fixed minor things in Makefile

diff --git a/AUTHORS b/AUTHORS
index c9a1837a966f2001e0c64bf0fface8d837d3974f..435431c9663d9fd55f5bc4dce07dad828a01fa49 100644 (file)
--- 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 86612c1b524b7185d9714b839067875b8bc85aa7..358120d97650b1391fc39c53ca448477e2d68da8 100644 (file)
--- 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 4b1bae5dd05e90b84895e8d7c7d6c0d76ace2550..1008e91cd10f13fd89ddb1ccaa5dac092ab3a337 100644 (file)
--- 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