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fix exit(1) for bin_only

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chhylp123
2023-01-23 15:25:01 -05:00
parent 25d6857d44
commit db2edc0ffb
4 changed files with 146 additions and 77 deletions
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CommandLines.h
+1 -1
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@@ -4,7 +4,7 @@
#include <pthread.h> #include <pthread.h>
#include <stdint.h> #include <stdint.h>
#define HA_VERSION "0.18.5-r499" #define HA_VERSION "0.18.5-r450"
#define VERBOSE 0 #define VERBOSE 0
Overlaps.cpp
+1 -1
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@@ -19082,7 +19082,7 @@ void write_all_data_to_disk(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sou
free(gfa_name); free(gfa_name);
fprintf(stderr, "bin files have been written.\n"); fprintf(stderr, "bin files have been written.\n");
if(asm_opt.bin_only) exit(1); if(asm_opt.bin_only) exit(0);
} }
int load_debug_graph(asg_t** sg, ma_hit_t_alloc** sources, ma_sub_t** coverage_cut, int load_debug_graph(asg_t** sg, ma_hit_t_alloc** sources, ma_sub_t** coverage_cut,
horder.cpp
+143 -74
View File
@@ -463,12 +463,9 @@ void idx_hits(kvec_pe_hit* hits, uint64_t n)
memset(hits->idx.a, 0, hits->idx.n*sizeof(uint64_t)); memset(hits->idx.a, 0, hits->idx.n*sizeof(uint64_t));
radix_sort_pe_hit_idx_hn1(hits->a.a, hits->a.a + hits->a.n); radix_sort_pe_hit_idx_hn1(hits->a.a, hits->a.a + hits->a.n);
for (k = 1, l = 0; k <= hits->a.n; ++k) for (k = 1, l = 0; k <= hits->a.n; ++k) {
{ if (k == hits->a.n || (get_hit_suid(*hits, k) != get_hit_suid(*hits, l))) {
if (k == hits->a.n || (get_hit_suid(*hits, k) != get_hit_suid(*hits, l)))
{
if (k - l > 1) radix_sort_pe_hit_idx_hn2(hits->a.a + l, hits->a.a + k); if (k - l > 1) radix_sort_pe_hit_idx_hn2(hits->a.a + l, hits->a.a + k);
hits->idx.a[get_hit_suid(*hits, l)] = (uint64_t)l << 32 | (k - l); hits->idx.a[get_hit_suid(*hits, l)] = (uint64_t)l << 32 | (k - l);
l = k; l = k;
} }
@@ -596,8 +593,7 @@ void get_r_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, asg_t* r_g, ma_ug_t* u
uint64_t k, l, i, r_i, offset, rid, rev, rBeg, rEnd, ubits, p_mode, upos, rpos, update; uint64_t k, l, i, r_i, offset, rid, rev, rBeg, rEnd, ubits, p_mode, upos, rpos, update;
ma_utg_t *u = NULL; ma_utg_t *u = NULL;
memset(r_hits, 0, sizeof(*r_hits)); memset(r_hits, 0, sizeof(*r_hits));
r_hits->uID_bits = uID_bits; r_hits->uID_bits = uID_bits; r_hits->pos_mode = pos_mode;
r_hits->pos_mode = pos_mode;
//reset for reads //reset for reads
for (ubits=1; (uint64_t)(1<<ubits)<(uint64_t)r_g->n_seq; ubits++); for (ubits=1; (uint64_t)(1<<ubits)<(uint64_t)r_g->n_seq; ubits++);
p_mode = ((uint64_t)-1) >> (ubits + 1); p_mode = ((uint64_t)-1) >> (ubits + 1);
@@ -605,30 +601,22 @@ void get_r_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, asg_t* r_g, ma_ug_t* u
kv_malloc(r_hits->a, u_hits->a.n); r_hits->a.n = r_hits->a.m = u_hits->a.n; kv_malloc(r_hits->a, u_hits->a.n); r_hits->a.n = r_hits->a.m = u_hits->a.n;
memcpy(r_hits->a.a, u_hits->a.a, r_hits->a.n*sizeof(pe_hit)); memcpy(r_hits->a.a, u_hits->a.a, r_hits->a.n*sizeof(pe_hit));
radix_sort_pe_hit_idx_hn1(r_hits->a.a, r_hits->a.a + r_hits->a.n); radix_sort_pe_hit_idx_hn1(r_hits->a.a, r_hits->a.a + r_hits->a.n);
for (k = 1, l = 0; k <= r_hits->a.n; ++k) for (k = 1, l = 0; k <= r_hits->a.n; ++k) {
{ if (k == r_hits->a.n || get_hit_suid(*r_hits, k) != get_hit_suid(*r_hits, l)) {//same suid
if (k == r_hits->a.n || get_hit_suid(*r_hits, k) != get_hit_suid(*r_hits, l))//same suid
{
///already sort by spos ///already sort by spos
u = &(ug->u.a[get_hit_suid(*r_hits, l)]); u = &(ug->u.a[get_hit_suid(*r_hits, l)]); update = 0;
update = 0; for (i = offset = 0, r_i = l; i < u->n; i++) {
for (i = offset = 0, r_i = l; i < u->n; i++)
{
rid = u->a[i]>>33; rid = u->a[i]>>33;
rBeg = offset; rBeg = offset;
rEnd = rBeg + r_g->seq[rid].len - 1; rEnd = rBeg + r_g->seq[rid].len - 1;
for (; r_i < k; r_i++) for (; r_i < k; r_i++) {
{
upos = get_hit_spos(*r_hits, r_i);///pos at unitig upos = get_hit_spos(*r_hits, r_i);///pos at unitig
if(upos > rEnd) break; if(upos > rEnd) break;
if(upos >= rBeg && upos <= rEnd) if(upos >= rBeg && upos <= rEnd) {
{ if(bub) {
if(bub)
{
r_hits->a.a[r_i].id = (uint32_t)r_hits->a.a[r_i].id; r_hits->a.a[r_i].id = (uint32_t)r_hits->a.a[r_i].id;
if(!IF_HOM(get_hit_suid(*r_hits, r_i), *bub)) if(!IF_HOM(get_hit_suid(*r_hits, r_i), *bub)) {
{
r_hits->a.a[r_i].id += ((uint64_t)(1)<<32); r_hits->a.a[r_i].id += ((uint64_t)(1)<<32);
} }
} }
@@ -642,38 +630,30 @@ void get_r_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, asg_t* r_g, ma_ug_t* u
} }
offset += (uint32_t)u->a[i]; offset += (uint32_t)u->a[i];
} }
assert((r_i == k) && (update == (k-l)));
if(r_i != k || update != k - l) fprintf(stderr, "ERROR-r_i\n"); // if(r_i != k || update != k - l) fprintf(stderr, "ERROR-r_i\n");
l = k; l = k;
} }
} }
radix_sort_pe_hit_idx_hn2(r_hits->a.a, r_hits->a.a + r_hits->a.n); radix_sort_pe_hit_idx_hn2(r_hits->a.a, r_hits->a.a + r_hits->a.n);
for (k = 1, l = 0; k <= r_hits->a.n; ++k) for (k = 1, l = 0; k <= r_hits->a.n; ++k) {
{ if (k == r_hits->a.n || get_hit_euid(*r_hits, k) != get_hit_euid(*r_hits, l)) {//same euid
if (k == r_hits->a.n || get_hit_euid(*r_hits, k) != get_hit_euid(*r_hits, l))//same euid
{
///already sort by epos ///already sort by epos
u = &(ug->u.a[get_hit_euid(*r_hits, l)]); u = &(ug->u.a[get_hit_euid(*r_hits, l)]); update = 0;
update = 0; for (i = offset = 0, r_i = l; i < u->n; i++) {
for (i = offset = 0, r_i = l; i < u->n; i++)
{
rid = u->a[i]>>33; rid = u->a[i]>>33;
rBeg = offset; rBeg = offset;
rEnd = rBeg + r_g->seq[rid].len - 1; rEnd = rBeg + r_g->seq[rid].len - 1;
for (; r_i < k; r_i++) for (; r_i < k; r_i++) {
{
upos = get_hit_epos(*r_hits, r_i);///pos at unitig upos = get_hit_epos(*r_hits, r_i);///pos at unitig
if(upos > rEnd) break; if(upos > rEnd) break;
if(upos >= rBeg && upos <= rEnd) if(upos >= rBeg && upos <= rEnd) {
{ if(bub) {
if(bub)
{
r_hits->a.a[r_i].id >>= 32; r_hits->a.a[r_i].id >>= 32;
r_hits->a.a[r_i].id <<= 32; r_hits->a.a[r_i].id <<= 32;
if(!IF_HOM(get_hit_euid(*r_hits, r_i), *bub)) if(!IF_HOM(get_hit_euid(*r_hits, r_i), *bub)) {
{
r_hits->a.a[r_i].id += 1; r_hits->a.a[r_i].id += 1;
} }
} }
@@ -687,8 +667,8 @@ void get_r_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, asg_t* r_g, ma_ug_t* u
} }
offset += (uint32_t)u->a[i]; offset += (uint32_t)u->a[i];
} }
assert((r_i == k) && (update == (k - l)));
if(r_i != k || update != k - l) fprintf(stderr, "ERROR-r_i\n"); // if(r_i != k || update != k - l) fprintf(stderr, "ERROR-r_i\n");
l = k; l = k;
} }
} }
@@ -822,34 +802,22 @@ static inline void asg_arc_unique_del(asg_t *g, uint32_t v, uint32_t w, int del)
} }
void horder_clean_sg_by_utg(asg_t *sg, ma_ug_t *ug) void horder_clean_sg_by_utg(asg_t *sg, ma_ug_t *ug)
{ {
uint32_t i, v, n_vx, w, k, m, nv, vx, wx; uint32_t i, v, w, k, nv, vx, wx;
asg_arc_t *av = NULL; asg_arc_t *av = NULL;
ma_utg_t *u = NULL; ma_utg_t *u = NULL;
n_vx = sg->n_seq<<1; for (i = 0; i < sg->n_arc; i++) sg->arc[i].del = (!!1);
for (v = 0; v < n_vx; v++) for (i = 0; i < sg->n_seq; i++) sg->seq[i].del = (!!1);
{
nv = asg_arc_n(sg, v);
av = asg_arc_a(sg, v);
for (m = 0; m < nv; m++) av[m].del = (!!1);
sg->seq[v>>1].del = (!!1);
}
for (i = 0; i < ug->g->n_seq; ++i) for (i = 0; i < ug->g->n_seq; ++i) {
{
if(ug->g->seq[i].del) continue; if(ug->g->seq[i].del) continue;
u = &(ug->u.a[i]); u = &(ug->u.a[i]);
for (k = 0; (k + 1) < u->n; k++) for (k = 0; (k + 1) < u->n; k++) {
{
v = u->a[k]>>32; w = u->a[k+1]>>32; v = u->a[k]>>32; w = u->a[k+1]>>32;
asg_arc_unique_del(sg, v, w, 0); asg_arc_unique_del(sg, v, w, 0);
asg_arc_unique_del(sg, w^1, v^1, 0); asg_arc_unique_del(sg, w^1, v^1, 0);
} }
for (k = 0; k < u->n; k++) for (k = 0; k < u->n; k++) sg->seq[u->a[k]>>33].del = (!!0);
{
sg->seq[u->a[k]>>33].del = (!!0);
}
v = i<<1; v = i<<1;
nv = asg_arc_n(ug->g, v); av = asg_arc_a(ug->g, v); nv = asg_arc_n(ug->g, v); av = asg_arc_a(ug->g, v);
@@ -2544,8 +2512,7 @@ dens_idx_t *build_interval_idx(kvec_pe_hit *hits, ma_ug_t *ug)
dens_idx_t *idx = NULL; dens_idx_t *idx = NULL;
CALLOC(idx, 1); CALLOC(idx, 1);
for (i = 0; i < hits->a.n; i++) for (i = 0; i < hits->a.n; i++) {
{
if(!hits->a.a[i].id) continue; if(!hits->a.a[i].id) continue;
suid = get_hit_suid(*hits, i); suid = get_hit_suid(*hits, i);
euid = get_hit_euid(*hits, i); euid = get_hit_euid(*hits, i);
@@ -2574,10 +2541,8 @@ dens_idx_t *build_interval_idx(kvec_pe_hit *hits, ma_ug_t *ug)
radix_sort_ho64(idx->pos.a, idx->pos.a + idx->pos.n); radix_sort_ho64(idx->pos.a, idx->pos.a + idx->pos.n);
idx->n = idx->m = ug->u.n; idx->n = idx->m = ug->u.n;
CALLOC(idx->a, idx->n); CALLOC(idx->a, idx->n);
for (k = 1, l = 0; k <= idx->pos.n; ++k) for (k = 1, l = 0; k <= idx->pos.n; ++k) {
{ if (k == idx->pos.n || ((idx->pos.a[k]>>32) != (idx->pos.a[l]>>32))) {
if (k == idx->pos.n || ((idx->pos.a[k]>>32) != (idx->pos.a[l]>>32)))
{
idx->a[idx->pos.a[l]>>32] = (uint64_t)l << 32 | (k - l); idx->a[idx->pos.a[l]>>32] = (uint64_t)l << 32 | (k - l);
l = k; l = k;
} }
@@ -2801,8 +2766,7 @@ void update_scg(horder_t *h, trans_col_t *t_idx)
osg_arc_t *p = NULL; osg_arc_t *p = NULL;
osg_destroy(h->sg.g); osg_destroy(h->sg.g);
h->sg.g = osg_init(); h->sg.g = osg_init();
for (i = 0; i < ug->u.n; i++) for (i = 0; i < ug->u.n; i++) {
{
osg_seq_set(h->sg.g, i, 0); osg_seq_set(h->sg.g, i, 0);
h->sg.g->seq[i].mw[0] = h->sg.g->seq[i].mw[1] = 0; h->sg.g->seq[i].mw[0] = h->sg.g->seq[i].mw[1] = 0;
h->sg.g->seq[i].ez[0] = ug->u.a[i].len>>1; h->sg.g->seq[i].ez[0] = ug->u.a[i].len>>1;
@@ -2810,8 +2774,7 @@ void update_scg(horder_t *h, trans_col_t *t_idx)
} }
idx = build_interval_idx(hits, ug);///idx is used to get density idx = build_interval_idx(hits, ug);///idx is used to get density
for (i = 0, e.n = 0; i < hits->a.n; i++) for (i = 0, e.n = 0; i < hits->a.n; i++) {
{
if(!hits->a.a[i].id) continue;//hom hits if(!hits->a.a[i].id) continue;//hom hits
suid = get_hit_suid(*hits, i); suid = get_hit_suid(*hits, i);
euid = get_hit_euid(*hits, i); euid = get_hit_euid(*hits, i);
@@ -2848,8 +2811,7 @@ void update_scg(horder_t *h, trans_col_t *t_idx)
ep->e = (v<<32)|w; ep->e = (v<<32)|w;
ep->d = (sd<<32)|ed; ep->d = (sd<<32)|ed;
if(v > w) if(v > w) {
{
ep->e = (w<<32)|v; ep->e = (w<<32)|v;
ep->d = (ed<<32)|sd; ep->d = (ed<<32)|sd;
} }
@@ -2926,6 +2888,7 @@ void update_scg(horder_t *h, trans_col_t *t_idx)
} }
if(bestAlt == 0) bestAlt = 1; if(bestAlt == 0) bestAlt = 1;
///if there is just one edges between p->u and p->v, then bestAlt -> p->nw <= 1; this is wrong
p->nw = p->w/bestAlt; p->nw = p->w/bestAlt;
if(p->nw > 1) eg_edges++; if(p->nw > 1) eg_edges++;
} }
@@ -3015,6 +2978,8 @@ void get_backbone_layout(horder_t *h, sc_lay_t *sl, osg_t *lg, uint8_t *vis)
memset(vis, 0, sizeof(uint8_t)*(lg->n_seq<<1)); memset(vis, 0, sizeof(uint8_t)*(lg->n_seq<<1));
for (k = 0; k < lg->n_seq; k++) for (k = 0; k < lg->n_seq; k++)
{ {
///I guess this should be (!!(asg_arc_n(lg, k<<1)))^(!!(asg_arc_n(lg, (k<<1)+1)))?
///no, since asg_arc_n is at most 1
if((asg_arc_n(lg, k<<1))^(asg_arc_n(lg, (k<<1)+1))) if((asg_arc_n(lg, k<<1))^(asg_arc_n(lg, (k<<1)+1)))
{ {
v = (asg_arc_n(lg, k<<1)?(k<<1):((k<<1)+1)); v = (asg_arc_n(lg, k<<1)?(k<<1):((k<<1)+1));
@@ -4089,7 +4054,111 @@ asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, ug_opt_t *opt)
sc_lay_t sl; kv_init(sl); sc_lay_t sl; kv_init(sl);
get_r_hits(i_hits, &(h->r_hits), i_rg, i_ug, bub, i_hits_uid_bits, i_hits_pos_mode); get_r_hits(i_hits, &(h->r_hits), i_rg, i_ug, bub, i_hits_uid_bits, i_hits_pos_mode);
h->r_g = copy_read_graph(i_rg); h->r_g = copy_read_graph(i_rg);
horder_clean_sg_by_utg(h->r_g, i_ug); horder_clean_sg_by_utg(h->r_g, i_ug);///udate rg by ug
h->ug = copy_untig_graph(i_ug); asg_destroy(h->ug->g); h->ug->g = NULL;
cpy_u_hits(&(h->u_hits), i_hits, h->ug->u.n);
update_scg(h, NULL);
layout_scg(h, ((double)1)/((double)0.75), 19, &sl);
renew_scaffold_utg(h, &sl, i_ug);
spg_t *scg = scf_g(&sl, i_ug);
destory_sc_lay_t(&sl);
destory_horder_t(&h);
return scg;
}
void gen_r_hits(kvec_pe_hit *u_hits, kvec_pe_hit *r_hits, asg_t* r_g, ma_ug_t* ug, bubble_type* bub, uint64_t uID_bits, uint64_t pos_mode)
{
uint64_t k, l, i, m, r_i, offset, rid, rev, rBeg, rEnd, ubits, p_mode, upos, rpos, update;
ma_utg_t *u = NULL;
memset(r_hits, 0, sizeof(*r_hits));
r_hits->uID_bits = uID_bits; r_hits->pos_mode = pos_mode;
//reset for reads
for (ubits=1; (uint64_t)(1<<ubits)<(uint64_t)r_g->n_seq; ubits++);
p_mode = ((uint64_t)-1) >> (ubits + 1);
kv_malloc(r_hits->a, u_hits->a.n); r_hits->a.n = r_hits->a.m = u_hits->a.n;
memcpy(r_hits->a.a, u_hits->a.a, r_hits->a.n*sizeof(pe_hit));
radix_sort_pe_hit_idx_hn1(r_hits->a.a, r_hits->a.a + r_hits->a.n);
for (k = 1, l = m = 0; k <= r_hits->a.n; ++k) {
if (k == r_hits->a.n || get_hit_suid(*r_hits, k) != get_hit_suid(*r_hits, l)) {//same suid
///already sort by spos
if((!bub) || ((!IF_HOM(get_hit_suid(*r_hits, l), *bub)))) {
u = &(ug->u.a[get_hit_suid(*r_hits, l)]); update = 0;
for (i = offset = 0, r_i = l; i < u->n; i++) {
rid = u->a[i]>>33;
rBeg = offset;
rEnd = rBeg + r_g->seq[rid].len - 1;
for (; r_i < k; r_i++) {
upos = get_hit_spos(*r_hits, r_i);///pos at unitig
if(upos > rEnd) break;
if(upos >= rBeg && upos <= rEnd) {
rpos = (((u->a[i]>>32)&1)? rEnd - upos : upos - rBeg);///pos at read
rev = ((u->a[i]>>32)&1) ^ (r_hits->a.a[r_i].s>>63);
r_hits->a.a[r_i].s = (rev<<63) | ((rid << (64-ubits))>>1) | (rpos & p_mode);
r_hits->a.a[r_i].id = 1; r_hits->a.a[m++] = r_hits->a.a[r_i];
update++;
}
}
offset += (uint32_t)u->a[i];
}
assert((r_i == k) && (update == (k-l)));
}
// if(r_i != k || update != k - l) fprintf(stderr, "ERROR-r_i\n");
l = k;
}
}
r_hits->a.n = m;
radix_sort_pe_hit_idx_hn2(r_hits->a.a, r_hits->a.a + r_hits->a.n);
for (k = 1, l = m = 0; k <= r_hits->a.n; ++k) {
if (k == r_hits->a.n || get_hit_euid(*r_hits, k) != get_hit_euid(*r_hits, l)) {//same euid
///already sort by epos
if((!bub) || ((!IF_HOM(get_hit_euid(*r_hits, l), *bub)))) {
u = &(ug->u.a[get_hit_euid(*r_hits, l)]); update = 0;
for (i = offset = 0, r_i = l; i < u->n; i++) {
rid = u->a[i]>>33;
rBeg = offset;
rEnd = rBeg + r_g->seq[rid].len - 1;
for (; r_i < k; r_i++) {
upos = get_hit_epos(*r_hits, r_i);///pos at unitig
if(upos > rEnd) break;
if(upos >= rBeg && upos <= rEnd) {
rpos = (((u->a[i]>>32)&1)? rEnd - upos : upos - rBeg);///pos at read
rev = ((u->a[i]>>32)&1) ^ (r_hits->a.a[r_i].e>>63);
r_hits->a.a[r_i].e = (rev<<63) | ((rid << (64-ubits))>>1) | (rpos & p_mode);
r_hits->a.a[r_i].id = 1; r_hits->a.a[m++] = r_hits->a.a[r_i];
update++;
}
}
offset += (uint32_t)u->a[i];
}
assert((r_i == k) && (update == (k - l)));
}
// if(r_i != k || update != k - l) fprintf(stderr, "ERROR-r_i\n");
l = k;
}
}
r_hits->a.n = m;
r_hits->uID_bits = ubits;
r_hits->pos_mode = p_mode;
idx_hits(r_hits, r_g->n_seq);
}
spg_t *horder_sensitive_utg(kvec_pe_hit *i_hits, uint64_t i_hits_uid_bits, uint64_t i_hits_pos_mode,
asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, ug_opt_t *opt)
{
horder_t *h = NULL; CALLOC(h, 1);
sc_lay_t sl; kv_init(sl);
gen_r_hits(i_hits, &(h->r_hits), i_rg, i_ug, bub, i_hits_uid_bits, i_hits_pos_mode);
h->r_g = copy_read_graph(i_rg);
horder_clean_sg_by_utg(h->r_g, i_ug);///udate rg by ug
h->ug = copy_untig_graph(i_ug); asg_destroy(h->ug->g); h->ug->g = NULL; h->ug = copy_untig_graph(i_ug); asg_destroy(h->ug->g); h->ug->g = NULL;
cpy_u_hits(&(h->u_hits), i_hits, h->ug->u.n); cpy_u_hits(&(h->u_hits), i_hits, h->ug->u.n);
inter.cpp
+1 -1
View File
@@ -15700,7 +15700,7 @@ int32_t write_all_ul_t(all_ul_t *x, char* file_name, ma_ug_t *ug)
fprintf(stderr, "[M::%s] Index has been written.\n", __func__); fprintf(stderr, "[M::%s] Index has been written.\n", __func__);
fclose(fp); fclose(fp);
if(asm_opt.bin_only) exit(1); if(asm_opt.bin_only) exit(0);
return 1; return 1;
} }