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Jeremiah Wala
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Jun 18, 2015
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -38,15 +38,16 @@ 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) \ | ||
| $(ACLOCAL_M4) | ||
| 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=\"[email protected]\" -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 \ | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| #!/bin/sh | ||
|
|
||
| set -ex | ||
| aclocal | ||
| autoconf | ||
| autoheader | ||
| automake -a |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 <boost/icl/interval_set.hpp> header file. */ | ||
| /* #undef HAVE_BOOST_ICL_INTERVAL_SET_HPP */ | ||
|
|
||
| /* clock_getttime found */ | ||
| #define HAVE_CLOCK_GETTIME 1 | ||
|
|
||
| /* Define to 1 if you have the <inttypes.h> header file. */ | ||
| #define HAVE_INTTYPES_H 1 | ||
|
|
||
| /* Define to 1 if you have the <memory.h> header file. */ | ||
| #define HAVE_MEMORY_H 1 | ||
|
|
||
| /* Define to 1 if you have the <stdint.h> header file. */ | ||
| #define HAVE_STDINT_H 1 | ||
|
|
||
| /* Define to 1 if you have the <stdlib.h> header file. */ | ||
| #define HAVE_STDLIB_H 1 | ||
|
|
||
| /* Define to 1 if you have the <strings.h> header file. */ | ||
| #define HAVE_STRINGS_H 1 | ||
|
|
||
| /* Define to 1 if you have the <string.h> header file. */ | ||
| #define HAVE_STRING_H 1 | ||
|
|
||
| /* Define to 1 if you have the <sys/stat.h> header file. */ | ||
| #define HAVE_SYS_STAT_H 1 | ||
|
|
||
| /* Define to 1 if you have the <sys/types.h> header file. */ | ||
| #define HAVE_SYS_TYPES_H 1 | ||
|
|
||
| /* Define to 1 if you have the <unistd.h> 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 "[email protected]" | ||
|
|
||
| /* 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" |
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