r315: move kopen.o out of libbwa.a

Makefile

@@ -3,9 +3,9 @@ CFLAGS=		-g -Wall -O2
 CXXFLAGS=	$(CFLAGS)
 AR=			ar
 DFLAGS=		-DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
-LOBJS=		utils.o kstring.o ksw.o kopen.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
+LOBJS=		utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
 AOBJS=		QSufSort.o bwt_gen.o stdaln.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
-			is.o bwtindex.o bwape.o \
+			is.o bwtindex.o bwape.o kopen.o \
 			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
 			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
 PROG=		bwa bwamem-lite

bwamem.h

@@ -109,7 +109,7 @@ extern "C" {
 	 * Find the aligned regions for one query sequence
 	 *
 	 * Note that this routine does not generate CIGAR. CIGAR should be
-	 * generated later by bwa_gen_cigar() defined in bwa.c.
+	 * generated later by mem_reg2aln() below.
 	 *
 	 * @param opt    alignment parameters
 	 * @param bwt    FM-index of the reference sequence
@@ -126,7 +126,6 @@ extern "C" {
 	 * Generate CIGAR and forward-strand position from alignment region
 	 *
 	 * @param opt    alignment parameters
-	 * @param bwt    FM-index of the reference sequence
 	 * @param bns    Information of the reference
 	 * @param pac    2-bit encoded reference
 	 * @param l_seq  length of query sequence

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.0-r314"
+#define PACKAGE_VERSION "0.7.0-r315"
 #endif
 
 static int usage()