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This commit is contained in:
Heng Li 2017-06-23 18:57:00 -04:00
parent 6c8368c24c
commit 4fea3d778a
5 changed files with 60 additions and 11 deletions
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3
Makefile
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@ -2,7 +2,8 @@ CC= gcc
CFLAGS= -g -Wall -O2 -Wc++-compat -Wno-unused-function
CPPFLAGS=
INCLUDES= -I.
OBJS= kalloc.o kthread.o misc.o bseq.o sketch.o chain.o align.o sdust.o index.o map.o
OBJS= kalloc.o kthread.o misc.o bseq.o sketch.o chain.o align.o sdust.o \
index.o map.o ksw2_extz2_sse.o
PROG= minimap2
PROG_EXTRA= sdust
LIBS= -lm -lz -lpthread

50
align.c
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@ -1,7 +1,26 @@
#include <assert.h>
#include <string.h>
#include "minimap.h"
#include "ksw2.h"
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b)
{
int i, j;
a = a < 0? -a : a;
b = b > 0? -b : b;
for (i = 0; i < m - 1; ++i) {
for (j = 0; j < m - 1; ++j)
mat[i * m + j] = i == j? a : b;
mat[i * m + m - 1] = 0;
}
for (j = 0; j < m; ++j)
mat[(m - 1) * m + j] = 0;
}
static inline void mm_seq_rev(uint32_t len, uint8_t *seq)
{
uint32_t i;
@ -10,13 +29,31 @@ static inline void mm_seq_rev(uint32_t len, uint8_t *seq)
t = seq[i], seq[i] = seq[len - 1 - i], seq[len - 1 - i] = t;
}
static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r2, mm128_t *a)
static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) // TODO: this calls the libc realloc()
{
if (r->cigar == 0) {
uint32_t m_cigar = n_cigar + 2;
kroundup32(m_cigar);
r->cigar = (mm_cigar_t*)malloc(m_cigar * 4);
r->cigar->n = 0, r->cigar->m = m_cigar;
} else if (r->cigar->n + n_cigar > r->cigar->m - 2) {
kroundup32(r->cigar->m);
r->cigar->m = r->cigar->n + n_cigar;
r->cigar = (mm_cigar_t*)realloc(r->cigar, r->cigar->m * 4);
}
memcpy(r->cigar->cigar + r->cigar->n, cigar, n_cigar * 4);
r->cigar->n += n_cigar;
}
static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r2, mm128_t *a, ksw_extz_t *ez)
{
int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
uint8_t *tseq, *qseq;
int32_t i, k, l, rs0, re0, qs0, qe0;
int32_t rs, re, qs, qe, ret;
mm_reg1_t r1;
int8_t mat[25];
ksw_gen_simple_mat(5, mat, opt->a, opt->b);
rs = (int32_t)a[r->as].x + 1; // NB: this is the same as r->{rs,re}
re = (int32_t)a[r->as + r->cnt - 1].x + 1;
@ -53,8 +90,11 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
fprintf(stderr, "===> [-1] %d-%d %c (%s:%d-%d) <===\n", qs0, qs, "+-"[rev], mi->seq[rid].name, rs0, rs);
for (k = 0; k < tl; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
for (k = 0; k < ql; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
ksw_extz2_sse(km, ql, qseq, tl, tseq, 5, mat, opt->q, opt->e, (int)(opt->bw * 1.5 + .499), opt->zdrop, KSW_EZ_EXTZ_ONLY|KSW_EZ_RIGHT|KSW_EZ_REV_CIGAR, ez);
mm_seq_rev(ql, qseq);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
}
for (i = 0; i < r->cigar->n; ++i) fprintf(stderr, "%d%c", r->cigar->cigar[i]>>4, "MID"[r->cigar->cigar[i]&0xf]); fputc('\n', stderr);
/*
for (i = 1; i < r->cnt; ++i) {
re = (int32_t)a[r->as + i].x + 1;
@ -79,7 +119,9 @@ void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
extern unsigned char seq_nt4_table[256];
int i, reg;
uint8_t *qseq0[2];
ksw_extz_t ez;
memset(&ez, 0, sizeof(ksw_extz_t));
qseq0[0] = (uint8_t*)kmalloc(km, qlen);
qseq0[1] = (uint8_t*)kmalloc(km, qlen);
for (i = 0; i < qlen; ++i) {
@ -89,8 +131,8 @@ void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
for (reg = 0; reg < n_regs; ++reg) {
mm_reg1_t r2;
mm_align1(km, opt, mi, qlen, qseq0, &regs[reg], &r2, a);
mm_align1(km, opt, mi, qlen, qseq0, &regs[reg], &r2, a, &ez);
}
kfree(km, qseq0[0]); kfree(km, qseq0[1]);
kfree(km, qseq0[0]); kfree(km, qseq0[1]); kfree(km, ez.cigar);
}

9
ksw2.h
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@ -10,6 +10,8 @@
#define KSW_EZ_GENERIC_SC 0x04 // without this flag: match/mismatch only; last symbol is a wildcard
#define KSW_EZ_GLOBAL_ONLY 0x08 // don't record best score and ignore z-drop; significantly faster
#define KSW_EZ_DYN_BAND 0x10 // once used, ksw_extz_t::{mqe,mte} may be wrong
#define KSW_EZ_EXTZ_ONLY 0x20 // only perform extension
#define KSW_EZ_REV_CIGAR 0x40 // reverse CIGAR in the output
typedef struct {
int max, max_q, max_t; // max extension score and coordinate
@ -88,7 +90,7 @@ static inline uint32_t *ksw_push_cigar(void *km, int *n_cigar, int *m_cigar, uin
return cigar;
}
static inline void ksw_backtrack(void *km, int is_rot, const uint8_t *p, const int *off, int n_col, int i0, int j0, int *m_cigar_, int *n_cigar_, uint32_t **cigar_)
static inline void ksw_backtrack(void *km, int is_rot, int is_rev, const uint8_t *p, const int *off, int n_col, int i0, int j0, int *m_cigar_, int *n_cigar_, uint32_t **cigar_)
{
int n_cigar = 0, m_cigar = *m_cigar_, which = 0, i = i0, j = j0, r;
uint32_t *cigar = *cigar_, tmp;
@ -104,8 +106,9 @@ static inline void ksw_backtrack(void *km, int is_rot, const uint8_t *p, const i
}
if (i >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 2, i + 1); // first deletion
if (j >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, j + 1); // first insertion
for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
if (!is_rev)
for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
*m_cigar_ = m_cigar, *n_cigar_ = n_cigar, *cigar_ = cigar;
}

7
ksw2_extz2_sse.c
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@ -272,8 +272,11 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
kfree(km, mem);
if (with_max) kfree(km, H);
if (with_cigar) { // backtrack
if (ez->score > KSW_NEG_INF) ksw_backtrack(km, 1, (uint8_t*)p, off, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
else ksw_backtrack(km, 1, (uint8_t*)p, off, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
int rev_cigar = !!(flag & KSW_EZ_REV_CIGAR);
if (ez->score > KSW_NEG_INF && !(flag&KSW_EZ_EXTZ_ONLY))
ksw_backtrack(km, 1, rev_cigar, (uint8_t*)p, off, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
else if (ez->max_t >= 0 && ez->max_q >= 0)
ksw_backtrack(km, 1, rev_cigar, (uint8_t*)p, off, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
kfree(km, mem2); kfree(km, off);
}
}

2
minimap.h
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@ -42,7 +42,7 @@ typedef struct {
} mm_idx_t;
typedef struct {
uint32_t n_cigar, m_cigar;
uint32_t n, m;
uint32_t cigar[];
} mm_cigar_t;