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r216: a bit cleanup; identical output to r215

This commit is contained in:
Heng Li 2017-07-28 11:54:18 -04:00
parent fc965805f7
commit 254280b8af
5 changed files with 14 additions and 7 deletions
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8
align.c
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@ -179,7 +179,7 @@ static void mm_filter_bad_seeds(void *km, int as1, int cnt1, mm128_t *a, int min
if (k == n || k >= max_en) { if (k == n || k >= max_en) {
if (max_en > 0) if (max_en > 0)
for (i = K[max_st]; i < K[max_en]; ++i) for (i = K[max_st]; i < K[max_en]; ++i)
a[as1 + i].y |= 1ULL << 41; a[as1 + i].y |= MM_SEED_IGNORE;
max = 0, max_st = max_en = -1; max = 0, max_st = max_en = -1;
if (k == n) break; if (k == n) break;
} }
@ -299,12 +299,12 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
assert(qs1 >= 0 && rs1 >= 0); assert(qs1 >= 0 && rs1 >= 0);
for (i = 1; i < cnt1; ++i) { // gap filling for (i = 1; i < cnt1; ++i) { // gap filling
if (a[as1+i].y>>41&1) continue; if (a[as1+i].y & MM_SEED_IGNORE) continue;
mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe); mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
re1 = re, qe1 = qe; re1 = re, qe1 = qe;
if (i == cnt1 - 1 || (a[as1+i].y>>40&1) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) { if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
int bw1 = bw; int bw1 = bw;
if (a[as1+i].y>>40&1) if (a[as1+i].y & MM_SEED_LONG_JOIN)
bw1 = qe - qs > re - rs? qe - qs : re - rs; bw1 = qe - qs > re - rs? qe - qs : re - rs;
qseq = &qseq0[rev][qs]; qseq = &qseq0[rev][qs];
mm_idx_getseq(mi, rid, rs, re, tseq); mm_idx_getseq(mi, rid, rs, re, tseq);

2
hit.c
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@ -266,7 +266,7 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
if (r1->re - r1->rs < max_gap>>1 || r1->qe - r1->qs < max_gap>>1) continue; if (r1->re - r1->rs < max_gap>>1 || r1->qe - r1->qs < max_gap>>1) continue;
// all conditions satisfied; join // all conditions satisfied; join
a[r1->as].y |= 1ULL<<40; a[r1->as].y |= MM_SEED_LONG_JOIN;
r0->cnt += r1->cnt, r0->score += r1->score; r0->cnt += r1->cnt, r0->score += r1->score;
mm_reg_set_coor(r0, qlen, a); mm_reg_set_coor(r0, qlen, a);
r1->cnt = 0; r1->cnt = 0;

2
main.c
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@ -8,7 +8,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r215-dirty" #define MM_VERSION "2.0-r216-dirty"
void liftrlimit() void liftrlimit()
{ {

5
map.c
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@ -209,8 +209,10 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
mm128_t *p = &b->mini.a[i + m_st]; mm128_t *p = &b->mini.a[i + m_st];
mm_match_t *q = &m[i]; mm_match_t *q = &m[i];
const uint64_t *r = q->x.cr; const uint64_t *r = q->x.cr;
int k, q_span = p->x & 0xff; int k, q_span = p->x & 0xff, is_tandem = 0;
if (q->n >= opt->mid_occ) continue; if (q->n >= opt->mid_occ) continue;
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;
for (k = 0; k < q->n; ++k) { for (k = 0; k < q->n; ++k) {
const char *tname = mi->seq[r[k]>>32].name; 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;
@ -227,6 +229,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
p->x = 1ULL<<63 | (r[k]&0xffffffff00000000ULL) | (uint32_t)r[k]>>1; p->x = 1ULL<<63 | (r[k]&0xffffffff00000000ULL) | (uint32_t)r[k]>>1;
p->y = (uint64_t)q_span << 32 | (qlen - ((q->qpos>>1) + 1 - q_span) - 1); p->y = (uint64_t)q_span << 32 | (qlen - ((q->qpos>>1) + 1 - q_span) - 1);
} }
if (is_tandem) p->y |= MM_SEED_TANDEM;
} }
} }
n_a = j; n_a = j;

4
mmpriv.h
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@ -12,6 +12,10 @@
#define MM_DBG_PRINT_QNAME 0x2 #define MM_DBG_PRINT_QNAME 0x2
#define MM_DBG_PRINT_SEED 0x4 #define MM_DBG_PRINT_SEED 0x4
#define MM_SEED_LONG_JOIN (1ULL<<40)
#define MM_SEED_IGNORE (1ULL<<41)
#define MM_SEED_TANDEM (1ULL<<42)
#ifndef kroundup32 #ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif #endif