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Heng Li
2017-09-20 14:35:46 -04:00
parent 5b39a1b34b
commit 9943e5fdd0
3 changed files with 118 additions and 51 deletions
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hit.c
+56 -8
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@@ -293,19 +293,67 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
mm_sync_regs(km, *n_regs_, regs);
}
}
/*
void mm_sep_seg(void *km, int n_segs, int qlen_sum, int n_regs0, mm_reg1_t *regs0, mm128_t *a, mm_segreg_t *seg)
{ // TODO: this implement is inefficient given a large n_segs
int s, i, j;
memset(seg, 0, n_segs * sizeof(mm_segreg_t));
mm_seg_t *mm_seg_gen(void *km, int n_segs, const int *qlens, int n_regs0, const mm_reg1_t *regs0, int *n_regs, mm_reg1_t **regs, const mm128_t *a)
{
int s, i, j, acc_qlen[MM_MAX_SEG+1], qlen_sum = 0;
mm_seg_t *seg;
assert(n_segs <= MM_MAX_SEG);
for (s = 1, acc_qlen[0] = 0; s < n_segs; ++s)
acc_qlen[s] = acc_qlen[s-1] + qlens[s-1];
qlen_sum = acc_qlen[n_segs - 1] + qlens[n_segs - 1];
seg = (mm_seg_t*)kcalloc(km, n_segs, sizeof(mm_seg_t));
for (s = 0; s < n_segs; ++s) {
seg[s].u = (uint64_t*)kmalloc(km, n_regs0 * 8);
for (i = 0; i < n_regs0; ++i)
seg[s].u[i] = (uint64_t)regs0[i].score << 32;
}
for (i = 0; i < n_regs0; ++i) {
mm_reg1_t *r = &regs0[i];
const mm_reg1_t *r = &regs0[i];
for (j = 0; j < r->cnt; ++j) {
++seg[(a[r->as + j].y&MM_SEED_SEG_MASK)>>MM_SEED_SEG_SHIFT].n_a;
int sid = (a[r->as + j].y&MM_SEED_SEG_MASK)>>MM_SEED_SEG_SHIFT;
++seg[sid].u[i];
++seg[sid].n_a;
}
}
for (s = 0; s < n_segs; ++s) {
mm_seg_t *sr = &seg[s];
for (i = 0, sr->n_u = 0; i < n_regs0; ++i) // squeeze out zero-length per-segment chains
if ((int32_t)sr->u[i] != 0)
sr->u[sr->n_u++] = sr->u[i];
sr->a = (mm128_t*)kmalloc(km, sr->n_a * sizeof(mm128_t));
sr->n_a = 0;
}
for (i = 0; i < n_regs0; ++i) {
const mm_reg1_t *r = &regs0[i];
for (j = 0; j < r->cnt; ++j) {
int sid = (a[r->as + j].y&MM_SEED_SEG_MASK)>>MM_SEED_SEG_SHIFT;
mm128_t a1 = a[r->as + j];
// on reverse strand, the segment position is:
// x_for_cat = qlen_sum - 1 - (int32_t)a1.y - 1 + q_span
// (int32_t)new_a1.y = qlens[sid] - (x_for_cat - acc_qlen[sid] + 1 - q_span) - 1 = (int32_t)a1.y - (qlen_sum - (qlens[sid] + acc_qlen[sid]))
a1.y -= a1.x>>63? qlen_sum - (qlens[sid] + acc_qlen[sid]) : acc_qlen[sid];
seg[sid].a[seg[sid].n_a++] = a1;
}
}
for (s = 0; s < n_segs; ++s) {
regs[s] = mm_gen_regs(km, qlens[s], seg[s].n_u, seg[s].u, seg[s].a);
n_regs[s] = seg[s].n_u;
}
return seg;
}
*/
void mm_seg_free(void *km, int n_segs, mm_seg_t *segs)
{
int i;
for (i = 0; i < n_segs; ++i) kfree(km, segs[i].u);
for (i = 0; i < n_segs; ++i) kfree(km, segs[i].a);
kfree(km, segs);
}
void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len)
{
static const float q_coef = 40.0f;