From b96f180a15fc182ba0c2b409df594a45aa02a56c Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Thu, 20 Oct 2011 11:56:24 -0400
Subject: [PATCH] move bwt_gen/* to the root directory

---
 Makefile                         | 26 +++++++-------------------
 bwt_gen/QSufSort.c => QSufSort.c |  0
 bwt_gen/QSufSort.h => QSufSort.h |  0
 bwt_gen/bwt_gen.c => bwt_gen.c   |  0
 4 files changed, 7 insertions(+), 19 deletions(-)
 rename bwt_gen/QSufSort.c => QSufSort.c (100%)
 rename bwt_gen/QSufSort.h => QSufSort.h (100%)
 rename bwt_gen/bwt_gen.c => bwt_gen.c (100%)

diff --git a/Makefile b/Makefile
index 53f241d..c9588f2 100644
--- a/Makefile
+++ b/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
diff --git a/bwt_gen/QSufSort.c b/QSufSort.c
similarity index 100%
rename from bwt_gen/QSufSort.c
rename to QSufSort.c
diff --git a/bwt_gen/QSufSort.h b/QSufSort.h
similarity index 100%
rename from bwt_gen/QSufSort.h
rename to QSufSort.h
diff --git a/bwt_gen/bwt_gen.c b/bwt_gen.c
similarity index 100%
rename from bwt_gen/bwt_gen.c
rename to bwt_gen.c