diff --git a/CommandLines.cpp b/CommandLines.cpp index a1d705a..90f605a 100644 --- a/CommandLines.cpp +++ b/CommandLines.cpp @@ -24,7 +24,7 @@ static ko_longopt_t long_options[] = { { "purge-cov", ko_required_argument, 309 }, { "pri-range", ko_required_argument, 310 }, { "high-het", ko_no_argument, 311 }, - { "pb-range", ko_required_argument, 312 }, + { "lowQ", ko_required_argument, 312 }, { 0, 0, 0 } }; @@ -60,7 +60,7 @@ void Print_H(hifiasm_opt_t* asm_opt) fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate); fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate); fprintf(stderr, " -u disable post join contigs step which may improve N50\n"); - fprintf(stderr, " --pb-range INT\n"); + fprintf(stderr, " --lowQ INT\n"); fprintf(stderr, " output contig regions with >=INT%% inconsistency in BED format; 0 to disable [%d]\n", asm_opt->bed_inconsist_rate); // fprintf(stderr, " --pri-range INT1[,INT2]\n"); // fprintf(stderr, " keep contigs with coverage in this range in p_ctg.gfa; -1 to disable [auto,inf]\n"); @@ -133,7 +133,7 @@ void init_opt(hifiasm_opt_t* asm_opt) asm_opt->recover_atg_cov_min = -1024; asm_opt->recover_atg_cov_max = INT_MAX; asm_opt->hom_global_coverage = -1; - asm_opt->bed_inconsist_rate = 0; + asm_opt->bed_inconsist_rate = 70; } void destory_opt(hifiasm_opt_t* asm_opt) diff --git a/CommandLines.h b/CommandLines.h index 7939a87..b130949 100644 --- a/CommandLines.h +++ b/CommandLines.h @@ -3,7 +3,7 @@ #include -#define HA_VERSION "0.13-r307" +#define HA_VERSION "0.13-r308" #define VERBOSE 0 diff --git a/Overlaps.cpp b/Overlaps.cpp index 1f09c6b..f86ac7c 100644 --- a/Overlaps.cpp +++ b/Overlaps.cpp @@ -27472,6 +27472,8 @@ ma_sub_t **coverage_cut_ptr, int debug_g) *coverage_cut_ptr = coverage_cut; *sg_ptr = sg; + + fprintf(stderr, "Inconsistency threshold for low-quality regions in BED files: %u%%\n", asm_opt.bed_inconsist_rate); } void build_string_graph_without_clean( diff --git a/hifiasm.1 b/hifiasm.1 index 0459286..e30c661 100644 --- a/hifiasm.1 +++ b/hifiasm.1 @@ -201,11 +201,11 @@ If INT2 is not specified, it is set to infinity. Set -1 to disable. .TP -.BI --pb-range \ INT +.BI --lowQ \ INT Output contig regions with >=INT% inconsistency to the bed file with suffix .B lowQ.bed -[0]. Set 0 to disable. +[70]. Set 0 to disable. .SS Trio-partition options