r1272: more stringent on @hd checking via -H

Author: lh3

Makefile

@@ -22,6 +22,11 @@ ifeq ($(shell uname -s),GNU/kFreeBSD)
 	LIBS += -lrt
 endif
 
+ifneq ($(asan),)
+	CFLAGS+=-fsanitize=address
+	LIBS+=-fsanitize=address -ldl
+endif
+
 .SUFFIXES:.c .o .cc
 
 .c.o:
@@ -81,7 +86,7 @@ fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h
 is.o: malloc_wrap.h
 kopen.o: malloc_wrap.h
 kstring.o: kstring.h malloc_wrap.h
-ksw.o: ksw.h neon_sse.h scalar_sse.h malloc_wrap.h
+ksw.o: scalar_sse.h ksw.h malloc_wrap.h
 main.o: kstring.h malloc_wrap.h utils.h
 malloc_wrap.o: malloc_wrap.h
 maxk.o: bwa.h bntseq.h bwt.h bwamem.h kseq.h malloc_wrap.h

README.md

@@ -6,8 +6,7 @@
 **Note: [minimap2][minimap2] has replaced BWA-MEM for __PacBio and Nanopore__ read
 alignment.** It retains all major BWA-MEM features, but is ~50 times as fast,
 more versatile, more accurate and produces better base-level alignment.
-A beta version of [BWA-MEM2][bwa-mem2] has been released for short-read mapping.
-BWA-MEM2 is about twice as fast as BWA-MEM and outputs near identical alignments.
+[BWA-MEM2][bwa-mem2] is 50-100% faster than BWA-MEM and outputs identical alignments.
 
 [minimap2]: https://github.com/lh3/minimap2
 [bwa-mem2]: https://github.com/bwa-mem2/bwa-mem2

bwa.1

@@ -359,7 +359,7 @@ uses soft clipping for the primary alignment and hard clipping for
 supplementary alignments.
 .TP
 .B -M
-Mark shorter split hits as secondary (for Picard compatibility).
+Mark shorter split hits as secondary
 .TP
 .BI -v \ INT
 Control the verbosity level of the output. This option has not been fully

bwa.c

@@ -412,9 +412,10 @@ void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
 	if (hdr_line) {
 		// check for HD line
 		const char *p = hdr_line;
-		if ((p = strstr(p, "@HD")) != 0) {
-			++n_HD;
-		}	
+		while ((p = strstr(p, "@HD\t")) != 0) {
+			if (p == hdr_line || *(p-1) == '\n') ++n_HD;
+			p += 4;
+		}
 		// check for SQ lines
 		p = hdr_line;
 		while ((p = strstr(p, "@SQ\t")) != 0) {

main.c

@@ -30,7 +30,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.18-r1271-dirty"
+#define PACKAGE_VERSION "0.7.18-r1272-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);