From 2bf5119bb50d332c76d9d6381189aab137b11bbe Mon Sep 17 00:00:00 2001 From: chhylp123 Date: Thu, 12 Jan 2023 01:22:34 -0500 Subject: [PATCH] update help information --- CommandLines.cpp | 15 ++++++++++----- CommandLines.h | 2 +- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/CommandLines.cpp b/CommandLines.cpp index d709b36..5cebb2f 100644 --- a/CommandLines.cpp +++ b/CommandLines.cpp @@ -51,6 +51,7 @@ static ko_longopt_t long_options[] = { { "dbg-het-cnt", ko_no_argument, 337}, { "ul-tip", ko_required_argument, 338}, { "low-het", ko_no_argument, 339}, + { "s-base", ko_required_argument, 340}, { 0, 0, 0 } }; @@ -120,7 +121,7 @@ void Print_H(hifiasm_opt_t* asm_opt) fprintf(stderr, " Purge-dups:\n"); fprintf(stderr, " -l INT purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 3 for unzip]\n"); - fprintf(stderr, " -s FLOAT similarity threshold for duplicate haplotigs [%g for -l1/-l2, %g for -l3]\n", + fprintf(stderr, " -s FLOAT similarity threshold for duplicate haplotigs in read-level [%g for -l1/-l2, %g for -l3]\n", asm_opt->purge_simi_rate_l2, asm_opt->purge_simi_rate_l3); fprintf(stderr, " -O INT min number of overlapped reads for duplicate haplotigs [%d]\n", asm_opt->purge_overlap_len); @@ -134,7 +135,9 @@ void Print_H(hifiasm_opt_t* asm_opt) fprintf(stderr, " --h1 FILEs file names of Hi-C R1 [r1_1.fq,r1_2.fq,...]\n"); fprintf(stderr, " --h2 FILEs file names of Hi-C R2 [r2_1.fq,r2_2.fq,...]\n"); fprintf(stderr, " --seed INT RNG seed [%lu]\n", asm_opt->seed); - + fprintf(stderr, " --s-base FLOAT\n"); + fprintf(stderr, " similarity threshold for homology detection in base-level;\n"); + fprintf(stderr, " -1 to disable [%.3g]; -s for read-level (see )\n", asm_opt->trans_base_rate_sec); fprintf(stderr, " --n-weight INT\n"); fprintf(stderr, " rounds of reweighting Hi-C links [%d]\n", asm_opt->n_weight); @@ -776,7 +779,10 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt) else if (c == 337) asm_opt->is_dbg_het_cnt = 1; else if (c == 338) asm_opt->max_short_ul_tip = atol(opt.arg); else if (c == 339) asm_opt->is_low_het_ul = 1; - else if (c == 'l') + else if (c == 340) { + asm_opt->trans_base_rate_sec = atof(opt.arg); + if(asm_opt->trans_base_rate_sec < 0) asm_opt->is_base_trans = 0; + } else if (c == 'l') { ///0: disable purge_dup; 1: purge containment; 2: purge overlap asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg); } @@ -793,10 +799,9 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt) return 1; } } - + if(asm_opt->purge_level_primary > 2) asm_opt->purge_simi_thres = asm_opt->purge_simi_rate_l3; else asm_opt->purge_simi_thres = asm_opt->purge_simi_rate_l2; - if (argc == opt.ind) { diff --git a/CommandLines.h b/CommandLines.h index 8d8776b..a61bff9 100644 --- a/CommandLines.h +++ b/CommandLines.h @@ -4,7 +4,7 @@ #include #include -#define HA_VERSION "0.18.4-r495" +#define HA_VERSION "0.18.4-r496" #define VERBOSE 0