-#CC= gcc
-#AR= ar
-CC= gccwine # on my laptop, this is an alias to [wine "c:/mingw/bin/gcc"]
-AR= arwine
+CC= gcc.exe
+AR= ar.exe
CFLAGS= -g -Wall -O2
-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_CURSES_LIB=0 #-D_USE_KNETFILE
+DFLAGS= -D_CURSES_LIB=2 -D_USE_KNETFILE
LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
- bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bam_sort.o
+ bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bam_sort.o \
+ knetfile.o
AOBJS= bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
bamtk.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; \
- $(MAKE) -f Makefile.mingw AR="$(AR)" CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
- INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
- cd $$wdir; \
- done;
-
all:$(PROG)
lib:libbam.a
libbam.a:$(LOBJS)
$(AR) -cru $@ $(LOBJS)
-### For the curses library: comment out `-lcurses' if you do not have curses installed
samtools:lib $(AOBJS)
- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LIBPATH) -lm -L. -lbam -Lwin32 -lz #-lcurses
+ $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LIBPATH) -lm -L. -lbam -Lwin32 -lz -lcurses -lws2_32
razip:razip.o razf.o
$(CC) $(CFLAGS) -o $@ razf.o razip.o -lz
faidx.o:faidx.h razf.h khash.h
faidx_main.o:faidx.h razf.h
-cleanlocal:
- rm -fr gmon.out *.o a.out *.dSYM razip $(PROG) *~ *.a
-
-clean:cleanlocal-recur
+clean:
+ rm -fr gmon.out *.o *.exe *.dSYM razip $(PROG) *~ *.a