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print misjoin debug

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chhylp123
2021-06-23 09:49:44 -04:00
parent 5a400af39d
commit 0410662841
3 changed files with 46 additions and 5 deletions
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2
CommandLines.h
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@@ -4,7 +4,7 @@
#include <pthread.h>
#include <stdint.h>
#define HA_VERSION "0.15.4-r342"
#define HA_VERSION "0.15.4-r343"
#define VERBOSE 0

7
hic.cpp
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@@ -16107,8 +16107,11 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
sl.hits.uID_bits = idx->uID_bits; sl.hits.pos_mode = idx->pos_mode;
update_switch_unitig(idx->ug, idx->read_g, &(sl.hits), &(idx->t_ch->k_trans), 10, 20, asm_opt.misjoin_len, 0.15);
renew_idx_para(idx, idx->ug);
if(asm_opt.misjoin_len > 0)
{
update_switch_unitig(idx->ug, idx->read_g, &(sl.hits), &(idx->t_ch->k_trans), 10, 20, asm_opt.misjoin_len, 0.15);
renew_idx_para(idx, idx->ug);
}
// print_hits_simp(idx, &sl.hits);
// print_kv_u_trans_t(&(idx->t_ch->k_trans));

42
horder.cpp
View File

@@ -1773,6 +1773,40 @@ int get_new_offset(kvec_pe_hit *hits, uint64_t id, uint64_t *index, h_covs *join
return 1;
}
void verbose_misjoin(uint64_t *a, uint64_t a_n)
{
radix_sort_ho64(a, a + a_n);
uint64_t k, l, i, len, s, C[2], N[2];
C[0] = C[1] = N[0] = N[1] = 0;
for (k = 1, l = 0; k <= a_n; ++k)
{
if (k == a_n || (a[k]>>63) != (a[l]>>63))
{
for (i = l, s = 0; i < k; i++) s += ((a[i]<<1)>>1);
len = s;
i = k; s = 0;
while (i > l)
{
i--;
s += ((a[i]<<1)>>1);
if(s >= (len>>1))
{
N[a[l]>>63] = ((a[i]<<1)>>1);
C[a[l]>>63] = k - l;
// fprintf(stderr, "[M::%s::] N50: %lu\n", __func__, b.a[i]);
break;
}
}
l = k;
}
}
fprintf(stderr, "[M::stat] # misjoined unitigs: %lu (N50: %lu); # corrected unitigs: %lu (N50: %lu)\n",
C[0], N[0], C[1], N[1]);
}
void break_phasing_utg(ma_ug_t *ug, asg_t *rg, kvec_pe_hit *hits, kv_u_trans_t *k_trans, h_covs *b_points)
{
if(b_points->n == 0) return;
@@ -1783,6 +1817,7 @@ void break_phasing_utg(ma_ug_t *ug, asg_t *rg, kvec_pe_hit *hits, kv_u_trans_t *
h_covs join; kv_init(join);
uint64_t k, l, i, idx, m, pidx, de_u, u_n, oug_n = ug->u.n, dug_n = 0, puid, pn, rsi, prid, nrid, x, y, *index = NULL;
kv_u_trans_t *n_trans = NULL; CALLOC(n_trans, 1);
kvec_t(uint64_t) dbg_N50; kv_init(dbg_N50);
/*******************************for debug************************************/
// debug_phasing_t *dbp = init_debug_phasing(ug, hits, k_trans, b_points);
/*******************************for debug************************************/
@@ -1806,6 +1841,7 @@ void break_phasing_utg(ma_ug_t *ug, asg_t *rg, kvec_pe_hit *hits, kv_u_trans_t *
kv_pushp(h_cov_t, join, &p);
p->dp = (b_points->a[l].s<<32)|(ug->u.n-1);
p->s = rsi; p->e = ug->u.a[ug->u.n-1].len;
kv_push(uint64_t, dbg_N50, (uint64_t)(ug->u.a[ug->u.n-1].len)+((uint64_t)(1)<<63));
}
}
pidx = idx;
@@ -1821,11 +1857,13 @@ void break_phasing_utg(ma_ug_t *ug, asg_t *rg, kvec_pe_hit *hits, kv_u_trans_t *
kv_pushp(h_cov_t, join, &p);
p->dp = (b_points->a[l].s<<32)|(ug->u.n-1);
p->s = rsi; p->e = ug->u.a[ug->u.n-1].len;
kv_push(uint64_t, dbg_N50, (uint64_t)(ug->u.a[ug->u.n-1].len)+((uint64_t)(1)<<63));
}
}
if(de_u)
{
kv_push(uint64_t, dbg_N50, ug->u.a[b_points->a[l].s].len);
update_nus(&(ug->u.a[b_points->a[l].s]), ug, join.a + pn, join.n - pn);
free(ug->u.a[b_points->a[l].s].a); free(ug->u.a[b_points->a[l].s].s);
memset(&(ug->u.a[b_points->a[l].s]), 0, sizeof(ug->u.a[b_points->a[l].s]));
@@ -1949,8 +1987,8 @@ void break_phasing_utg(ma_ug_t *ug, asg_t *rg, kvec_pe_hit *hits, kv_u_trans_t *
// debug_debug_phasing_t(dbp, ug, hits, k_trans, &join, index);
// destory_debug_phasing_t(&dbp);
/*******************************for debug************************************/
kv_destroy(join); kv_destroy(kv); free(index);
verbose_misjoin(dbg_N50.a, dbg_N50.n);
kv_destroy(join); kv_destroy(kv); free(index); kv_destroy(dbg_N50);
}
///min_ulen = BREAK_THRES