From 1e4d67ee645619bd0bff7f34a988acc8c4567191 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 19 Jul 2020 13:43:30 -0400 Subject: [PATCH] r288: reorganized command line help messages --- CommandLines.cpp | 78 +++++++++++++++++++++++------------------------- CommandLines.h | 2 +- 2 files changed, 38 insertions(+), 42 deletions(-) diff --git a/CommandLines.cpp b/CommandLines.cpp index 302e8ea..ae8f5bd 100644 --- a/CommandLines.cpp +++ b/CommandLines.cpp @@ -21,8 +21,8 @@ static ko_longopt_t long_options[] = { { "max-od-final", ko_no_argument, 306 }, { "ex-list", ko_required_argument, 307 }, { "ex-iter", ko_required_argument, 308 }, - { "purge-cov", ko_required_argument, 309 }, - { "pri-range", ko_required_argument, 310 }, + { "purge-cov", ko_required_argument, 309 }, + { "pri-range", ko_required_argument, 310 }, { 0, 0, 0 } }; @@ -37,50 +37,46 @@ void Print_H(hifiasm_opt_t* asm_opt) { fprintf(stderr, "Usage: hifiasm [options] <...>\n"); fprintf(stderr, "Options:\n"); + fprintf(stderr, " Input/Output:\n"); + fprintf(stderr, " -o STR prefix of output files [%s]\n", asm_opt->output_file_name); + fprintf(stderr, " -i ignore saved read correction and overlaps\n"); + fprintf(stderr, " -t INT number of threads [%d]\n", asm_opt->thread_num); + fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen); + fprintf(stderr, " --version show version number\n"); + fprintf(stderr, " Overlap/Error correction:\n"); + fprintf(stderr, " -k INT k-mer length (must be <64) [%d]\n", asm_opt->k_mer_length); + fprintf(stderr, " -w INT minimizer window size [%d]\n", asm_opt->mz_win); + fprintf(stderr, " -f INT number of bits for bloom filter; 0 to disable [%d]\n", asm_opt->bf_shift); + fprintf(stderr, " -D FLOAT drop k-mers occurring >FLOAT*coverage times [%.1f]\n", asm_opt->high_factor); + fprintf(stderr, " -N INT consider up to max(-D*coverage,-N) overlaps for each oriented read [%d]\n", asm_opt->max_n_chain); + fprintf(stderr, " -r INT round of correction [%d]\n", asm_opt->number_of_round); fprintf(stderr, " Assembly:\n"); - fprintf(stderr, " -o FILE prefix of output files [%s]\n", asm_opt->output_file_name); - fprintf(stderr, " -t INT number of threads [%d]\n", asm_opt->thread_num); - fprintf(stderr, " -r INT round of correction [%d]\n", asm_opt->number_of_round); - fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round); - fprintf(stderr, " -k INT k-mer length (must be <64) [%d]\n", asm_opt->k_mer_length); - fprintf(stderr, " -w INT minimizer window size [%d]\n", asm_opt->mz_win); - fprintf(stderr, " -f INT number of bits for bloom filter; 0 to disable [%d]\n", asm_opt->bf_shift); - fprintf(stderr, " -D FLOAT drop k-mers occuring >FLOAT*coverage times [%.1f]\n", asm_opt->high_factor); - fprintf(stderr, " -N INT consider up to max(-D*coverage,-N) overlaps for each oriented read [%d]\n", asm_opt->max_n_chain); - fprintf(stderr, " -i ignore saved overlaps in *.ovlp* files\n"); - fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen); - fprintf(stderr, " -m INT size of popped large bubbles for contig graph [%lld]\n", asm_opt->large_pop_bubble_size); - fprintf(stderr, " -p INT size of popped small bubbles for haplotype-resolved unitig graph [%lld]\n", asm_opt->small_pop_bubble_size); - fprintf(stderr, " -n INT small removed unitig threshold [%d]\n", asm_opt->max_short_tip); - 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, " --pri-range INT1[,INT2]\n\ - keep contigs with coverage in this range at p_ctg.gfa. Inferred automatically in default\n\ - If INT2 is not specified, it is set to infinity. Set -1 to disable\n"); - - - fprintf(stderr, " -u disable post join contigs step which may improve N50. Don't disable in default.\n"); - fprintf(stderr, " --version show version number\n"); - fprintf(stderr, " -h show help information\n"); + fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round); + fprintf(stderr, " -m INT pop bubbles of large_pop_bubble_size); + fprintf(stderr, " -p INT pop bubbles of small_pop_bubble_size); + fprintf(stderr, " -n INT remove tip unitigs composed of <=INT reads [%d]\n", asm_opt->max_short_tip); + 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, " --pri-range INT1[,INT2]\n"); +// fprintf(stderr, " keep contigs with coverage in this range in p_ctg.gfa; -1 to disable [auto,inf]\n"); fprintf(stderr, " Trio-partition:\n"); - fprintf(stderr, " -1 FILE hap1/paternal k-mer dump generated by \"yak count\" []\n"); - fprintf(stderr, " -2 FILE hap2/maternal k-mer dump generated by \"yak count\" []\n"); - fprintf(stderr, " -3 FILE list of hap1/paternal read names []\n"); - fprintf(stderr, " -4 FILE list of hap2/maternal read names []\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); + fprintf(stderr, " -1 FILE hap1/paternal k-mer dump generated by \"yak count\" []\n"); + fprintf(stderr, " -2 FILE hap2/maternal k-mer dump generated by \"yak count\" []\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); + fprintf(stderr, " -3 FILE list of hap1/paternal read names []\n"); + fprintf(stderr, " -4 FILE list of hap2/maternal read names []\n"); fprintf(stderr, " Purge-dups:\n"); - fprintf(stderr, " -l INT level of purge-dup. In default, [%d] for non-trio; [%d] for trio (see hifiasm.1 for details)\n", - asm_opt->purge_level_primary, asm_opt->purge_level_trio); - fprintf(stderr, " -s FLOAT similarity threshold for duplicate haplotigs [%g]\n", - asm_opt->purge_simi_rate); - fprintf(stderr, " -O INT min number of overlapped reads for duplicate haplotigs [%d]\n", - asm_opt->purge_overlap_len); - fprintf(stderr, " --purge-cov INT\n\ - coverage upper bound of Purge-dups, which is inferred automatically in default.\n"); - + fprintf(stderr, " -l INT purge level. 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip]\n"); + fprintf(stderr, " -s FLOAT similarity threshold for duplicate haplotigs [%g]\n", + asm_opt->purge_simi_rate); + fprintf(stderr, " -O INT min number of overlapped reads for duplicate haplotigs [%d]\n", + asm_opt->purge_overlap_len); + fprintf(stderr, " --purge-cov INT\n"); + fprintf(stderr, " coverage upper bound of Purge-dups [auto]\n"); fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n"); fprintf(stderr, "See `man ./hifiasm.1' for detailed description of these command-line options.\n"); diff --git a/CommandLines.h b/CommandLines.h index 6740089..e34511e 100644 --- a/CommandLines.h +++ b/CommandLines.h @@ -3,7 +3,7 @@ #include -#define HA_VERSION "0.9-r287-dirty" +#define HA_VERSION "0.9-r288-dirty" #define VERBOSE 0