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release v0.13

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chhylp123
2020-10-21 21:57:43 -04:00
parent 04f94514ee
commit 91d4915da7
4 changed files with 323 additions and 20 deletions
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CommandLines.cpp
+11 -1
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@@ -24,6 +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 },
{ 0, 0, 0 }
};
@@ -59,6 +60,8 @@ 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, " 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");
@@ -130,6 +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;
}
void destory_opt(hifiasm_opt_t* asm_opt)
@@ -319,6 +323,12 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if(asm_opt->bed_inconsist_rate < 0 || asm_opt->bed_inconsist_rate > 100)
{
fprintf(stderr, "[ERROR] inconsistency rate should be [0, 100] (--pb-range)\n");
return 0;
}
if(asm_opt->fn_bin_yak[0] != NULL && check_file(asm_opt->fn_bin_yak[0], "YAK1") == 0) return 0;
if(asm_opt->fn_bin_yak[1] != NULL && check_file(asm_opt->fn_bin_yak[1], "YAK2") == 0) return 0;
@@ -438,6 +448,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
}
}
else if (c == 311) asm_opt->flag |= HA_F_HIGH_HET;
else if (c == 312) asm_opt->bed_inconsist_rate = atoi(opt.arg);
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);
@@ -462,7 +473,6 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
Print_H(asm_opt);
return 0;
}
///fprintf(stderr, "max_ov_diff_ec: %f, max_ov_diff_final: %f\n", asm_opt->max_ov_diff_ec, asm_opt->max_ov_diff_final);
get_queries(argc, argv, &opt, asm_opt);