79 lines
2.6 KiB
Text
79 lines
2.6 KiB
Text
--- Makefile.orig 2017-09-28 11:22:48 UTC
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+++ Makefile
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@@ -22,10 +22,10 @@
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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# DEALINGS IN THE SOFTWARE.
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-CC = gcc
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-CPPFLAGS =
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-CFLAGS = -g -Wall -Wc++-compat -O2
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-LDFLAGS =
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+CC ?= cc
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+CPPFLAGS +=
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+CFLAGS += -Wall
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+LDFLAGS +=
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LIBS =
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DYNAMIC_FLAGS = -rdynamic
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@@ -42,26 +42,25 @@ OBJS = main.o vcfindex.o tabix.o \
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vcfsort.o \
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ccall.o em.o prob1.o kmin.o # the original samtools calling
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-prefix = /usr/local
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+prefix = ${PREFIX}
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exec_prefix = $(prefix)
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bindir = $(exec_prefix)/bin
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libdir = $(exec_prefix)/lib
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libexecdir = $(exec_prefix)/libexec
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-mandir = $(prefix)/share/man
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+mandir = $(prefix)/man
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man1dir = $(mandir)/man1
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# Installation location for $(PLUGINS)
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plugindir = $(libexecdir)/bcftools
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pluginpath = $(plugindir)
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# Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
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-misc_bindir = $(bindir)
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+misc_bindir = $(bindir)/samtools_misc
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MKDIR_P = mkdir -p
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-INSTALL = install -p
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-INSTALL_DATA = $(INSTALL) -m 644
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-INSTALL_DIR = $(MKDIR_P) -m 755
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-INSTALL_MAN = $(INSTALL_DATA)
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-INSTALL_PROGRAM = $(INSTALL)
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-INSTALL_SCRIPT = $(INSTALL_PROGRAM)
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+INSTALL_DATA = ${BSD_INSTALL_DATA}
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+INSTALL_DIR = $(MKDIR_P)
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+INSTALL_MAN = ${BSD_INSTALL_MAN}
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+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
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+INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT}
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PROGRAMS = bcftools
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MISC_SCRIPTS = \
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@@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin
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ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
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ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS)
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-ALL_LIBS = -lz -ldl $(LIBS)
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+ALL_LIBS = -lz $(LIBS)
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# Usually config.mk and config.h are generated by running configure
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# or config.status, but if those aren't used create defaults here.
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@@ -131,7 +130,7 @@ print-version:
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ifdef USE_GPL
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main.o : EXTRA_CPPFLAGS += -DUSE_GPL
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OBJS += polysomy.o peakfit.o
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- GSL_LIBS ?= -lgsl -lcblas
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+ GSL_LIBS ?= -lgsl -lgslcblas
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endif
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bcftools: $(OBJS) $(HTSLIB)
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@@ -273,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html
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# Since there is no make dependency, bcftools.1 can be out-of-date and
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# make docs can be run to update if asciidoc is available
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install: $(PROG) $(PLUGINS)
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- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
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+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
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$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
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$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
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$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
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