Add the header line to the output SAM

In particular, this defines the output SAM to be unsorted BUT also query grouped.  The latter is very important to explicitly define so downstream tools that don't make assumptions know that reads from the same template are grouped.

bwa.c

@@ -406,10 +406,17 @@ int bwa_idx2mem(bwaidx_t *idx)
 
 void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
 {
-	int i, n_SQ = 0;
+	int i, n_HD = 0, n_SQ = 0;
 	extern char *bwa_pg;
+
 	if (hdr_line) {
+		// check for HD line
 		const char *p = hdr_line;
+		if ((p = strstr(p, "@HD")) != 0) {
+			++n_HD;
+		}	
+		// check for SQ lines
+		p = hdr_line;
 		while ((p = strstr(p, "@SQ\t")) != 0) {
 			if (p == hdr_line || *(p-1) == '\n') ++n_SQ;
 			p += 4;
@@ -423,6 +430,9 @@ void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
 		}
 	} else if (n_SQ != bns->n_seqs && bwa_verbose >= 2)
 		fprintf(stderr, "[W::%s] %d @SQ lines provided with -H; %d sequences in the index. Continue anyway.\n", __func__, n_SQ, bns->n_seqs);
+	if (n_HD == 0) {
+		err_printf("@HD\tVN:1.5\tSO:unsorted\tGO:query\n");
+	}
 	if (hdr_line) err_printf("%s\n", hdr_line);
 	if (bwa_pg) err_printf("%s\n", bwa_pg);
 }