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fixed build
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Jeremiah Wala committed Jun 18, 2015
1 parent 961e322 commit 16f1ab3
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Showing 9 changed files with 839 additions and 79 deletions.
13 changes: 7 additions & 6 deletions src/GenomicRegionCollection.cpp
Original file line number Diff line number Diff line change
@@ -1,12 +1,14 @@
//#include "SnowTools/GenomicRegionCollection.h"
#include "SnowTools/GenomicRegionCollection.h"

#include <iostream>
#include <sstream>
#include <cassert>
#include "SnowTools/gzstream.h"
#include <set>


#ifdef HAVE_BOOST_ICL_INTERVAL_SET_HPP
#include <boost/icl/interval_set.hpp>
#endif

//#define DEBUG_OVERLAPS 1

Expand Down Expand Up @@ -414,12 +416,11 @@ GRC GenomicRegionCollection<T>::intersection(GRC& subject, bool ignore_strand /*
template<class T>
GRC GenomicRegionCollection<T>::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<int> TIntervalSet;

Expand Down Expand Up @@ -462,8 +463,8 @@ GRC GenomicRegionCollection<T>::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

}
Expand Down
57 changes: 38 additions & 19 deletions src/Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -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 = $(noinst_LIBRARIES)
AR = ar
Expand Down Expand Up @@ -85,7 +86,7 @@ am_snowtools_OBJECTS = snowtools-SnowTools.$(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) \
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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`; \
Expand All @@ -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 | \
Expand All @@ -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 | \
Expand Down Expand Up @@ -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)$(bindir)"; do \
Expand Down Expand Up @@ -1020,7 +1039,7 @@ distclean: distclean-recursive
-rm -rf ./$(DEPDIR)
-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
distclean-tags
distclean-hdr distclean-tags

dvi: dvi-recursive

Expand Down Expand Up @@ -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 \
Expand Down
53 changes: 36 additions & 17 deletions src/Makefile.in
Original file line number Diff line number Diff line change
Expand Up @@ -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 = $(noinst_LIBRARIES)
AR = ar
Expand Down Expand Up @@ -85,7 +86,7 @@ am_snowtools_OBJECTS = snowtools-SnowTools.$(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) \
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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`; \
Expand All @@ -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 | \
Expand All @@ -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 | \
Expand Down Expand Up @@ -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)$(bindir)"; do \
Expand Down Expand Up @@ -1020,7 +1039,7 @@ distclean: distclean-recursive
-rm -rf ./$(DEPDIR)
-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
distclean-tags
distclean-hdr distclean-tags

dvi: dvi-recursive

Expand Down Expand Up @@ -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 \
Expand Down
7 changes: 7 additions & 0 deletions src/autogen.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
#!/bin/sh

set -ex
aclocal
autoconf
autoheader
automake -a
59 changes: 59 additions & 0 deletions src/config.h
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 "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"
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