From: Heng Li <lh3@live.co.uk>
Date: Tue, 24 Mar 2009 11:50:32 +0000 (+0000)
Subject: rename Makefile.std as Makefile. GNU building systerm is not ready and may take some... 
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=54ce06b07cc86f7e2c5fbeb5333bc8fb99552cc3

rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
---

diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..d4a4101
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,64 @@
+CC=			gcc
+CXX=		g++
+CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
+CXXFLAGS=	$(CFLAGS)
+DFLAGS=		-D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
+OBJS=		bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
+			razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
+			bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o
+PROG=		razip bgzip samtools
+INCLUDES=	
+LIBS=		-lm -lz
+SUBDIRS=	. misc
+
+.SUFFIXES:.c .o
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+		@target=`echo $@ | sed s/-recur//`; \
+		wdir=`pwd`; \
+		list='$(SUBDIRS)'; for subdir in $$list; do \
+			cd $$subdir; \
+			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+				INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \
+			cd $$wdir; \
+		done;
+
+all:$(PROG)
+
+lib:libbam.a
+
+libbam.a:$(OBJS)
+		$(AR) -cru $@ $(OBJS)
+
+samtools:lib bamtk.o
+		$(CC) $(CFLAGS) -o $@ bamtk.o $(LIBS) -L. -lbam -lcurses
+
+razip:razip.o razf.o
+		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(LIBS)
+
+bgzip:bgzip.o bgzf.o
+		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(LIBS)
+
+razip.o:razf.h
+bam.o:bam.h razf.h bam_endian.h
+bam_import.o:bam.h kseq.h khash.h razf.h
+bam_pileup.o:bam.h razf.h ksort.h
+bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h
+bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
+bam_lpileup.o:bam.h ksort.h
+bam_tview.o:bam.h faidx.h bam_maqcns.h
+bam_maqcns.o:bam.h ksort.h bam_maqcns.h
+bam_sort.o:bam.h ksort.h razf.h
+razf.o:razf.h
+glf.o:glf.h
+
+faidx.o:faidx.h razf.h khash.h
+faidx_main.o:faidx.h razf.h
+
+cleanlocal:
+		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
+
+clean:cleanlocal-recur
diff --git a/Makefile.std b/Makefile.std
deleted file mode 100644
index d4a4101..0000000
--- a/Makefile.std
+++ /dev/null
@@ -1,64 +0,0 @@
-CC=			gcc
-CXX=		g++
-CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
-CXXFLAGS=	$(CFLAGS)
-DFLAGS=		-D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
-OBJS=		bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
-			razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
-			bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o
-PROG=		razip bgzip samtools
-INCLUDES=	
-LIBS=		-lm -lz
-SUBDIRS=	. misc
-
-.SUFFIXES:.c .o
-
-.c.o:
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-
-all-recur lib-recur clean-recur cleanlocal-recur install-recur:
-		@target=`echo $@ | sed s/-recur//`; \
-		wdir=`pwd`; \
-		list='$(SUBDIRS)'; for subdir in $$list; do \
-			cd $$subdir; \
-			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-				INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \
-			cd $$wdir; \
-		done;
-
-all:$(PROG)
-
-lib:libbam.a
-
-libbam.a:$(OBJS)
-		$(AR) -cru $@ $(OBJS)
-
-samtools:lib bamtk.o
-		$(CC) $(CFLAGS) -o $@ bamtk.o $(LIBS) -L. -lbam -lcurses
-
-razip:razip.o razf.o
-		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(LIBS)
-
-bgzip:bgzip.o bgzf.o
-		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(LIBS)
-
-razip.o:razf.h
-bam.o:bam.h razf.h bam_endian.h
-bam_import.o:bam.h kseq.h khash.h razf.h
-bam_pileup.o:bam.h razf.h ksort.h
-bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h
-bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
-bam_lpileup.o:bam.h ksort.h
-bam_tview.o:bam.h faidx.h bam_maqcns.h
-bam_maqcns.o:bam.h ksort.h bam_maqcns.h
-bam_sort.o:bam.h ksort.h razf.h
-razf.o:razf.h
-glf.o:glf.h
-
-faidx.o:faidx.h razf.h khash.h
-faidx_main.o:faidx.h razf.h
-
-cleanlocal:
-		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
-
-clean:cleanlocal-recur
diff --git a/misc/Makefile b/misc/Makefile
new file mode 100644
index 0000000..0f65881
--- /dev/null
+++ b/misc/Makefile
@@ -0,0 +1,58 @@
+CC=			gcc
+CXX=		g++
+CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
+CXXFLAGS=	$(CFLAGS)
+DFLAGS=		#-D_FILE_OFFSET_BITS=64
+OBJS=		
+PROG=		faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
+INCLUDES=	-I..
+LIBS=		-lm -lz
+SUBDIRS=	.
+
+.SUFFIXES:.c .o
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+lib-recur all-recur clean-recur cleanlocal-recur install-recur:
+		@target=`echo $@ | sed s/-recur//`; \
+		wdir=`pwd`; \
+		list='$(SUBDIRS)'; for subdir in $$list; do \
+			cd $$subdir; \
+			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+				INCLUDES="$(INCLUDES)" $$target || exit 1; \
+			cd $$wdir; \
+		done;
+
+lib:
+
+wgsim:wgsim.o
+		$(CC) $(CFLAGS) -o $@ wgsim.o -lm
+
+faidx:../faidx.c ../faidx.h
+		$(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
+
+md5fa:md5.o md5fa.o md5.h ../kseq.h
+		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
+
+md5sum-lite:md5sum-lite.o
+		$(CC) $(CFLAGS) -o $@ md5sum-lite.o
+
+md5sum-lite.o:md5.c md5.h
+		$(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
+
+maq2sam-short:maq2sam.c
+		$(CC) $(CFLAGS) -o $@ maq2sam.c -lz
+
+maq2sam-long:maq2sam.c
+		$(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
+
+md5fa.o:md5.h md5fa.c
+		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
+
+cleanlocal:
+		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
+
+clean:cleanlocal-recur
diff --git a/misc/Makefile.std b/misc/Makefile.std
deleted file mode 100644
index 0f65881..0000000
--- a/misc/Makefile.std
+++ /dev/null
@@ -1,58 +0,0 @@
-CC=			gcc
-CXX=		g++
-CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
-CXXFLAGS=	$(CFLAGS)
-DFLAGS=		#-D_FILE_OFFSET_BITS=64
-OBJS=		
-PROG=		faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
-INCLUDES=	-I..
-LIBS=		-lm -lz
-SUBDIRS=	.
-
-.SUFFIXES:.c .o
-
-.c.o:
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-
-all:$(PROG)
-
-lib-recur all-recur clean-recur cleanlocal-recur install-recur:
-		@target=`echo $@ | sed s/-recur//`; \
-		wdir=`pwd`; \
-		list='$(SUBDIRS)'; for subdir in $$list; do \
-			cd $$subdir; \
-			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-				INCLUDES="$(INCLUDES)" $$target || exit 1; \
-			cd $$wdir; \
-		done;
-
-lib:
-
-wgsim:wgsim.o
-		$(CC) $(CFLAGS) -o $@ wgsim.o -lm
-
-faidx:../faidx.c ../faidx.h
-		$(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
-
-md5fa:md5.o md5fa.o md5.h ../kseq.h
-		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
-
-md5sum-lite:md5sum-lite.o
-		$(CC) $(CFLAGS) -o $@ md5sum-lite.o
-
-md5sum-lite.o:md5.c md5.h
-		$(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
-
-maq2sam-short:maq2sam.c
-		$(CC) $(CFLAGS) -o $@ maq2sam.c -lz
-
-maq2sam-long:maq2sam.c
-		$(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
-
-md5fa.o:md5.h md5fa.c
-		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
-
-cleanlocal:
-		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
-
-clean:cleanlocal-recur