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move bwt_gen/* to the root directory

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commit b96f180a15fc182ba0c2b409df594a45aa02a56c 1 parent 70da24e
Heng Li authored
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26 Makefile
@@ -3,14 +3,14 @@ CXX= g++
CFLAGS= -g -Wall -O2
CXXFLAGS= $(CFLAGS)
DFLAGS= -DHAVE_PTHREAD #-D_FILE_OFFSET_BITS=64
-OBJS= utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o \
- bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o \
+OBJS= QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o \
+ is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o \
bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
bwtsw2_chain.o bamlite.o
PROG= bwa
INCLUDES=
-LIBS= -lm -lz -lpthread -Lbwt_gen -lbwtgen
+LIBS= -lm -lz -lpthread
SUBDIRS= . bwt_gen
.SUFFIXES:.c .o .cc
@@ -22,21 +22,11 @@ SUBDIRS= . bwt_gen
all:$(PROG)
-lib-recur all-recur clean-recur cleanlocal-recur install-recur:
- @target=`echo $@ | sed s/-recur//`; \
- wdir=`pwd`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
- cd $$subdir; \
- $(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
- INCLUDES="$(INCLUDES)" $$target || exit 1; \
- cd $$wdir; \
- done;
-
-lib:
-
-bwa:lib-recur $(OBJS) main.o
+bwa:$(OBJS) main.o
$(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS)
+QSufSort.o:QSufSort.h
+
bwt.o:bwt.h
bwtio.o:bwt.h
bwtaln.o:bwt.h bwtaln.h kseq.h
@@ -49,7 +39,5 @@ bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
bwtsw2_main.o:bwtsw2.h
-cleanlocal:
+clean:
rm -f gmon.out *.o a.out $(PROG) *~ *.a
-
-clean:cleanlocal-recur
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0  bwt_gen/QSufSort.c → QSufSort.c
File renamed without changes
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0  bwt_gen/QSufSort.h → QSufSort.h
File renamed without changes
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0  bwt_gen/bwt_gen.c → bwt_gen.c
File renamed without changes
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