works

[samtools.git] / Makefile.mingw

diff --git a/Makefile.mingw b/Makefile.mingw
index ffa1422043908dbb38ccae530166e176d7148925..7a57ffc0c7457c5fcfb65dd8585bd3ee3cb1114c 100644 (file)
--- a/Makefile.mingw
+++ b/Makefile.mingw
@@ -1,69 +1,63 @@
-#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_USE_KNETFILE -D_CURSES_LIB=2
+KNETFILE_O=    knetfile.o
 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
-AOBJS=         bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
+                       bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \
+                       $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bedidx.o
+AOBJS=         bam_tview.o bam_plcmd.o sam_view.o \
                        bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o     \
-                       bamtk.o
-PROG=          samtools
-INCLUDES=      -Iwin32
+                       bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
+                       cut_target.o phase.o bam_cat.o bam2depth.o
+BCFOBJS=       bcftools/bcf.o bcftools/fet.o bcftools/bcf2qcall.o bcftools/bcfutils.o \
+                       bcftools/call1.o bcftools/index.o bcftools/kfunc.o bcftools/em.o \
+                       bcftools/kmin.o bcftools/prob1.o bcftools/vcf.o bcftools/mut.o
+PROG=          samtools.exe bcftools.exe
+INCLUDES=      -I. -Iwin32
 SUBDIRS=       .
-LIBPATH=       
+LIBPATH=
 
 .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; \
-                       $(MAKE) -f Makefile.mingw AR="$(AR)" CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-                               INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
-                       cd $$wdir; \
-               done;
-
 all:$(PROG)
 
+.PHONY:all lib clean cleanlocal
+.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
+
 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) $(LIBPATH) -lm -L. -lbam -Lwin32 -lz #-lcurses
+samtools.exe:$(AOBJS) libbam.a $(BCFOBJS)
+               $(CC) $(CFLAGS) -o $@ $(AOBJS) $(BCFOBJS) $(LIBPATH) -lm -L. -lbam -Lwin32 -lz -lcurses -lws2_32
 
-razip:razip.o razf.o
-               $(CC) $(CFLAGS) -o $@ razf.o razip.o -lz
-
-bgzip:bgzip.o bgzf.o
-               $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -lz
+bcftools.exe:$(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o
+               $(CC) $(CFLAGS) -o $@ $(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o -lm -Lwin32 -lz -lws2_32
 
 razip.o:razf.h
-bam.o:bam.h razf.h bam_endian.h kstring.h
+bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
 sam.o:sam.h bam.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_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.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_tview.o:bam.h faidx.h
 bam_sort.o:bam.h ksort.h razf.h
 bam_md.o:bam.h faidx.h
-glf.o:glf.h
+sam_header.o:sam_header.h khash.h
+bcf.o:bcftools/bcf.h
+bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
+bam2bcf_indel.o:bam2bcf.h
+errmod.o:errmod.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 razip $(PROG) *~ *.a
-
-clean:cleanlocal-recur
+clean:
+               rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib