From 17514ff7dafaf019828c50df8869df6bb9f0e331 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Fri, 12 Jun 2009 14:21:21 +0000
Subject: [PATCH] fixed minor things in Makefile

---
 AUTHORS       |  8 ++++----
 Makefile      | 11 +++++------
 misc/Makefile | 14 +++++---------
 3 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/AUTHORS b/AUTHORS
index c9a1837..435431c 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -7,10 +7,10 @@ underlying indexable compression format for the BAM format. BGZF does
 not support arithmetic between file offsets.
 
 Jue Ruan for the Beijing Genome Institute designed and implemented the
-RAZF format. This is an alternative indexable compression format. It
-supports arithmetic between file offsets, at the cost of increased index
-file size and the full compatibility with gzip. RAZF is optional and
-only used in `faidx' for indexing RAZF compressed fasta files.
+RAZF format, an alternative indexable compression format. RAZF supports
+arithmetic between file offsets, at the cost of increased index file
+size and the full compatibility with gzip. RAZF is optional and only
+used in `faidx' for indexing RAZF compressed fasta files.
 
 Colin Hercus updated novo2sam.pl to support gapped alignment by
 novoalign.
diff --git a/Makefile b/Makefile
index 86612c1..358120d 100644
--- a/Makefile
+++ b/Makefile
@@ -10,7 +10,6 @@ OBJS=		bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
 			bam_rmdupse.o
 PROG=		razip bgzip samtools
 INCLUDES=	-Izlib
-LIBS=		-lm -Lzlib -lz
 SUBDIRS=	zlib . misc
 
 .SUFFIXES:.c .o
@@ -23,8 +22,8 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
 		wdir=`pwd`; \
 		list='$(SUBDIRS)'; for subdir in $$list; do \
 			cd $$subdir; \
-			$(MAKE) -f Makefile CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-				INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \
+			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+				INCLUDES="$(INCLUDES)" $$target || exit 1; \
 			cd $$wdir; \
 		done;
 
@@ -37,13 +36,13 @@ libbam.a:$(OBJS)
 
 ### For ncurses: comment out `-lcurses' if you do not have ncurses installed
 samtools:lib bamtk.o
-		$(CC) $(CFLAGS) -o $@ bamtk.o $(LIBS) -L. -lbam -lcurses
+		$(CC) $(CFLAGS) -o $@ bamtk.o -lm -L. -lbam -lcurses -Lzlib -lz
 
 razip:razip.o razf.o
-		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(LIBS)
+		$(CC) $(CFLAGS) -o $@ razf.o razip.o -Lzlib -lz
 
 bgzip:bgzip.o bgzf.o
-		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(LIBS)
+		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -Lzlib -lz
 
 razip.o:razf.h
 bam.o:bam.h razf.h bam_endian.h kstring.h
diff --git a/misc/Makefile b/misc/Makefile
index 4b1bae5..1008e91 100644
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -4,9 +4,8 @@ CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
 CXXFLAGS=	$(CFLAGS)
 DFLAGS=		-D_FILE_OFFSET_BITS=64
 OBJS=		
-PROG=		faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
+PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
 INCLUDES=	-I..
-LIBS=		-lm -lz
 SUBDIRS=	.
 
 .SUFFIXES:.c .o
@@ -21,7 +20,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
 		wdir=`pwd`; \
 		list='$(SUBDIRS)'; for subdir in $$list; do \
 			cd $$subdir; \
-			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
 				INCLUDES="$(INCLUDES)" $$target || exit 1; \
 			cd $$wdir; \
 		done;
@@ -31,11 +30,8 @@ lib:
 wgsim:wgsim.o
 		$(CC) $(CFLAGS) -o $@ wgsim.o -lm
 
-faidx:../faidx.c ../faidx.h
-		$(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
-
 md5fa:md5.o md5fa.o md5.h ../kseq.h
-		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
+		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -L../zlib -lz
 
 md5sum-lite:md5sum-lite.o
 		$(CC) $(CFLAGS) -o $@ md5sum-lite.o
@@ -44,10 +40,10 @@ md5sum-lite.o:md5.c md5.h
 		$(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
 
 maq2sam-short:maq2sam.c
-		$(CC) $(CFLAGS) -o $@ maq2sam.c -lz
+		$(CC) $(CFLAGS) -I../zlib -o $@ maq2sam.c -L../zlib -lz
 
 maq2sam-long:maq2sam.c
-		$(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
+		$(CC) $(CFLAGS) -I../zlib -DMAQ_LONGREADS -o $@ maq2sam.c -L../zlib -lz
 
 md5fa.o:md5.h md5fa.c
 		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
-- 
2.39.2