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r344: avoid unnecessary refName retrieval

This commit is contained in:
Heng Li 2017-09-08 22:44:14 -04:00
parent ef3f7ea2f2
commit f422175e4e
2 changed files with 8 additions and 6 deletions
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2
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.1.1-r341" #define MM_VERSION "2.1.1-r344-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

8
map.c
View File

@ -217,13 +217,15 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
if (i > 0 && p->x>>8 == b->mini.a[m_st + i - 1].x>>8) is_tandem = 1; if (i > 0 && p->x>>8 == b->mini.a[m_st + i - 1].x>>8) is_tandem = 1;
if (i < n - 1 && p->x>>8 == b->mini.a[m_st + i + 1].x>>8) is_tandem = 1; if (i < n - 1 && p->x>>8 == b->mini.a[m_st + i + 1].x>>8) is_tandem = 1;
for (k = 0; k < q->n; ++k) { for (k = 0; k < q->n; ++k) {
const char *tname = mi->seq[r[k]>>32].name;
int32_t rpos = (uint32_t)r[k] >> 1; int32_t rpos = (uint32_t)r[k] >> 1;
mm128_t *p; mm128_t *p;
if (qname && (opt->flag&MM_F_NO_SELF) && strcmp(qname, tname) == 0 && rpos == (q->qpos>>1)) // avoid the diagonal if (qname && (opt->flag&(MM_F_NO_SELF|MM_F_AVA))) {
const char *tname = mi->seq[r[k]>>32].name;
if ((opt->flag&MM_F_NO_SELF) && strcmp(qname, tname) == 0 && rpos == (q->qpos>>1)) // avoid the diagonal
continue; continue;
if (qname && (opt->flag&MM_F_AVA) && strcmp(qname, tname) > 0) // all-vs-all mode: map once if ((opt->flag&MM_F_AVA) && strcmp(qname, tname) > 0) // all-vs-all mode: map once
continue; continue;
}
p = &a[j++]; p = &a[j++];
if ((r[k]&1) == (q->qpos&1)) { // forward strand if ((r[k]&1) == (q->qpos&1)) { // forward strand
p->x = (r[k]&0xffffffff00000000ULL) | (uint32_t)r[k]>>1; p->x = (r[k]&0xffffffff00000000ULL) | (uint32_t)r[k]>>1;