* samtools-0.1.4-9 (r340)

[samtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 358120d97650b1391fc39c53ca448477e2d68da8..724552f1c85961d6c441396b8f363b4602c94ec2 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -2,15 +2,14 @@ CC=                   gcc
 CXX=           g++
 CFLAGS=                -g -Wall -O2 #-m64 #-arch ppc
 CXXFLAGS=      $(CFLAGS)
-### For ncurses: please apply `-D_NO_CURSES' if you do not have ncurses installed
 DFLAGS=                -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-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 bam_md.o sam.o sam_view.o \
                        bam_rmdupse.o
-PROG=          razip bgzip samtools
-INCLUDES=      -Izlib
-SUBDIRS=       zlib . misc
+PROG=          bgzip samtools
+INCLUDES=      
+SUBDIRS=       . misc
 
 .SUFFIXES:.c .o
 
@@ -34,15 +33,15 @@ lib:libbam.a
 libbam.a:$(OBJS)
                $(AR) -cru $@ $(OBJS)
 
-### For ncurses: comment out `-lcurses' if you do not have ncurses installed
+### For the curses library: comment out `-lcurses' if you do not have curses installed
 samtools:lib bamtk.o
-               $(CC) $(CFLAGS) -o $@ bamtk.o -lm -L. -lbam -lcurses -Lzlib -lz
+               $(CC) $(CFLAGS) -o $@ bamtk.o -lm -L. -lbam -lcurses -lz
 
 razip:razip.o razf.o
-               $(CC) $(CFLAGS) -o $@ razf.o razip.o -Lzlib -lz
+               $(CC) $(CFLAGS) -o $@ razf.o razip.o -lz
 
 bgzip:bgzip.o bgzf.o
-               $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -Lzlib -lz
+               $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -lz
 
 razip.o:razf.h
 bam.o:bam.h razf.h bam_endian.h kstring.h
@@ -56,13 +55,12 @@ 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
 bam_md.o:bam.h faidx.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
+               rm -fr gmon.out *.o a.out *.dSYM razip $(PROG) *~ *.a
 
 clean:cleanlocal-recur