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Merge branch 'master' into dev-lh3

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This commit is contained in:
Heng Li
2021-03-18 16:11:43 -04:00
parent 8e98fb2276 e6e6dbf7b3
commit 863b20773a
8 changed files with 5650 additions and 2397 deletions
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37
CommandLines.cpp
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@@ -23,7 +23,7 @@ static ko_longopt_t long_options[] = {
{ "ex-iter", ko_required_argument, 308 },
{ "purge-cov", ko_required_argument, 309 },
{ "pri-range", ko_required_argument, 310 },
{ "high-het", ko_no_argument, 311 },
///{ "high-het", ko_no_argument, 311 },
{ "lowQ", ko_required_argument, 312 },
{ "min-hist-cnt", ko_required_argument, 313 },
{ "h1", ko_required_argument, 314 },
@@ -89,14 +89,14 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -4 FILE list of hap2/maternal read names []\n");
fprintf(stderr, " Purge-dups:\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, " -l INT purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 2 for unzip]\n");
fprintf(stderr, " -s FLOAT similarity threshold for duplicate haplotigs [%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);
fprintf(stderr, " --purge-cov INT\n");
fprintf(stderr, " coverage upper bound of Purge-dups [auto]\n");
fprintf(stderr, " --high-het enable this mode for high heterozygosity sample [experimental, not stable]\n");
///fprintf(stderr, " --high-het enable this mode for high heterozygosity sample [experimental, not stable]\n");
fprintf(stderr, " Hi-C-partition [experimental, not stable]:\n");
fprintf(stderr, " --h1 FILEs file names of Hi-C R1 [r1_1.fq,r1_2.fq,...]\n");
@@ -151,10 +151,11 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->mid_cnt = 5;
asm_opt->purge_level_primary = 2;
asm_opt->purge_level_trio = 0;
asm_opt->purge_simi_rate = 0.75;
asm_opt->purge_simi_rate_hic = 0.85;
asm_opt->purge_simi_rate_l2 = 0.75;
asm_opt->purge_simi_rate_l3 = 0.55;
///asm_opt->purge_simi_rate_hic = 0.85;
asm_opt->purge_overlap_len = 1;
asm_opt->purge_overlap_len_hic = 50;
///asm_opt->purge_overlap_len_hic = 50;
asm_opt->recover_atg_cov_min = -1024;
asm_opt->recover_atg_cov_max = INT_MAX;
asm_opt->hom_global_coverage = -1;
@@ -165,6 +166,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->b_low_cov = 0;
asm_opt->b_high_cov = -1;
asm_opt->m_rate = 0.75;
asm_opt->hap_occ = 1;
}
void destory_enzyme(enzyme* f)
@@ -361,9 +363,9 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if(asm_opt->purge_level_primary < 0 || asm_opt->purge_level_primary > 2)
if(asm_opt->purge_level_primary < 0 || asm_opt->purge_level_primary > 3)
{
fprintf(stderr, "[ERROR] the level of purge-dup should be [0, 2] (-l)\n");
fprintf(stderr, "[ERROR] the level of purge-dup should be [0, 3] (-l)\n");
return 0;
}
@@ -454,6 +456,12 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if(asm_opt->purge_simi_thres < 0)
{
fprintf(stderr, "[ERROR] [-s] must >= 0\n");
return 0;
}
// fprintf(stderr, "input file num: %d\n", asm_opt->num_reads);
// fprintf(stderr, "output file: %s\n", asm_opt->output_file_name);
// fprintf(stderr, "number of threads: %d\n", asm_opt->thread_num);
@@ -471,7 +479,7 @@ int check_option(hifiasm_opt_t* asm_opt)
// fprintf(stderr, "mid_cnt: %d\n", asm_opt->mid_cnt);
// fprintf(stderr, "purge_level_primary: %d\n", asm_opt->purge_level_primary);
// fprintf(stderr, "purge_level_trio: %d\n", asm_opt->purge_level_trio);
// fprintf(stderr, "purge_simi_rate: %f\n", asm_opt->purge_simi_rate);
// fprintf(stderr, "purge_simi_thres: %f\n", asm_opt->purge_simi_thres);
// fprintf(stderr, "purge_overlap_len: %d\n", asm_opt->purge_overlap_len);
return 1;
@@ -621,7 +629,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
asm_opt->recover_atg_cov_min = asm_opt->recover_atg_cov_max = -1;
}
}
else if (c == 311) asm_opt->flag |= HA_F_HIGH_HET;
///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 == 313) asm_opt->min_hist_kmer_cnt = atoi(opt.arg);
else if (c == 314) get_hic_enzymes(opt.arg, &(asm_opt->hic_reads[0]), 0);
@@ -634,7 +642,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
{ ///0: disable purge_dup; 1: purge containment; 2: purge overlap
asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);
}
else if (c == 's') asm_opt->purge_simi_rate = atof(opt.arg);
else if (c == 's') asm_opt->purge_simi_rate_l2 = asm_opt->purge_simi_rate_l3 = atof(opt.arg);
else if (c == 'O') asm_opt->purge_overlap_len = atoll(opt.arg);
else if (c == ':')
{
@@ -648,6 +656,9 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
}
}
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)
{