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

diff --git a/Makefile b/Makefile
new file mode 100644 (file)
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 (file)
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 (file)
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 (file)
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