X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Makefile;h=25897dbf2f1dfe9a5ec690b5883aed8e606d140a;hb=99a3d0d13f7668b26ec6b47b100ee6232d49d336;hp=32e4c41aa15cb717424cf85f5459b9510db712b1;hpb=f93dae0d03856955f9424e8b2aaf261304ca647e;p=samtools.git

diff --git a/Makefile b/Makefile
index 32e4c41..25897db 100644
--- a/Makefile
+++ b/Makefile
@@ -2,9 +2,10 @@ CC=			gcc
 CXX=		g++
 CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
 CXXFLAGS=	$(CFLAGS)
-DFLAGS=		-D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -DHAVE_RAZF #-D_NO_CURSES
+DFLAGS=		-D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
 OBJS=		bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
-			razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o
+			razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
+			bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o bam_md.o
 PROG=		razip bgzip samtools
 INCLUDES=	
 LIBS=		-lm -lz
@@ -21,7 +22,7 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
 		list='$(SUBDIRS)'; for subdir in $$list; do \
 			cd $$subdir; \
 			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-				INCLUDES="$(INCLUDES)" $$target || exit 1; \
+				INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \
 			cd $$wdir; \
 		done;
 
@@ -45,13 +46,15 @@ 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
+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
+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