r342: bugfix in bwasw - AS is off by one

but I do not understand why the old code does not have the same problem.

Makefile

@@ -1,8 +1,7 @@
 CC=			gcc
 CFLAGS=		-g -Wall -O2
-CXXFLAGS=	$(CFLAGS)
 AR=			ar
-DFLAGS=		-DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
+DFLAGS=		-DHAVE_PTHREAD
 LOBJS=		utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
 AOBJS=		QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
 			is.o bwtindex.o bwape.o kopen.o pemerge.o \
@@ -17,8 +16,6 @@ SUBDIRS=	.
 
 .c.o:
 		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-.cc.o:
-		$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
 
 all:$(PROG)
 

bwtsw2_aux.c

@@ -153,7 +153,7 @@ void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq,
 		for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
 			target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
 		lt = j;
-		score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, -1, 1, &qle, &tle, 0, 0, 0);
+		score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, -1, 1, &qle, &tle, 0, 0, 0) - 1;
 //		if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G);
 		if (score >= p->G) {
 			p->G = score;

main.c

@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.0-r341-beta"
+#define PACKAGE_VERSION "0.7.0-r342-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);