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phasing speedup

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chhylp123
2026-04-11 22:33:18 -04:00
parent 815d709fb9
commit ba8627fb23
13 changed files with 1055 additions and 186 deletions
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Overlaps.cpp
+4 -3
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@@ -13918,9 +13918,9 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
ug = ma_ug_gen(sg);
ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0, 1);
// if(asm_opt.dbg_bam) {
// gen_gfa_bam(ug);
// }
if(asm_opt.dbg_bam) {
gen_gfa_bam(ug, R_INF.total_reads);
}
fprintf(stderr, "Writing raw unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
@@ -40260,6 +40260,7 @@ long long bubble_dist, int read_graph, int write)
for (j = 0; j < reverse_sources[i].length; j++) reverse_sources[i].buffer[j].del = 0;
}
if(asm_opt.is_ont) cmk = gen_chemical_arc_rf(asm_opt.thread_num, R_INF.total_reads);
if(asm_opt.del_hf) clean_arc_rf(asm_opt.thread_num, R_INF.total_reads);
}
try_rescue_overlaps(sources, reverse_sources, n_read, 4, asm_opt.is_ont);