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r215: prepare for list-based binning

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Heng Li
2020-04-10 00:12:19 -04:00
parent 7a35bd7fcc
commit f32bfc904a
6 changed files with 50 additions and 33 deletions
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4
Assembly.cpp
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@@ -1156,7 +1156,7 @@ 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)) {
ovlp_loaded = 1;
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)) trio_partition();
if (!(asm_opt.flag & HA_F_SKIP_TRIOBIN)) ha_triobin(&asm_opt);
if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();
if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
}
@@ -1187,7 +1187,7 @@ int ha_assemble(void)
ha_print_ovlp_stat(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads);
ha_ft_destroy(ha_flt_tab);
if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
trio_partition();
ha_triobin(&asm_opt);
}
build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,