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Merge branch 'master' into dev-lh3

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This commit is contained in:
Heng Li
2020-04-11 00:08:35 -04:00
parent c710c6ea48 20c6c1d2e6
commit 54fa1a9aed
3 changed files with 17 additions and 31 deletions
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Assembly.cpp
+2 -1
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@@ -1156,7 +1156,8 @@ int ha_assemble(void)
if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name)) { if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name)) {
ovlp_loaded = 1; ovlp_loaded = 1;
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> loaded corrected reads and overlaps from disk\n", __func__, yak_realtime(), yak_cpu_usage()); fprintf(stderr, "[M::%s::%.3f*%.2f] ==> loaded corrected reads and overlaps from disk\n", __func__, yak_realtime(), yak_cpu_usage());
if (!(asm_opt.flag & HA_F_SKIP_TRIOBIN)) ha_triobin(&asm_opt); //if (!(asm_opt.flag & HA_F_SKIP_TRIOBIN)) ha_triobin(&asm_opt);
if (!(asm_opt.flag & HA_F_SKIP_TRIOBIN)&&!(asm_opt.flag&HA_F_VERBOSE_GFA)) ha_triobin(&asm_opt);
if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads(); if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();
if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF(); if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
} }
Overlaps.cpp
+14 -13
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@@ -13467,9 +13467,10 @@ kvec_asg_arc_t_warp* new_rtg_edges)
delete_useless_nodes(ug); delete_useless_nodes(ug);
deduplicate(*ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, 1); // purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
// min_ovlp, bubble_dist, drop_ratio, 1);
delete_useless_nodes(ug); // deduplicate(*ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, 1);
// delete_useless_nodes(ug);
update_unitig_graph((*ug), read_g, reverse_sources, ruIndex, flag, drop_rate); update_unitig_graph((*ug), read_g, reverse_sources, ruIndex, flag, drop_rate);
@@ -13485,17 +13486,17 @@ kvec_asg_arc_t_warp* new_rtg_edges)
renew_utg(ug, read_g, new_rtg_edges); renew_utg(ug, read_g, new_rtg_edges);
update_unitig_graph((*ug), read_g, reverse_sources, ruIndex, flag, drop_rate);
renew_utg(ug, read_g, new_rtg_edges);
delete_useless_nodes(ug);
purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
min_ovlp, bubble_dist, drop_ratio, 1);
delete_useless_nodes(ug);
set_drop_trio_flag(*ug); set_drop_trio_flag(*ug);
n_vtx = read_g->n_seq;
for (v = 0; v < n_vtx; v++)
{
if(read_g->seq[v].c == HAP_LABLE)
{
read_g->seq[v].c = PRIMARY_LABLE;
}
}
/** /**
kv_destroy(new_rtg_nodes.a); kv_destroy(new_rtg_nodes.a);
Purge_Dups.cpp
+1 -17
View File
@@ -3574,7 +3574,7 @@ uint32_t just_contain)
asg_t *purge_g = NULL; asg_t *purge_g = NULL;
purge_g = asg_init(); purge_g = asg_init();
asg_t* nsg = ug->g; asg_t* nsg = ug->g;
uint32_t v, rId, uId, i, k, offset; uint32_t v, rId, uId, i, offset;
ma_utg_t* reads = NULL; ma_utg_t* reads = NULL;
// kvec_t_u64_warp u_vecs; // kvec_t_u64_warp u_vecs;
@@ -3600,22 +3600,6 @@ uint32_t just_contain)
asg_arc_t* p = NULL; asg_arc_t* p = NULL;
int r; int r;
hap_alignment_struct_pip hap_buf; hap_alignment_struct_pip hap_buf;
/****************************may have bugs********************************/
for (v = 0; v < nsg->n_seq; ++v)
{
uId = v;
if(nsg->seq[uId].c != HAP_LABLE) continue;
reads = &(ug->u.a[uId]);
for (k = 0; k < reads->n; k++)
{
rId = reads->a[k]>>33;
read_g->seq[reads->a[k]>>33].c = HAP_LABLE;
}
}
/****************************may have bugs********************************/
for (v = 0; v < nsg->n_seq; v++) for (v = 0; v < nsg->n_seq; v++)
{ {