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chhylp123
2021-04-16 20:28:48 -04:00
parent 1e86e3dc02
commit f8ee584291
9 changed files with 1805 additions and 221 deletions
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134
CommandLines.cpp
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@@ -34,6 +34,10 @@ static ko_longopt_t long_options[] = {
{ "m-rate", ko_required_argument, 319 },
{ "b-partition", ko_no_argument, 320 },
{ "t-occ", ko_required_argument, 321 },
{ "seed", ko_required_argument, 322 },
{ "n-perturb", ko_required_argument, 323 },
{ "f-perturb", ko_required_argument, 324 },
{ "n-hap", ko_required_argument, 325 },
{ 0, 0, 0 }
};
@@ -49,64 +53,71 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, "Usage: hifiasm [options] <in_1.fq> <in_2.fq> <...>\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, " -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, " -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, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round);
fprintf(stderr, " -m INT pop bubbles of <INT in size in contig graphs [%lld]\n", asm_opt->large_pop_bubble_size);
fprintf(stderr, " -p INT pop bubbles of <INT in size in unitig graphs [%lld]\n", asm_opt->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, " --lowQ 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, " --b-cov INT\n");
fprintf(stderr, " break contigs at positions with <INT-fold coverage; work with '--m-rate'; 0 to disable [%d]\n", asm_opt->b_low_cov);
fprintf(stderr, " --h-cov INT\n");
fprintf(stderr, " break contigs at positions with >INT-fold coverage; work with '--m-rate'; -1 to disable [%d]\n", asm_opt->b_high_cov);
fprintf(stderr, " --m-rate FLOAT\n");
fprintf(stderr, " break contigs at positions with <=FLOAT*coverage exact overlaps;\n");
fprintf(stderr, " only work with '--b-cov' or '--h-cov'[%.2f]\n", asm_opt->m_rate);
fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round);
fprintf(stderr, " -m INT pop bubbles of <INT in size in contig graphs [%lld]\n", asm_opt->large_pop_bubble_size);
fprintf(stderr, " -p INT pop bubbles of <INT in size in unitig graphs [%lld]\n", asm_opt->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, " --lowQ 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, " --b-cov INT\n");
fprintf(stderr, " break contigs at positions with <INT-fold coverage; work with '--m-rate'; 0 to disable [%d]\n", asm_opt->b_low_cov);
fprintf(stderr, " --h-cov INT\n");
fprintf(stderr, " break contigs at positions with >INT-fold coverage; work with '--m-rate'; -1 to disable [%d]\n", asm_opt->b_high_cov);
fprintf(stderr, " --m-rate FLOAT\n");
fprintf(stderr, " break contigs at positions with <=FLOAT*coverage exact overlaps;\n");
fprintf(stderr, " only work with '--b-cov' or '--h-cov'[%.2f]\n", asm_opt->m_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");
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, " -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, " --t-occ INT\n");
fprintf(stderr, " force remove unitigs with >INT unexpected haplotype-specific reads;\n");
fprintf(stderr, " ignore graph topology; [%d]\n", asm_opt->trio_flag_occ_thres);
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, " --t-occ INT\n");
fprintf(stderr, " force remove unitigs with >INT unexpected haplotype-specific reads;\n");
fprintf(stderr, " ignore graph topology; [%d]\n", asm_opt->trio_flag_occ_thres);
fprintf(stderr, " Purge-dups:\n");
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, " -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",
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, " --n-hap INT\n");
fprintf(stderr, " number of haplotypes [%d]\n", asm_opt->polyploidy);
fprintf(stderr, " Hi-C-partition [experimental, not stable]:\n");
// fprintf(stderr, " Hi-C-partition [experimental, not stable]:\n");
fprintf(stderr, " Hi-C-partition:\n");
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, " --n-perturb INT\n");
fprintf(stderr, " rounds of perturbation [%d]\n", asm_opt->n_perturb);
fprintf(stderr, " --f-perturb FLOAT\n");
fprintf(stderr, " fraction to flip for perturbation [%.3g]\n", asm_opt->f_perturb);
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");
@@ -154,7 +165,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->max_short_tip = 3;
asm_opt->min_cnt = 2;
asm_opt->mid_cnt = 5;
asm_opt->purge_level_primary = 2;
asm_opt->purge_level_primary = 3;
asm_opt->purge_level_trio = 0;
asm_opt->purge_simi_rate_l2 = 0.75;
asm_opt->purge_simi_rate_l3 = 0.55;
@@ -175,6 +186,9 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->hap_occ = 1;
asm_opt->polyploidy = 2;
asm_opt->trio_flag_occ_thres = 60;
asm_opt->seed = 11;
asm_opt->n_perturb = 50000;
asm_opt->f_perturb = 0.1;
}
void destory_enzyme(enzyme* f)
@@ -469,27 +483,7 @@ int check_option(hifiasm_opt_t* asm_opt)
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);
// fprintf(stderr, "number of rounds for correction: %d\n", asm_opt->number_of_round);
// fprintf(stderr, "number of rounds for assembly cleaning: %d\n", asm_opt->clean_round);
// fprintf(stderr, "length of removed adapters: %d\n", asm_opt->adapterLen);
// fprintf(stderr, "length of k_mer: %d\n", asm_opt->k_mer_length);
// fprintf(stderr, "min overlap drop ratio: %.2g\n", asm_opt->min_drop_rate);
// fprintf(stderr, "max overlap drop ratio: %.2g\n", asm_opt->max_drop_rate);
// fprintf(stderr, "size of popped small bubbles: %lld\n", asm_opt->small_pop_bubble_size);
// fprintf(stderr, "size of popped large bubbles: %lld\n", asm_opt->large_pop_bubble_size);
// fprintf(stderr, "small removed unitig threshold: %d\n", asm_opt->max_short_tip);
// fprintf(stderr, "small removed unitig threshold: %d\n", asm_opt->max_short_tip);
// fprintf(stderr, "min_cnt: %d\n", asm_opt->min_cnt);
// 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_thres: %f\n", asm_opt->purge_simi_thres);
// fprintf(stderr, "purge_overlap_len: %d\n", asm_opt->purge_overlap_len);
return 1;
}
@@ -652,6 +646,10 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 319) asm_opt->m_rate = atof(opt.arg);
else if (c == 320) asm_opt->flag |= HA_F_PARTITION;
else if (c == 321) asm_opt->trio_flag_occ_thres = atoi(opt.arg);
else if (c == 322) asm_opt->seed = atol(opt.arg);
else if (c == 323) asm_opt->n_perturb = atoi(opt.arg);
else if (c == 324) asm_opt->f_perturb = atof(opt.arg);
else if (c == 325) asm_opt->polyploidy = 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);