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Merge pull request #349 from chhylp123/hifiasm_dev_debug

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bugs for bubble/hom assembly
This commit is contained in:
chhylp123
2022-11-17 18:01:50 -05:00
committed by GitHub
parent a1867ec9a2 553a8745cc
commit b4b53b8efd
3 changed files with 18 additions and 2 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 "0.17.3-r452"
#define HA_VERSION "0.17.3-r453"
#define VERBOSE 0

2
README.md
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@@ -150,7 +150,7 @@ Hifiasm could integrate ultra-long ONT reads to improve the assembly quality:
```sh
hifiasm -o NA12878.asm -t32 --ul ul.fq.gz HiFi-reads.fq.gz
```
Please note that this mode is not stable right now.
Please note that this mode is not stable right now. We have only tested with >=100kb UL reads.
### <a name="output"></a>Output files

16
gfa_ut.cpp
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@@ -2598,6 +2598,12 @@ bubble_type *gen_bubble_chain(asg_t *sg, ma_ug_t *ug, ug_opt_t *uopt, uint8_t **
identify_bubbles(ug, bub, (*ir_het), NULL);
kv_destroy(new_rtg_edges.a); destory_hap_cov_t(&cov);
if(asm_opt.purge_level_primary == 0) {///all nodes are het
uint32_t k;
for (k = 0; k < ug->g->n_seq; k++) {
if(IF_HOM(k, *bub)) bub->index[k] = bub->f_bub+1;
}
}
return bub;
}
@@ -12865,6 +12871,11 @@ void renew_usg_t_bub(ul_resolve_t *uidx, usg_t *ng, uint32_t *id_map, uint8_t *f
// fprintf(stderr, "1[M::%s::] f[51]::%u\n", __func__, ff[51]);
free(uidx->bub->index); MALLOC(uidx->bub->index, ng->n);
memcpy(uidx->bub->index, id_map, sizeof((*id_map))*ng->n);
if(asm_opt.purge_level_primary == 0) {///all nodes are het
for (k = 0; k < ug->g->n_seq; k++) {
if(IF_HOM(k, *(uidx->bub))) uidx->bub->index[k] = uidx->bub->f_bub+1;
}
}
ma_ug_destroy(ug);
}
@@ -13635,6 +13646,11 @@ void u2g_hybrid_detan_iter(ul_resolve_t *uidx, usg_t *ng, uint32_t max_ext, uint
// prt_usg_t(uidx, ng, "ng0");
ncut += ug_ext_free(ob, ub, uidx, ng, max_ext, &ff, &ng_occ, &i_idx, &b64, &ub64, 48);
ncut += ug_ext_free(ob, ub, uidx, ng, max_ext, &ff, &ng_occ, &i_idx, &b64, &ub64, 16);
///renew bubble for ug_ext_strict
n_vtx = ng->n<<1;
REALLOC(ff, n_vtx); REALLOC(ng_occ, n_vtx); REALLOC(i_idx, n_vtx);
renew_usg_t_bub(uidx, ng, ng_occ, ff, 0);
}
// // ug_ext_strict(ob, ub, uidx, ng, max_ext, &ff, &ng_occ, &i_idx, &b64, &ub64);
// ncut += ug_ext_free(ob, ub, uidx, ng, max_ext, &ff, &ng_occ, &i_idx, &b64, &ub64, 50);