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Merge branch 'dev' into short

This commit is contained in:
Heng Li 2017-09-11 09:32:28 -04:00
parent 87a278d06a c7c3585531
commit eea9e851d8
2 changed files with 16 additions and 22 deletions
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2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.1.1-r344-dirty"
#define MM_VERSION "2.1.1-r347-dirty"
#ifdef __linux__
#include <sys/resource.h>

36
map.c
View File

@ -48,7 +48,7 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
}
typedef struct {
uint32_t n:31, is_alloc:1;
uint32_t n;
uint32_t qpos;
union {
const uint64_t *cr;
@ -103,21 +103,28 @@ static void mm_dust_minier(mm128_v *mini, int l_seq, const char *seq, int sdust_
mini->n = k;
}
mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint32_t m_st, uint32_t m_en, const char *qname, int qlen, const char *seq, int *n_regs)
mm_reg1_t *mm_map(const mm_idx_t *mi, int qlen, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
int i, n = m_en - m_st, j, n_u, max_gap_ref;
int i, n, j, n_u, max_gap_ref;
int64_t n_a;
uint64_t *u;
mm_match_t *m;
mm128_t *a;
mm_reg1_t *regs;
// collect minimizers
b->mini.n = 0;
mm_sketch(b->km, seq, qlen, mi->w, mi->k, 0, mi->is_hpc, &b->mini);
n = b->mini.n;
if (opt->sdust_thres > 0)
mm_dust_minier(&b->mini, qlen, seq, opt->sdust_thres, b->sdb);
// convert to local representation
m = (mm_match_t*)kmalloc(b->km, n * sizeof(mm_match_t));
for (i = 0; i < n; ++i) {
int t;
mm128_t *p = &b->mini.a[i + m_st];
m[i].is_alloc = 0;
mm128_t *p = &b->mini.a[i];
m[i].qpos = (uint32_t)p->y;
m[i].x.cr = mm_idx_get(mi, p->x>>8, &t);
m[i].n = t;
@ -128,13 +135,13 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
if (m[i].n < opt->mid_occ) n_a += m[i].n;
a = (mm128_t*)kmalloc(b->km, n_a * sizeof(mm128_t));
for (i = j = 0; i < n; ++i) {
mm128_t *p = &b->mini.a[i + m_st];
mm128_t *p = &b->mini.a[i];
mm_match_t *q = &m[i];
const uint64_t *r = q->x.cr;
int k, q_span = p->x & 0xff, is_tandem = 0;
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;
if (i > 0 && p->x>>8 == b->mini.a[i - 1].x>>8) is_tandem = 1;
if (i < n - 1 && p->x>>8 == b->mini.a[i + 1].x>>8) is_tandem = 1;
for (k = 0; k < q->n; ++k) {
int32_t rpos = (uint32_t)r[k] >> 1;
mm128_t *p;
@ -158,8 +165,6 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
}
n_a = j;
radix_sort_128x(a, a + n_a);
for (i = 0; i < n; ++i)
if (m[i].is_alloc) kfree(b->km, m[i].x.r);
kfree(b->km, m);
if (mm_dbg_flag & MM_DBG_PRINT_SEED)
@ -200,17 +205,6 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
return regs;
}
mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
mm_reg1_t *regs;
b->mini.n = 0;
mm_sketch(b->km, seq, l_seq, mi->w, mi->k, 0, mi->is_hpc, &b->mini);
if (opt->sdust_thres > 0)
mm_dust_minier(&b->mini, l_seq, seq, opt->sdust_thres, b->sdb);
regs = mm_map_frag(opt, mi, b, 0, b->mini.n, qname, l_seq, seq, n_regs);
return regs;
}
/**************************
* Multi-threaded mapping *
**************************/