* This revision is SERIOUSLY BUGGY. Please NOT use it.

[samtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 0a2791e8810435f244e310ec8e64aaa46331269a..ad2cfb122502c5ac984f8ebfa16a56adc9056f73 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,16 +1,17 @@
 CC=                    gcc
-CXX=           g++
-CFLAGS=                -g -Wall -O2 #-m64 #-arch ppc
-CXXFLAGS=      $(CFLAGS)
-DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE #-D_NO_CURSES
+CFLAGS=                -g -Wall #-O2 #-m64 #-arch ppc
+DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1
 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 knetfile.o
-AOBJS=         bam_sort.o bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o      \
+                       bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o     \
+                       bam_sort.o sam_header.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
+                       bamtk.o kaln.o
 PROG=          samtools
-INCLUDES=      
+INCLUDES=
 SUBDIRS=       . misc
+LIBPATH=
+LIBCURSES=     -lcurses # -lXCurses
 
 .SUFFIXES:.c .o
 
@@ -23,7 +24,7 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
                list='$(SUBDIRS)'; for subdir in $$list; do \
                        cd $$subdir; \
                        $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-                               INCLUDES="$(INCLUDES)" $$target || exit 1; \
+                               INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
                        cd $$wdir; \
                done;
 
@@ -34,9 +35,8 @@ 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) -lm -lcurses -lz -L. -lbam
+               $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam
 
 razip:razip.o razf.o
                $(CC) $(CFLAGS) -o $@ razf.o razip.o -lz
@@ -45,7 +45,7 @@ bgzip:bgzip.o bgzf.o
                $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -lz
 
 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
@@ -57,6 +57,7 @@ bam_maqcns.o:bam.h ksort.h bam_maqcns.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
 
 faidx.o:faidx.h razf.h khash.h
 faidx_main.o:faidx.h razf.h