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r108: refactoring, move reg1 routines to hit.c

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This commit is contained in:
Heng Li
2017-06-29 19:44:11 -04:00
parent ecedfe5788
commit 4cd456b9ba
6 changed files with 30 additions and 44 deletions
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align.c
+2 -34
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@@ -26,23 +26,6 @@ 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_reg_split(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
{
if (n <= 0 || n >= r->cnt) return;
*r2 = *r;
r2->id = -1;
r2->p = 0;
r2->cnt = r->cnt - n;
r2->score = (int32_t)(r->score * ((float)r2->cnt / r->cnt) + .499);
r2->as = r->as + n;
r2->parent = -2;
mm_reg_set_coor(r2, qlen, a);
r->cnt -= r2->cnt;
r->score -= r2->score;
mm_reg_set_coor(r, qlen, a);
r->split = r2->split = 1;
}
static inline int test_zdrop_aux(int32_t score, int i, int j, int32_t *max, int *max_i, int *max_j, int e, int zdrop)
{
if (score < *max) {
@@ -250,7 +233,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
re1 = rs + (ez->max_t + 1);
qe1 = qs + (ez->max_q + 1);
if (r->cnt - (j + 1) >= opt->min_cnt) {
mm_reg_split(r, r2, j + 1, qlen, a);
mm_split_reg(r, r2, j + 1, qlen, a);
if (j + 1 < opt->min_cnt)
r2->id = r->id, r->id = -1;
}
@@ -325,22 +308,7 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
else if (i < r) regs[i++] = regs[r]; // NB: this also move the regs[r].p pointer
else ++i;
}
// remap mm_reg1_t::{id,parent}
if (i < n_regs || n_regs != *n_regs_) { // there are region splits or drops
int32_t *id;
n_regs = i;
id = (int32_t*)kmalloc(km, *n_regs_ * 4);
for (r = 0; r < *n_regs_; ++r) id[r] = -1;
for (r = 0; r < n_regs; ++r) {
if (regs[r].id >= 0) id[regs[r].id] = r;
regs[r].id = r;
}
for (r = 0; r < n_regs; ++r)
if (regs[r].parent >= 0)
regs[r].parent = id[regs[r].parent];
kfree(km, id);
}
*n_regs_ = n_regs;
mm_sync_regs(km, n_regs, regs);
return regs;
}