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keep l1 trans

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chhylp123
2021-04-04 14:00:28 -04:00
parent ebfc04d253
commit 8e75eb5a05
6 changed files with 356 additions and 72 deletions
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partig.cpp
+46 -18
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@@ -721,6 +721,7 @@ int8_t *s)
}
}
void clean_ovlp(ma_ug_t *ug, asg_t *read_g, hap_overlaps_list* ha, pt_g_t *pg, int8_t* s)
{
uint32_t v, i, k, qn, tn, types[4];
@@ -751,11 +752,35 @@ void clean_ovlp(ma_ug_t *ug, asg_t *read_g, hap_overlaps_list* ha, pt_g_t *pg, i
}
}
// for (v = 0; v < ha->num; v++)
// {
// for (i = k = 0; i < ha->x[v].a.n; i++)
// {
// if(ha->x[v].a.a[i].status != FLIP)
// {
// if(s[ha->x[v].a.a[i].xUid]*s[ha->x[v].a.a[i].yUid] == -1)
// {
// fprintf(stderr, "\ns[0]=%d, s[1]=%d\n", s[ha->x[v].a.a[i].xUid], s[ha->x[v].a.a[i].yUid]);
// print_hap_paf(ug, &(ha->x[v].a.a[i]));
// }
// continue;
// }
// ha->x[v].a.a[k] = ha->x[v].a.a[i];
// k++;
// }
// ha->x[v].a.n = k;
// }
for (v = 0; v < ha->num; v++)
{
for (i = k = 0; i < ha->x[v].a.n; i++)
{
if(ha->x[v].a.a[i].status != FLIP) continue;
ha->x[v].a.a[k] = ha->x[v].a.a[i];
k++;
}
@@ -775,28 +800,31 @@ void pt_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, ma_ug_t *ug, asg_t *re
pt_cc(pg->e);
s = pt_solve_core(&opt, pg->e);
if(asm_opt.flag & HA_F_PARTITION)
{
MALLOC(buf, pg->e->ma.n); // FIXME: this is over-allocation for convenience
for (i = 0; i < pg->e->n_seq; ++i) {
uint64_t z[2];
uint32_t o = pg->e->idx.a[i] >> 32;
uint32_t n = (uint32_t)pg->e->idx.a[i], j;
MALLOC(buf, pg->e->ma.n); // FIXME: this is over-allocation for convenience
for (i = 0; i < pg->e->n_seq; ++i) {
uint64_t z[2];
uint32_t o = pg->e->idx.a[i] >> 32;
uint32_t n = (uint32_t)pg->e->idx.a[i], j;
set_trio_flag(ug, read_g, i, trio_flag, t_ch, ovlp, pg->e, s[i]);
set_trio_flag(ug, read_g, i, trio_flag, t_ch, ovlp, pg->e, s[i]);
pg->info.a[i].s = s[i];
for (j = 0; j < n; ++j) {
const pt_match1_t *m = &pg->e->ma.a[o + j];
buf[j] = (uint64_t)((uint32_t)-1 - m->w) << 32 | (o + j);
pg->info.a[i].s = s[i];
for (j = 0; j < n; ++j) {
const pt_match1_t *m = &pg->e->ma.a[o + j];
buf[j] = (uint64_t)((uint32_t)-1 - m->w) << 32 | (o + j);
}
radix_sort_gfa64(buf, buf + n);
for (j = 0, z[0] = z[1] = 0; j < n; ++j) {
const pt_match1_t *m = &pg->e->ma.a[(uint32_t)buf[j]];
if (s[m->sid[1]] > 0) z[0] += m->w;
else if (s[m->sid[1]] < 0) z[1] += m->w;
}
pg->info.a[i].m[0] = z[0], pg->info.a[i].m[1] = z[1];
}
radix_sort_gfa64(buf, buf + n);
for (j = 0, z[0] = z[1] = 0; j < n; ++j) {
const pt_match1_t *m = &pg->e->ma.a[(uint32_t)buf[j]];
if (s[m->sid[1]] > 0) z[0] += m->w;
else if (s[m->sid[1]] < 0) z[1] += m->w;
}
pg->info.a[i].m[0] = z[0], pg->info.a[i].m[1] = z[1];
}
clean_ovlp(ug, read_g, ovlp, pg, s);