r860: MD/cs not working with --eqx

Illumina · Oct 27, 2018 · 9ed56b4 · 9ed56b4
1 parent ecb6c5c
commit 9ed56b4
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/format.c b/format.c
@@ -139,8 +139,8 @@ static void write_cs_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq
 	if (write_tag) mm_sprintf_lite(s, "\tcs:Z:");
 	for (i = q_off = t_off = 0; i < (int)r->p->n_cigar; ++i) {
 		int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
-		assert(op >= 0 && op <= 3);
-		if (op == 0) { // match
+		assert((op >= 0 && op <= 3) || op == 7 || op == 8);
+		if (op == 0 || op == 7 || op == 8) { // match
 			int l_tmp = 0;
 			for (j = 0; j < len; ++j) {
 				if (qseq[q_off + j] != tseq[t_off + j]) {
@@ -187,8 +187,8 @@ static void write_MD_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq
 	if (write_tag) mm_sprintf_lite(s, "\tMD:Z:");
 	for (i = q_off = t_off = 0; i < (int)r->p->n_cigar; ++i) {
 		int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
-		assert(op >= 0 && op <= 3);
-		if (op == 0) { // match
+		assert((op >= 0 && op <= 3) || op == 7 || op == 8);
+		if (op == 0 || op == 7 || op == 8) { // match
 			for (j = 0; j < len; ++j) {
 				if (qseq[q_off + j] != tseq[t_off + j]) {
 					mm_sprintf_lite(s, "%d%c", l_MD, "ACGTN"[tseq[t_off + j]]);

diff --git a/main.c b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.13-r858-dirty"
+#define MM_VERSION "2.13-r860-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>