&2;} +fi + +done + + ac_config_files="$ac_config_files Makefile" @@ -4488,38 +4644,7 @@ s/^[^=]*=[ ]*$//; }' fi -# Transform confdefs.h into DEFS. -# Protect against shell expansion while executing Makefile rules. -# Protect against Makefile macro expansion. -# -# If the first sed substitution is executed (which looks for macros that -# take arguments), then we branch to the quote section. Otherwise, -# look for a macro that doesn't take arguments. -cat >confdef2opt.sed <<\_ACEOF -t clear -: clear -s,^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\),-D\1=\2,g -t quote -s,^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\),-D\1=\2,g -t quote -d -: quote -s,[ `~#$^&*(){}\\|;'"<>?],\\&,g -s,\[,\\&,g -s,\],\\&,g -s,\$,$$,g -p -_ACEOF -# We use echo to avoid assuming a particular line-breaking character. -# The extra dot is to prevent the shell from consuming trailing -# line-breaks from the sub-command output. A line-break within -# single-quotes doesn't work because, if this script is created in a -# platform that uses two characters for line-breaks (e.g., DOS), tr -# would break. -ac_LF_and_DOT=`echo; echo .` -DEFS=`sed -n -f confdef2opt.sed confdefs.h | tr "$ac_LF_and_DOT" ' .'` -rm -f confdef2opt.sed - +DEFS=-DHAVE_CONFIG_H ac_libobjs= ac_ltlibobjs= @@ -4874,10 +4999,15 @@ Usage: $0 [OPTIONS] [FILE]... --recheck update $as_me by reconfiguring in the same conditions --file=FILE[:TEMPLATE] instantiate the configuration file FILE + --header=FILE[:TEMPLATE] + instantiate the configuration header FILE Configuration files: $config_files +Configuration headers: +$config_headers + Configuration commands: $config_commands @@ -4998,6 +5128,7 @@ do # Handling of arguments. "Makefile" ) CONFIG_FILES="$CONFIG_FILES Makefile" ;; "depfiles" ) CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; + "config.h" ) CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;; *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 echo "$as_me: error: invalid argument: $ac_config_target" >&2;} { (exit 1); exit 1; }; };; @@ -5010,6 +5141,7 @@ done # bizarre bug on SunOS 4.1.3. if $ac_need_defaults; then test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files + test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands fi @@ -5373,6 +5505,251 @@ done _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF +# +# CONFIG_HEADER section. +# + +# These sed commands are passed to sed as "A NAME B NAME C VALUE D", where +# NAME is the cpp macro being defined and VALUE is the value it is being given. +# +# ac_d sets the value in "#define NAME VALUE" lines. +ac_dA='s,^\([ ]*\)#\([ ]*define[ ][ ]*\)' +ac_dB='[ ].*$,\1#\2' +ac_dC=' ' +ac_dD=',;t' +# ac_u turns "#undef NAME" without trailing blanks into "#define NAME VALUE". +ac_uA='s,^\([ ]*\)#\([ ]*\)undef\([ ][ ]*\)' +ac_uB='$,\1#\2define\3' +ac_uC=' ' +ac_uD=',;t' + +for ac_file in : $CONFIG_HEADERS; do test "x$ac_file" = x: && continue + # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in". + case $ac_file in + - | *:- | *:-:* ) # input from stdin + cat >$tmp/stdin + ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'` + ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;; + *:* ) ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'` + ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;; + * ) ac_file_in=$ac_file.in ;; + esac + + test x"$ac_file" != x- && { echo "$as_me:$LINENO: creating $ac_file" >&5 +echo "$as_me: creating $ac_file" >&6;} + + # First look for the input files in the build tree, otherwise in the + # src tree. + ac_file_inputs=`IFS=: + for f in $ac_file_in; do + case $f in + -) echo $tmp/stdin ;; + [\\/$]*) + # Absolute (can't be DOS-style, as IFS=:) + test -f "$f" || { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + # Do quote $f, to prevent DOS paths from being IFS'd. + echo "$f";; + *) # Relative + if test -f "$f"; then + # Build tree + echo "$f" + elif test -f "$srcdir/$f"; then + # Source tree + echo "$srcdir/$f" + else + # /dev/null tree + { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5 +echo "$as_me: error: cannot find input file: $f" >&2;} + { (exit 1); exit 1; }; } + fi;; + esac + done` || { (exit 1); exit 1; } + # Remove the trailing spaces. + sed 's/[ ]*$//' $ac_file_inputs >$tmp/in + +_ACEOF + +# Transform confdefs.h into two sed scripts, `conftest.defines' and +# `conftest.undefs', that substitutes the proper values into +# config.h.in to produce config.h. The first handles `#define' +# templates, and the second `#undef' templates. +# And first: Protect against being on the right side of a sed subst in +# config.status. Protect against being in an unquoted here document +# in config.status. +rm -f conftest.defines conftest.undefs +# Using a here document instead of a string reduces the quoting nightmare. +# Putting comments in sed scripts is not portable. +# +# `end' is used to avoid that the second main sed command (meant for +# 0-ary CPP macros) applies to n-ary macro definitions. +# See the Autoconf documentation for `clear'. +cat >confdef2sed.sed <<\_ACEOF +s/[\\&,]/\\&/g +s,[\\$`],\\&,g +t clear +: clear +s,^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*\)\(([^)]*)\)[ ]*\(.*\)$,${ac_dA}\1${ac_dB}\1\2${ac_dC}\3${ac_dD},gp +t end +s,^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)$,${ac_dA}\1${ac_dB}\1${ac_dC}\2${ac_dD},gp +: end +_ACEOF +# If some macros were called several times there might be several times +# the same #defines, which is useless. Nevertheless, we may not want to +# sort them, since we want the *last* AC-DEFINE to be honored. +uniq confdefs.h | sed -n -f confdef2sed.sed >conftest.defines +sed 's/ac_d/ac_u/g' conftest.defines >conftest.undefs +rm -f confdef2sed.sed + +# This sed command replaces #undef with comments. This is necessary, for +# example, in the case of _POSIX_SOURCE, which is predefined and required +# on some systems where configure will not decide to define it. +cat >>conftest.undefs <<\_ACEOF +s,^[ ]*#[ ]*undef[ ][ ]*[a-zA-Z_][a-zA-Z_0-9]*,/* & */, +_ACEOF + +# Break up conftest.defines because some shells have a limit on the size +# of here documents, and old seds have small limits too (100 cmds). +echo ' # Handle all the #define templates only if necessary.' >>$CONFIG_STATUS +echo ' if grep "^[ ]*#[ ]*define" $tmp/in >/dev/null; then' >>$CONFIG_STATUS +echo ' # If there are no defines, we may have an empty if/fi' >>$CONFIG_STATUS +echo ' :' >>$CONFIG_STATUS +rm -f conftest.tail +while grep . conftest.defines >/dev/null +do + # Write a limited-size here document to $tmp/defines.sed. + echo ' cat >$tmp/defines.sed <>$CONFIG_STATUS + # Speed up: don't consider the non `#define' lines. + echo '/^[ ]*#[ ]*define/!b' >>$CONFIG_STATUS + # Work around the forget-to-reset-the-flag bug. + echo 't clr' >>$CONFIG_STATUS + echo ': clr' >>$CONFIG_STATUS + sed ${ac_max_here_lines}q conftest.defines >>$CONFIG_STATUS + echo 'CEOF + sed -f $tmp/defines.sed $tmp/in >$tmp/out + rm -f $tmp/in + mv $tmp/out $tmp/in +' >>$CONFIG_STATUS + sed 1,${ac_max_here_lines}d conftest.defines >conftest.tail + rm -f conftest.defines + mv conftest.tail conftest.defines +done +rm -f conftest.defines +echo ' fi # grep' >>$CONFIG_STATUS +echo >>$CONFIG_STATUS + +# Break up conftest.undefs because some shells have a limit on the size +# of here documents, and old seds have small limits too (100 cmds). +echo ' # Handle all the #undef templates' >>$CONFIG_STATUS +rm -f conftest.tail +while grep . conftest.undefs >/dev/null +do + # Write a limited-size here document to $tmp/undefs.sed. + echo ' cat >$tmp/undefs.sed <>$CONFIG_STATUS + # Speed up: don't consider the non `#undef' + echo '/^[ ]*#[ ]*undef/!b' >>$CONFIG_STATUS + # Work around the forget-to-reset-the-flag bug. + echo 't clr' >>$CONFIG_STATUS + echo ': clr' >>$CONFIG_STATUS + sed ${ac_max_here_lines}q conftest.undefs >>$CONFIG_STATUS + echo 'CEOF + sed -f $tmp/undefs.sed $tmp/in >$tmp/out + rm -f $tmp/in + mv $tmp/out $tmp/in +' >>$CONFIG_STATUS + sed 1,${ac_max_here_lines}d conftest.undefs >conftest.tail + rm -f conftest.undefs + mv conftest.tail conftest.undefs +done +rm -f conftest.undefs + +cat >>$CONFIG_STATUS <<\_ACEOF + # Let's still pretend it is `configure' which instantiates (i.e., don't + # use $as_me), people would be surprised to read: + # /* config.h. Generated by config.status. */ + if test x"$ac_file" = x-; then + echo "/* Generated by configure. */" >$tmp/config.h + else + echo "/* $ac_file. Generated by configure. */" >$tmp/config.h + fi + cat $tmp/in >>$tmp/config.h + rm -f $tmp/in + if test x"$ac_file" != x-; then + if diff $ac_file $tmp/config.h >/dev/null 2>&1; then + { echo "$as_me:$LINENO: $ac_file is unchanged" >&5 +echo "$as_me: $ac_file is unchanged" >&6;} + else + ac_dir=`(dirname "$ac_file") 2>/dev/null || +$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$ac_file" : 'X\(//\)[^/]' \| \ + X"$ac_file" : 'X\(//\)$' \| \ + X"$ac_file" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$ac_file" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + { if $as_mkdir_p; then + mkdir -p "$ac_dir" + else + as_dir="$ac_dir" + as_dirs= + while test ! -d "$as_dir"; do + as_dirs="$as_dir $as_dirs" + as_dir=`(dirname "$as_dir") 2>/dev/null || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'` + done + test ! -n "$as_dirs" || mkdir $as_dirs + fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5 +echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;} + { (exit 1); exit 1; }; }; } + + rm -f $ac_file + mv $tmp/config.h $ac_file + fi + else + cat $tmp/config.h + rm -f $tmp/config.h + fi +# Compute $ac_file's index in $config_headers. +_am_stamp_count=1 +for _am_header in $config_headers :; do + case $_am_header in + $ac_file | $ac_file:* ) + break ;; + * ) + _am_stamp_count=`expr $_am_stamp_count + 1` ;; + esac +done +echo "timestamp for $ac_file" >`(dirname $ac_file) 2>/dev/null || +$as_expr X$ac_file : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X$ac_file : 'X\(//\)[^/]' \| \ + X$ac_file : 'X\(//\)$' \| \ + X$ac_file : 'X\(/\)' \| \ + . : '\(.\)' 2>/dev/null || +echo X$ac_file | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } + /^X\(\/\/\)[^/].*/{ s//\1/; q; } + /^X\(\/\/\)$/{ s//\1/; q; } + /^X\(\/\).*/{ s//\1/; q; } + s/.*/./; q'`/stamp-h$_am_stamp_count +done +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF + # # CONFIG_COMMANDS section. # diff --git a/src/configure.ac b/src/configure.ac index 281280736..40fe31bb5 100644 --- a/src/configure.ac +++ b/src/configure.ac @@ -4,7 +4,7 @@ AC_PREREQ(2.59) ## specificy version of autoconf AC_INIT(snowtools, 1.0, jwala@broadinstitute.org) AM_INIT_AUTOMAKE(foreign) AC_CONFIG_SRCDIR([SnowTools.cpp]) -##AC_CONFIG_HEADER([config.h]) +AC_CONFIG_HEADER([config.h]) ##m4_include([m4/m4_ax_openmp.m4]) # Checks for programs. @@ -105,6 +105,9 @@ AC_SUBST(LIBS, "$LIBS") # Make sure the HTSlib headers can be found #AC_CHECK_HEADERS([htslib/hts.h],,[AC_MSG_ERROR([The HTSlib library must be installed. You can specify its path with the --with-htslib=PATH option])]) +# Make sure the bamtools headers can be found +AC_CHECK_HEADERS([boost/icl/interval_set.hpp],,[AC_MSG_WARN([The Boost library must be installed for a few of the interval operations. NOT REQUIRED for VariantBam. Specify its path with the --with-boost=PATH option])]) + AC_CONFIG_FILES([Makefile]) AC_OUTPUT