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r860: MD/cs not working with --eqx

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Heng Li
2018-10-26 23:23:53 -04:00
parent ecb6c5c36c
commit 9ed56b4a25
2 changed files with 5 additions and 5 deletions
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format.c
+4 -4
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@@ -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:"); if (write_tag) mm_sprintf_lite(s, "\tcs:Z:");
for (i = q_off = t_off = 0; i < (int)r->p->n_cigar; ++i) { 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; int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
assert(op >= 0 && op <= 3); assert((op >= 0 && op <= 3) || op == 7 || op == 8);
if (op == 0) { // match if (op == 0 || op == 7 || op == 8) { // match
int l_tmp = 0; int l_tmp = 0;
for (j = 0; j < len; ++j) { for (j = 0; j < len; ++j) {
if (qseq[q_off + j] != tseq[t_off + 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:"); if (write_tag) mm_sprintf_lite(s, "\tMD:Z:");
for (i = q_off = t_off = 0; i < (int)r->p->n_cigar; ++i) { 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; int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
assert(op >= 0 && op <= 3); assert((op >= 0 && op <= 3) || op == 7 || op == 8);
if (op == 0) { // match if (op == 0 || op == 7 || op == 8) { // match
for (j = 0; j < len; ++j) { for (j = 0; j < len; ++j) {
if (qseq[q_off + j] != tseq[t_off + j]) { if (qseq[q_off + j] != tseq[t_off + j]) {
mm_sprintf_lite(s, "%d%c", l_MD, "ACGTN"[tseq[t_off + j]]); mm_sprintf_lite(s, "%d%c", l_MD, "ACGTN"[tseq[t_off + j]]);
main.c
+1 -1
View File
@@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.13-r858-dirty" #define MM_VERSION "2.13-r860-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>