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chhylp123
2023-01-12 01:22:34 -05:00
parent 197cd4d77e
commit 2bf5119bb5
2 changed files with 11 additions and 6 deletions
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15
CommandLines.cpp
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@@ -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 <Purge-dups>)\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)
{