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r985: optionally report cs/cg on the query strand

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PAF only; not well tested
This commit is contained in:
Heng Li
2020-04-21 12:37:35 -04:00
parent 29f67a1666
commit da7109fd29
9 changed files with 114 additions and 42 deletions
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hit.c
+9 -9
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@@ -20,14 +20,14 @@ static inline void mm_cal_fuzzy_len(mm_reg1_t *r, const mm128_t *a)
}
}
static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a, int is_qstrand)
{ // NB: r->as and r->cnt MUST BE set correctly for this function to work
int32_t k = r->as, q_span = (int32_t)(a[k].y>>32&0xff);
r->rev = a[k].x>>63;
r->rid = a[k].x<<1>>33;
r->rs = (int32_t)a[k].x + 1 > q_span? (int32_t)a[k].x + 1 - q_span : 0; // NB: target span may be shorter, so this test is necessary
r->re = (int32_t)a[k + r->cnt - 1].x + 1;
if (!r->rev) {
if (!r->rev || is_qstrand) {
r->qs = (int32_t)a[k].y + 1 - q_span;
r->qe = (int32_t)a[k + r->cnt - 1].y + 1;
} else {
@@ -49,7 +49,7 @@ static inline uint64_t hash64(uint64_t key)
return key;
}
mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u, mm128_t *a) // convert chains to hits
mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u, mm128_t *a, int is_qstrand) // convert chains to hits
{
mm128_t *z, tmp;
mm_reg1_t *r;
@@ -81,7 +81,7 @@ mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u,
ri->cnt = (int32_t)z[i].y;
ri->as = z[i].y >> 32;
ri->div = -1.0f;
mm_reg_set_coor(ri, qlen, a);
mm_reg_set_coor(ri, qlen, a, is_qstrand);
}
kfree(km, z);
return r;
@@ -103,7 +103,7 @@ static inline int mm_alt_score(int score, float alt_diff_frac)
return score > 0? score : 1;
}
void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a, int is_qstrand)
{
if (n <= 0 || n >= r->cnt) return;
*r2 = *r;
@@ -115,10 +115,10 @@ void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
r2->score = (int32_t)(r->score * ((float)r2->cnt / r->cnt) + .499);
r2->as = r->as + n;
if (r->parent == r->id) r2->parent = MM_PARENT_TMP_PRI;
mm_reg_set_coor(r2, qlen, a);
mm_reg_set_coor(r2, qlen, a, is_qstrand);
r->cnt -= r2->cnt;
r->score -= r2->score;
mm_reg_set_coor(r, qlen, a);
mm_reg_set_coor(r, qlen, a, is_qstrand);
r->split |= 1, r2->split |= 2;
}
@@ -350,7 +350,7 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
// all conditions satisfied; join
a[r1->as].y |= MM_SEED_LONG_JOIN;
r0->cnt += r1->cnt, r0->score += r1->score;
mm_reg_set_coor(r0, qlen, a);
mm_reg_set_coor(r0, qlen, a, opt->flag&MM_F_QSTRAND);
r1->cnt = 0;
r1->parent = r0->id;
++n_drop;
@@ -416,7 +416,7 @@ mm_seg_t *mm_seg_gen(void *km, uint32_t hash, int n_segs, const int *qlens, int
}
}
for (s = 0; s < n_segs; ++s) {
regs[s] = mm_gen_regs(km, hash, qlens[s], seg[s].n_u, seg[s].u, seg[s].a);
regs[s] = mm_gen_regs(km, hash, qlens[s], seg[s].n_u, seg[s].u, seg[s].a, 0);
n_regs[s] = seg[s].n_u;
for (i = 0; i < n_regs[s]; ++i) {
regs[s][i].seg_split = 1;