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r445: pair coordinate adjustment working

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Next: mapq adjustment, which will be tricky...
This commit is contained in:
Heng Li
2017-09-27 15:38:18 -04:00
parent a349d85280
commit 7e0d70bfd3
5 changed files with 76 additions and 14 deletions
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pe.c
+65 -10
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@@ -1,5 +1,6 @@
#include <stdlib.h>
#include "mmpriv.h"
#include "kalloc.h"
void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r)
{
@@ -43,29 +44,83 @@ void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int
#include "ksort.h"
typedef struct {
int s;
int s, rev;
uint64_t key;
mm_reg1_t *r;
} pair_arr_t;
#define sort_key_pair(a) ((a).key)
KRADIX_SORT_INIT(pair, pair_arr_t, sort_key_pair, 8)
/*
void mm_pair(void *km, int max_gap_ref, int *n_regs, mm_reg1_t **regs)
void mm_pair(void *km, int max_gap_ref, int pe_bonus, const int *qlens, int *n_regs, mm_reg1_t **regs)
{
int i, j, s, n, last = -1;
int i, j, s, n, last[2], dp_thres, segs = 0, n_pairs = 0, max_idx[2];
int64_t max, max2;
pair_arr_t *a;
a = (pair_arr_t*)kmalloc(km, (n_regs[0] + n_regs[1]) * sizeof(pair_arr_t));
for (s = n = 0; s < 2; ++s)
for (s = n = 0, dp_thres = 0; s < 2; ++s) {
int max = 0;
for (i = 0; i < n_regs[s]; ++i) {
a[n].s = s;
a[n].r = &regs[s][i];
a[n++].key = (uint64_t)a[n].r->rid << 32 | a[n].r->rs;
a[n].rev = a[n].r->rev;
a[n].key = (uint64_t)a[n].r->rid << 32 | a[n].r->rs<<1 | (s^a[n].rev);
max = max > a[n].r->p->dp_max? max : a[n].r->p->dp_max;
++n;
segs |= 1<<s;
}
radix_sort_pair(n, a);
for (i = 0; i < n; ++i) {
int pre_dir = seg_rev? !a[i].r->rev : a[i].r->rev;
dp_thres += max;
}
if (segs != 3) {
kfree(km, a); // only one end is mapped
return;
}
dp_thres -= pe_bonus;
if (dp_thres < 0) dp_thres = 0;
radix_sort_pair(a, a + n);
max = max2 = -1;
max_idx[0] = max_idx[1] = -1;
last[0] = last[1] = -1;
for (i = 0; i < n; ++i) {
if (a[i].key & 1) { // reverse first read or forward second read
mm_reg1_t *q, *r;
if (last[a[i].rev] < 0) continue;
r = a[i].r;
q = a[last[a[i].rev]].r;
if (r->rid != q->rid || r->rs - q->re > max_gap_ref) continue;
for (j = last[a[i].rev]; j >= 0; --j) {
int sum;
if (a[j].rev != a[i].rev || a[j].s == a[i].s) continue;
q = a[j].r;
if (r->rid != q->rid || r->rs - q->re > max_gap_ref) break;
if (r->p->dp_max + q->p->dp_max < dp_thres) continue;
++n_pairs;
sum = r->p->dp_max + q->p->dp_max;
if (sum > max) {
max_idx[a[j].s] = j, max_idx[a[i].s] = i;
max2 = max;
max = sum;
} else if (sum > max2)
max2 = sum;
}
} else { // forward first read or reverse second read
last[a[i].rev] = i;
}
}
if (max > 0) {
for (s = 0; s < 2; ++s) {
mm_reg1_t *r = a[max_idx[s]].r;
if (r->id != r->parent) {
mm_reg1_t *p = &regs[s][r->parent];
for (i = 0; i < n_regs[s]; ++i)
if (regs[s][i].parent == p->id)
regs[s][i].parent = r->id;
}
}
}
kfree(km, a);
}
*/