diff --git a/CommandLines.cpp b/CommandLines.cpp index e4e080b..8734c47 100644 --- a/CommandLines.cpp +++ b/CommandLines.cpp @@ -45,7 +45,7 @@ void Print_H(hifiasm_opt_t* asm_opt) fprintf(stderr, " Trio-partition:\n"); fprintf(stderr, " -P FILE paternal trio index generated by \"yak count\" [NULL]\n"); - fprintf(stderr, " -M FILE Maternal trio index generated by \"yak count\" [NULL]\n"); + fprintf(stderr, " -M FILE maternal trio index generated by \"yak count\" [NULL]\n"); fprintf(stderr, " -c INT lower bound of the binned k-mer's frequency [%d]\n", asm_opt->min_cnt); fprintf(stderr, " -d INT upper bound of the binned k-mer's frequency [%d]\n", asm_opt->mid_cnt); @@ -253,6 +253,11 @@ int check_option(hifiasm_opt_t* asm_opt) // fprintf(stderr, "size of popped small bubbles: %lld\n", asm_opt->small_pop_bubble_size); // fprintf(stderr, "size of popped large bubbles: %lld\n", asm_opt->large_pop_bubble_size); // fprintf(stderr, "small removed unitig threshold: %d\n", asm_opt->max_short_tip); + // fprintf(stderr, "small removed unitig threshold: %d\n", asm_opt->max_short_tip); + // fprintf(stderr, "pat_index: %s\n", asm_opt->pat_index); + // fprintf(stderr, "mat_index: %s\n", asm_opt->mat_index); + // fprintf(stderr, "min_cnt: %d\n", asm_opt->min_cnt); + // fprintf(stderr, "mid_cnt: %d\n", asm_opt->mid_cnt); return 1; } diff --git a/Overlaps.cpp b/Overlaps.cpp index 71d9d57..c2deb22 100644 --- a/Overlaps.cpp +++ b/Overlaps.cpp @@ -25060,11 +25060,14 @@ ma_sub_t* coverage_cut, int debug_g) asg_arc_del_simple_circle_untig(sources, coverage_cut, sg, 100, 0); - - /*******************************for debug***************************************/ - write_debug_graph(sg, sources, coverage_cut, output_file_name, n_read, reverse_sources, ruIndex); - debug_gfa:; - /*******************************for debug***************************************/ + if(VERBOSE_GFA >= 1) + { + /*******************************for debug***************************************/ + write_debug_graph(sg, sources, coverage_cut, output_file_name, n_read, reverse_sources, ruIndex); + debug_gfa:; + /*******************************for debug***************************************/ + } + /** debug_ma_hit_t(sources, coverage_cut, n_read, max_hang_length, mini_overlap_length); @@ -25137,20 +25140,23 @@ long long bubble_dist, int read_graph, int write) ///actually min_thres = asm_opt.max_short_tip + 1 there are asm_opt.max_short_tip reads min_thres = asm_opt.max_short_tip + 1; - - if(load_debug_graph(&sg, &sources, &coverage_cut, output_file_name, &reverse_sources, &ruIndex)) + if(VERBOSE_GFA >= 1) { - fprintf(stderr, "debug gfa has been loaded\n"); - - clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length, - max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio, - output_file_name, bubble_dist, read_graph, &ruIndex, sg, coverage_cut, 1); - asg_destroy(sg); - free(coverage_cut); - destory_R_to_U(&ruIndex); - return; + if(load_debug_graph(&sg, &sources, &coverage_cut, output_file_name, &reverse_sources, &ruIndex)) + { + fprintf(stderr, "debug gfa has been loaded\n"); + + clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length, + max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio, + output_file_name, bubble_dist, read_graph, &ruIndex, sg, coverage_cut, 1); + asg_destroy(sg); + free(coverage_cut); + destory_R_to_U(&ruIndex); + return; + } } + if (asm_opt.write_index_to_disk && write) {