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
 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.
 
 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
                        bam_rmdupse.o
 PROG=          razip bgzip samtools
 INCLUDES=      -Izlib

-LIBS=          -lm -Lzlib -lz

 SUBDIRS=       zlib . misc
 
 .SUFFIXES:.c .o
 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; \
                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;
 
                        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
 
 ### 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
 
 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
 
 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
 
 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=          
 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..
 INCLUDES=      -I..

-LIBS=          -lm -lz

 SUBDIRS=       .
 
 .SUFFIXES:.c .o
 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; \
                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;
                                INCLUDES="$(INCLUDES)" $$target || exit 1; \
                        cd $$wdir; \
                done;


@@ -31,11 +30,8 @@ lib:
 wgsim:wgsim.o
                $(CC) $(CFLAGS) -o $@ wgsim.o -lm
 
 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
 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
 
 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) -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
 
 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
 
 md5fa.o:md5.h md5fa.c
                $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c