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move bwt_gen/* to the root directory

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commit b96f180a15fc182ba0c2b409df594a45aa02a56c 1 parent 70da24e
authored October 20, 2011
26  Makefile
@@ -3,14 +3,14 @@ CXX=		g++
3 3
 CFLAGS=		-g -Wall -O2
4 4
 CXXFLAGS=	$(CFLAGS)
5 5
 DFLAGS=		-DHAVE_PTHREAD #-D_FILE_OFFSET_BITS=64
6  
-OBJS=		utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o \
7  
-			bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o \
  6
+OBJS=		QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o \
  7
+			is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o \
8 8
 			bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
9 9
 			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
10 10
 			bwtsw2_chain.o bamlite.o
11 11
 PROG=		bwa
12 12
 INCLUDES=	
13  
-LIBS=		-lm -lz -lpthread -Lbwt_gen -lbwtgen
  13
+LIBS=		-lm -lz -lpthread
14 14
 SUBDIRS=	. bwt_gen
15 15
 
16 16
 .SUFFIXES:.c .o .cc
@@ -22,21 +22,11 @@ SUBDIRS=	. bwt_gen
22 22
 
23 23
 all:$(PROG)
24 24
 
25  
-lib-recur all-recur clean-recur cleanlocal-recur install-recur:
26  
-		@target=`echo $@ | sed s/-recur//`; \
27  
-		wdir=`pwd`; \
28  
-		list='$(SUBDIRS)'; for subdir in $$list; do \
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-			cd $$subdir; \
30  
-			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
31  
-				INCLUDES="$(INCLUDES)" $$target || exit 1; \
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-			cd $$wdir; \
33  
-		done;
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-
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-lib:
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-
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-bwa:lib-recur $(OBJS) main.o
  25
+bwa:$(OBJS) main.o
38 26
 		$(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS)
39 27
 
  28
+QSufSort.o:QSufSort.h
  29
+
40 30
 bwt.o:bwt.h
41 31
 bwtio.o:bwt.h
42 32
 bwtaln.o:bwt.h bwtaln.h kseq.h
@@ -49,7 +39,5 @@ bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
49 39
 bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
50 40
 bwtsw2_main.o:bwtsw2.h
51 41
 
52  
-cleanlocal:
  42
+clean:
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 		rm -f gmon.out *.o a.out $(PROG) *~ *.a
54  
-
55  
-clean:cleanlocal-recur
0  bwt_gen/QSufSort.c → QSufSort.c
File renamed without changes
0  bwt_gen/QSufSort.h → QSufSort.h
File renamed without changes
0  bwt_gen/bwt_gen.c → bwt_gen.c
File renamed without changes

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