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CommandLines.cpp
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#define __STDC_LIMIT_MACROS
#include <zlib.h>
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <limits.h>
#include <sys/time.h>
#include "CommandLines.h"
#include "ketopt.h"
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
#define DEFAULT_OUTPUT "hifiasm.asm"
hifiasm_opt_t asm_opt;
static ko_longopt_t long_options[] = {
{ "version", ko_no_argument, 300 },
{ "dbg-gfa", ko_no_argument, 301 },
{ "write-paf", ko_no_argument, 302 },
{ "write-ec", ko_no_argument, 303 },
{ "skip-triobin", ko_no_argument, 304 },
{ "max-od-ec", ko_required_argument, 305 },
{ "max-od-final", ko_required_argument, 306 },
{ "ex-list", ko_required_argument, 307 },
{ "ex-iter", ko_required_argument, 308 },
{ "hom-cov", ko_required_argument, 309 },
{ "pri-range", ko_required_argument, 310 },
{ "lowQ", ko_required_argument, 312 },
{ "min-hist-cnt", ko_required_argument, 313 },
{ "h1", ko_required_argument, 314 },
{ "h2", ko_required_argument, 315 },
{ "enzyme", ko_required_argument, 316 },
{ "b-cov", ko_required_argument, 317 },
{ "h-cov", ko_required_argument, 318 },
{ "m-rate", ko_required_argument, 319 },
{ "primary", 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 },
{ "n-weight", ko_required_argument, 326 },
{ "l-msjoin", ko_required_argument, 327 },
{ "purge-max", ko_required_argument, 328 },
{ "fast", ko_no_argument, 329 },
{ "dp-er", ko_required_argument, 330},
{ "max-kocc", ko_required_argument, 331},
{ "hg-size", ko_required_argument, 332},
{ "ul", ko_required_argument, 333},
{ "unskew", ko_no_argument, 334},
{ "kpt-rate", ko_required_argument, 335},
{ "ul-rate", ko_required_argument, 336},
{ "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},
{ "bin-only", ko_no_argument, 341},
{ "ul-round", ko_required_argument, 342},
{ "prt-raw", ko_no_argument, 343},
{ "integer-correct", ko_required_argument, 344},
{ "dbg-ovec", ko_no_argument, 345},
{ "path-max", ko_required_argument, 346},
{ "path-min", ko_required_argument, 347},
{ "trio-dual", ko_no_argument, 348},
{ "ul-cut", ko_required_argument, 349},
{ "dual-scaf", ko_no_argument, 350},
{ "scaf-gap", ko_required_argument, 351},
{ "sec-in", ko_required_argument, 352},
{ "somatic-cov", ko_required_argument, 353},
{ "telo-m", ko_required_argument, 354},
{ "telo-p", ko_required_argument, 355},
{ "telo-d", ko_required_argument, 356},
{ "telo-s", ko_required_argument, 357},
{ "ctg-n", ko_required_argument, 358},
{ "ont", ko_no_argument, 359},
// { "sc-n", ko_no_argument, 360},
{ "chem-c", ko_required_argument, 361},
{ "chem-f", ko_required_argument, 362},
{ "ul-m", ko_required_argument, 363},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
double Get_T(void)
{
struct timeval t;
gettimeofday(&t, NULL);
return t.tv_sec+t.tv_usec/1000000.0;
}
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, " -t INT number of threads [%d]\n", asm_opt->thread_num);
fprintf(stderr, " -h show help information\n");
fprintf(stderr, " --version show version number\n");
fprintf(stderr, " Preset options:\n");
fprintf(stderr, " --ont assemble Oxford Nanopore reads\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, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " --max-kocc INT\n");
fprintf(stderr, " employ k-mers occurring <INT times to rescue repetitive overlaps [%d]\n", asm_opt->max_kmer_cnt);
fprintf(stderr, " --hg-size INT(k, m or g)\n");
fprintf(stderr, " estimated haploid genome size used for inferring read coverage [auto]\n");
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, " -i ignore saved read correction and overlaps\n");
fprintf(stderr, " -u post-join step for contigs which may improve N50; 0 to disable; 1 to enable\n");
fprintf(stderr, " [%u] and [%u] in default for the UL+HiFi assembly and the HiFi assembly, respectively\n",
asm_opt->ul_pst_join, asm_opt->hifi_pst_join);
fprintf(stderr, " --hom-cov INT\n");
fprintf(stderr, " homozygous read coverage [auto]\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, " --primary output a primary assembly and an alternate assembly\n");
fprintf(stderr, " --ctg-n INT\n");
fprintf(stderr, " remove tip contigs composed of <=INT reads [%d]\n", asm_opt->max_contig_tip);
// 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, " -3 FILE list of hap1/paternal read names []\n");
fprintf(stderr, " -4 FILE list of hap2/maternal read names []\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, " --t-occ INT\n");
fprintf(stderr, " forcedly remove unitigs with >INT unexpected haplotype-specific reads;\n");
fprintf(stderr, " ignore graph topology; [%d]\n", asm_opt->trio_flag_occ_thres);
fprintf(stderr, " --trio-dual utilize homology information to correct trio phasing errors\n");
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 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);
fprintf(stderr, " --purge-max 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:\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, " --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);
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, " --l-msjoin INT\n");
fprintf(stderr, " detect misjoined unitigs of >=INT in size; 0 to disable [%lu]\n", asm_opt->misjoin_len);
fprintf(stderr, " Ultra-Long-integration:\n");
fprintf(stderr, " --ul FILEs file names of Ultra-Long reads [r1.fq,r2.fq,...]\n");
///pending for integration
/**
fprintf(stderr, " --ul-m INT\n");
fprintf(stderr, " hybrid assembly mode. 0: fast and memory efficent; 1: may produce better assembly with ONT R10 [%d]\n", asm_opt->ul_mod);
**/
fprintf(stderr, " --ul-rate FLOAT\n");
fprintf(stderr, " error rate of Ultra-Long reads [%.3g]\n", asm_opt->ul_error_rate);
fprintf(stderr, " --ul-tip INT\n");
fprintf(stderr, " remove tip unitigs composed of <=INT reads for the UL assembly [%d]\n", asm_opt->max_short_ul_tip);
fprintf(stderr, " --path-max FLOAT\n");
fprintf(stderr, " max path drop ratio [%.2g]; higher number may make the assembly cleaner\n", asm_opt->max_path_drop_rate);
fprintf(stderr, " but may lead to more misassemblies\n");
fprintf(stderr, " --path-min FLOAT\n");
fprintf(stderr, " min path drop ratio [%.2g]; higher number may make the assembly cleaner\n", asm_opt->min_path_drop_rate);
fprintf(stderr, " but may lead to more misassemblies\n");
fprintf(stderr, " --ul-cut INT\n");
fprintf(stderr, " filter out <INT UL reads during the UL assembly [%d]\n", asm_opt->ul_min_base);
// fprintf(stderr, " --low-het enable it for genomes with very low het heterozygosity rate (<0.0001%%)\n");
fprintf(stderr, " Dual-Scaffolding:\n");
fprintf(stderr, " --dual-scaf output scaffolding\n");
fprintf(stderr, " --scaf-gap INT\n");
fprintf(stderr, " max gap size for scaffolding [%ld]\n", asm_opt->self_scaf_gap_max);
fprintf(stderr, " Telomere-identification:\n");
fprintf(stderr, " --telo-m STR\n");
fprintf(stderr, " telomere motif at 5'-end; CCCTAA for human [%s]\n", ((asm_opt->telo_motif)?(asm_opt->telo_motif):("NULL")));///5'-end, check CCCTAA
fprintf(stderr, " --telo-p INT\n");
fprintf(stderr, " non-telomeric penalty [%ld]\n", asm_opt->telo_pen);
fprintf(stderr, " --telo-d INT\n");
fprintf(stderr, " max drop [%ld]\n", asm_opt->telo_drop);
fprintf(stderr, " --telo-s INT\n");
fprintf(stderr, " min score for telomere reads [%ld]\n", asm_opt->telo_mic_sc);
fprintf(stderr, " ONT simplex assembly (beta):\n");
fprintf(stderr, " --ont assemble ONT simplex reads in fastq format\n");
// fprintf(stderr, " --sc-n consider base qual value for assembly\n");
fprintf(stderr, " --chem-c INT\n");
fprintf(stderr, " detect chimeric reads with <=INT other reads support [%lu]\n", asm_opt->chemical_cov);
fprintf(stderr, " --chem-f INT\n");
fprintf(stderr, " length of flanking regions for chimeric read detection [%lu]\n", asm_opt->chemical_flank);
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
fprintf(stderr, "See `https://hifiasm.readthedocs.io/en/latest/' or `man ./hifiasm.1' for complete documentation.\n");
}
void init_opt(hifiasm_opt_t* asm_opt)
{
memset(asm_opt, 0, sizeof(hifiasm_opt_t));
///asm_opt->flag = 0;
asm_opt->flag = HA_F_PARTITION;
asm_opt->coverage = -1;
asm_opt->num_reads = 0;
asm_opt->read_file_names = NULL;
asm_opt->output_file_name = (char*)(DEFAULT_OUTPUT);
asm_opt->required_read_name = NULL;
asm_opt->hic_enzymes = NULL;
asm_opt->hic_reads[0] = NULL;
asm_opt->hic_reads[1] = NULL;
asm_opt->fn_bin_poy = NULL;
asm_opt->ar = NULL;
asm_opt->thread_num = 1;
asm_opt->k_mer_length = 51;
asm_opt->hic_mer_length = 31;
asm_opt->ul_mer_length = 19;
asm_opt->trans_mer_length = 31;
asm_opt->mz_win = 51;
asm_opt->ul_mz_win = 19;
asm_opt->trans_win = 31;
asm_opt->mz_rewin = 1000;
asm_opt->ul_mz_rewin = 360;
asm_opt->mz_sample_dist = 500;
asm_opt->bf_shift = 37;
asm_opt->max_kmer_cnt = 2000;
asm_opt->high_factor = 5.0;
asm_opt->max_ov_diff_ec = 0.04;
asm_opt->max_ov_diff_final = 0.03;
asm_opt->hom_cov = 20;
asm_opt->het_cov = -1024;
asm_opt->max_n_chain = MIN_N_CHAIN;
asm_opt->min_hist_kmer_cnt = 5;
asm_opt->load_index_from_disk = 1;
asm_opt->write_index_to_disk = 1;
asm_opt->number_of_round = 3;
asm_opt->number_of_pround = 0/**3**/;
asm_opt->adapterLen = 0;
asm_opt->clean_round = 4;
///asm_opt->small_pop_bubble_size = 100000;
asm_opt->small_pop_bubble_size = 0;
asm_opt->large_pop_bubble_size = 10000000;
asm_opt->min_drop_rate = 0.2;
asm_opt->max_drop_rate = 0.8;
asm_opt->max_hang_Len = 1000;
asm_opt->max_hang_rate = 0.8;
asm_opt->gap_fuzz = 1000;
asm_opt->min_overlap_Len = 50;
asm_opt->min_overlap_coverage = 0;
asm_opt->max_short_tip = 3;
asm_opt->max_short_ul_tip = 6;
asm_opt->max_contig_tip = 3;
asm_opt->min_cnt = 2;
asm_opt->mid_cnt = 5;
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;
asm_opt->trans_base_rate = 0.93;
asm_opt->trans_base_rate_sec = 0.5;
asm_opt->purge_overlap_len = 1;
///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;
asm_opt->hom_global_coverage_set = 0;
asm_opt->pur_global_coverage = -1;
asm_opt->bed_inconsist_rate = 70;
asm_opt->hic_inconsist_rate = 30;
///asm_opt->bub_mer_length = 3;
asm_opt->bub_mer_length = 1000000;
asm_opt->b_low_cov = 0;
asm_opt->b_high_cov = -1;
asm_opt->m_rate = 0.75;
asm_opt->hap_occ = 1;
asm_opt->polyploidy = 2;
asm_opt->trio_flag_occ_thres = 60;
asm_opt->seed = 11;
asm_opt->n_perturb = 10000;
asm_opt->f_perturb = 0.1;
asm_opt->n_weight = 3;
asm_opt->is_alt = 0;
asm_opt->misjoin_len = 500000;
asm_opt->scffold = 0;
asm_opt->dp_min_len = 2000;
asm_opt->dp_e = 0.0025;
asm_opt->hg_size = -1;
asm_opt->kpt_rate = -1;
asm_opt->infor_cov = 3;
asm_opt->s_hap_cov = 3;
asm_opt->ul_error_rate = 0.2/**0.15**/;
asm_opt->ul_error_rate_low = 0.1;
asm_opt->ul_error_rate_hpc = 0.2;
asm_opt->ul_ec_round = 3;
asm_opt->is_dbg_het_cnt = 0;
asm_opt->is_low_het_ul = 0;
asm_opt->is_base_trans = 1;
asm_opt->is_read_trans = 1;
asm_opt->is_topo_trans = 1;
asm_opt->is_bub_trans = 1;
asm_opt->bin_only = 0;
asm_opt->ul_clean_round = 1;
asm_opt->prt_dbg_gfa = 0;
asm_opt->integer_correct_round = 0;
asm_opt->dbg_ovec_cal = 0;
asm_opt->min_path_drop_rate = 0.2;
asm_opt->max_path_drop_rate = 0.6;
asm_opt->hifi_pst_join = 1;
asm_opt->ul_pst_join = 1;
asm_opt->trio_cov_het_ovlp = -1;
asm_opt->ul_min_base = 0;
asm_opt->self_scaf = 0;
asm_opt->self_scaf_min = 250000;
asm_opt->self_scaf_reliable_min = 5000000;
asm_opt->self_scaf_gap_max = 3000000;
asm_opt->sec_in = NULL;
asm_opt->somatic_cov = -1;
asm_opt->telo_motif = NULL;
asm_opt->telo_pen = 1;
asm_opt->telo_drop = 2000;
asm_opt->telo_mic_sc = 500;
asm_opt->is_ont = 0;
asm_opt->is_sc = 0;
asm_opt->chemical_cov = 1;
asm_opt->chemical_flank = 256;
asm_opt->ul_mod = 0;
}
void destory_enzyme(enzyme* f)
{
int i;
if(f != NULL)
{
for (i = 0; i < f->n; i++)
{
free(f->a[i]);
}
free(f->a);
free(f->l);
free(f);
}
}
void destory_opt(hifiasm_opt_t* asm_opt)
{
if(asm_opt->read_file_names != NULL) free(asm_opt->read_file_names);
if(asm_opt->hic_enzymes != NULL) destory_enzyme(asm_opt->hic_enzymes);
if(asm_opt->hic_reads[0] != NULL) destory_enzyme(asm_opt->hic_reads[0]);
if(asm_opt->hic_reads[1] != NULL) destory_enzyme(asm_opt->hic_reads[1]);
if(asm_opt->ar != NULL) destory_enzyme(asm_opt->ar);
}
void ha_opt_reset_to_round(hifiasm_opt_t* asm_opt, int round)
{
asm_opt->num_bases = 0;
asm_opt->num_corrected_bases = 0;
asm_opt->num_recorrected_bases = 0;
asm_opt->mem_buf = 0;
asm_opt->roundID = round;
}
void ha_opt_update_cov(hifiasm_opt_t *opt, int hom_cov)
{
int max_n_chain = (int)(hom_cov * opt->high_factor + .499);
opt->hom_cov = hom_cov;
if (opt->max_n_chain < max_n_chain)
opt->max_n_chain = max_n_chain;
fprintf(stderr, "[M::%s] updated max_n_chain to %d\n", __func__, opt->max_n_chain);
}
void ha_opt_update_cov_min(hifiasm_opt_t *opt, int hom_cov, int min_chain)
{
int max_n_chain = (int)(hom_cov * opt->high_factor + .499);
opt->hom_cov = hom_cov; opt->max_n_chain = max_n_chain;
if(opt->max_n_chain < min_chain) opt->max_n_chain = min_chain;
fprintf(stderr, "[M::%s] updated max_n_chain to %d\n", __func__, opt->max_n_chain);
}
static int check_file(char* name, const char* opt)
{
if(!name)
{
fprintf(stderr, "[ERROR] file does not exist (-%s)\n", opt);
return 0;
}
FILE* is_exist = NULL;
is_exist = fopen(name,"r");
if(!is_exist)
{
fprintf(stderr, "[ERROR] %s does not exist (-%s)\n", name, opt);
return 0;
}
fclose(is_exist);
return 1;
}
static int check_hic_reads(enzyme* f, const char* opt)
{
int32_t i;
for (i = 0; i < f->n; i++) {
if(check_file(f->a[i], opt) == 0) return 0;
}
return 1;
}
static int check_fq_files(enzyme* f, const char* opt, int32_t is_fq)
{
int32_t i, ret; gzFile dfp; kseq_t *ks = NULL;
for (i = 0; i < f->n; i++) {
if(!(f->a[i])) {
fprintf(stderr, "[ERROR] input file does not exist (%s)\n", opt);
return 0;
}
dfp = gzopen(f->a[i], "r");
if (dfp == 0) {
fprintf(stderr, "[ERROR] Cannot find the input file: %s (%s)\n", f->a[i], opt);
return 0;
} else if(is_fq){
ks = kseq_init(dfp);
while (((ret = kseq_read(ks)) >= 0)) {
if((ks->qual.l == 0) || (ks->qual.s == NULL)) {
fprintf(stderr, "[ERROR] %s is in fasta format rather than fastq format (%s)\n", f->a[i], opt);
fprintf(stderr, "[ERROR] set --ul-m 0 for fasta files\n");
return 0;
}
break;
}
kseq_destroy(ks); ks = NULL;
}
gzclose(dfp);
}
return 1;
}
int check_option(hifiasm_opt_t* asm_opt)
{
if(asm_opt->read_file_names == NULL || asm_opt->num_reads == 0)
{
fprintf(stderr, "[ERROR] missing input: please specify a read file\n");
return 0;
}
if(asm_opt->output_file_name == NULL)
{
fprintf(stderr, "[ERROR] missing output: please specify the output name (-o)\n");
return 0;
}
if(asm_opt->thread_num < 1)
{
fprintf(stderr, "[ERROR] the number of threads must be > 0 (-t)\n");
return 0;
}
if(asm_opt->number_of_round < 1)
{
fprintf(stderr, "[ERROR] the number of rounds for correction must be > 0 (-r)\n");
return 0;
}
if(asm_opt->clean_round < 1)
{
fprintf(stderr, "[ERROR] the number of rounds for assembly cleaning must be > 0 (-a)\n");
return 0;
}
if(asm_opt->adapterLen < 0)
{
fprintf(stderr, "[ERROR] the length of removed adapters must be >= 0 (-z)\n");
return 0;
}
if(asm_opt->k_mer_length >= 64)
{
fprintf(stderr, "[ERROR] the length of k_mer must be < 64 (-k)\n");
return 0;
}
if(asm_opt->max_drop_rate < 0 || asm_opt->max_drop_rate >= 1 )
{
fprintf(stderr, "[ERROR] max overlap drop ratio must be [0.0, 1.0) (-x)\n");
return 0;
}
if(asm_opt->min_drop_rate < 0 || asm_opt->min_drop_rate >= 1)
{
fprintf(stderr, "[ERROR] min overlap drop ratio must be [0.0, 1.0) (-y)\n");
return 0;
}
if(asm_opt->max_drop_rate <= asm_opt->min_drop_rate)
{
fprintf(stderr, "[ERROR] min overlap drop ratio must be less than max overlap drop ratio (-x/-y)\n");
return 0;
}
if(asm_opt->small_pop_bubble_size < 0)
{
fprintf(stderr, "[ERROR] the size of popped small bubbles must be >= 0 (-p)\n");
return 0;
}
if(asm_opt->large_pop_bubble_size < 0)
{
fprintf(stderr, "[ERROR] the size of popped large bubbles must be >= 0 (-m)\n");
return 0;
}
if(asm_opt->max_hang_Len < 0)
{
fprintf(stderr, "[ERROR] max_hang_Len must be >= 0\n");
return 0;
}
if(asm_opt->max_hang_rate < 0)
{
fprintf(stderr, "[ERROR] max_hang_rate must be >= 0\n");
return 0;
}
if(asm_opt->gap_fuzz < 0)
{
fprintf(stderr, "[ERROR] gap_fuzz must be >= 0\n");
return 0;
}
if(asm_opt->min_overlap_Len < 0)
{
fprintf(stderr, "[ERROR] min_overlap_Len must be >= 0\n");
return 0;
}
if(asm_opt->min_overlap_coverage < 0)
{
fprintf(stderr, "[ERROR] min_overlap_coverage must be >= 0\n");
return 0;
}
if (asm_opt->max_ov_diff_ec < asm_opt->max_ov_diff_final) {
fprintf(stderr, "[ERROR] max_ov_diff_ec shouldn't be smaller than max_ov_diff_final\n");
return 0;
}
if (asm_opt->max_ov_diff_ec < HA_MIN_OV_DIFF) {
fprintf(stderr, "[ERROR] max_ov_diff_ec shouldn't be smaller than %g\n", HA_MIN_OV_DIFF);
return 0;
}
if(asm_opt->max_short_tip < 0)
{
fprintf(stderr, "[ERROR] the length of removal tips must be >= 0 (-n)\n");
return 0;
}
if(asm_opt->purge_level_primary < 0 || asm_opt->purge_level_primary > 3)
{
fprintf(stderr, "[ERROR] the level of purge-dup should be [0, 3] (-l)\n");
return 0;
}
if(ha_opt_triobin(asm_opt) && ((asm_opt->purge_level_trio < 0 || asm_opt->purge_level_trio > 1)))
{
fprintf(stderr, "[ERROR] the level of purge-dup for trio should be [0, 1] (-l)\n");
return 0;
}
if(asm_opt->hom_global_coverage < 0 && asm_opt->hom_global_coverage != -1)
{
fprintf(stderr, "[ERROR] homozygous read coverage should be >= 0 (--hom-cov)\n");
return 0;
}
if(asm_opt->pur_global_coverage < 0 && asm_opt->pur_global_coverage != -1)
{
fprintf(stderr, "[ERROR] purge duplication coverage threshold should be >= 0 (--purge-max)\n");
return 0;
}
if(asm_opt->bed_inconsist_rate < 0 || asm_opt->bed_inconsist_rate > 100)
{
fprintf(stderr, "[ERROR] inconsistency rate should be [0, 100] (--lowQ)\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;
if(asm_opt->fn_bin_list[0] != NULL && check_file(asm_opt->fn_bin_list[0], "LIST1") == 0) return 0;
if(asm_opt->fn_bin_list[1] != NULL && check_file(asm_opt->fn_bin_list[1], "LIST2") == 0) return 0;
if(asm_opt->required_read_name != NULL && check_file(asm_opt->required_read_name, "b") == 0) return 0;
if(asm_opt->hic_reads[0] != NULL && check_hic_reads(asm_opt->hic_reads[0], "HIC1") == 0) return 0;
if(asm_opt->hic_reads[1] != NULL && check_hic_reads(asm_opt->hic_reads[1], "HIC2") == 0) return 0;
if(asm_opt->hic_reads[0] != NULL && asm_opt->hic_reads[1] == NULL)
{
fprintf(stderr, "[ERROR] lack r2 of HiC reads (--h2)\n");
return 0;
}
if(asm_opt->hic_reads[1] != NULL && asm_opt->hic_reads[0] == NULL)
{
fprintf(stderr, "[ERROR] lack r1 of HiC reads (--h1)\n");
return 0;
}
if(asm_opt->hic_reads[0] != NULL && asm_opt->hic_reads[1] != NULL &&
asm_opt->hic_reads[0]->n != asm_opt->hic_reads[1]->n)
{
fprintf(stderr, "[ERROR] wrong r1 and r2 of HiC reads (--h1 && --h2)\n");
return 0;
}
if(asm_opt->hic_enzymes != NULL && asm_opt->hic_enzymes->n == 0)
{
fprintf(stderr, "[ERROR] wrong HiC enzymes (--enzyme)\n");
return 0;
}
if(asm_opt->hic_reads[0] != NULL && asm_opt->hic_reads[0]->n == 0)
{
fprintf(stderr, "[ERROR] wrong r1 of HiC reads (--h1)\n");
return 0;
}
if(asm_opt->hic_reads[1] != NULL && asm_opt->hic_reads[1]->n == 0)
{
fprintf(stderr, "[ERROR] wrong r2 of HiC reads (--h2)\n");
return 0;
}
if(asm_opt->ar != NULL && check_fq_files(asm_opt->ar, "--ul", asm_opt->ul_mod) == 0) return 0;
if(asm_opt->ar != NULL && asm_opt->ar->n == 0)
{
fprintf(stderr, "[ERROR] wrong UL reads (--ul)\n");
return 0;
}
if(asm_opt->b_low_cov < 0)
{
fprintf(stderr, "[ERROR] must >= 0 (--b-cov)\n");
return 0;
}
if(asm_opt->b_high_cov != -1 && asm_opt->b_high_cov < 0)
{
fprintf(stderr, "[ERROR] must >= 0 (--h-cov)\n");
return 0;
}
if(asm_opt->m_rate < 0)
{
fprintf(stderr, "[ERROR] must >= 0 (--m-rate)\n");
return 0;
}
if(asm_opt->b_high_cov != -1 && asm_opt->b_high_cov <= asm_opt->b_low_cov)
{
fprintf(stderr, "[ERROR] [--h-cov] must >= [--b-cov]\n");
return 0;
}
if(asm_opt->purge_simi_thres < 0)
{
fprintf(stderr, "[ERROR] [-s] must >= 0\n");
return 0;
}
if(asm_opt->max_kmer_cnt < 0)
{
fprintf(stderr, "[ERROR] [--max-kocc] must >= 0\n");
return 0;
}
if(asm_opt->hg_size < -1)
{
fprintf(stderr, "[ERROR] [--hg-size] wrong genome size\n");
return 0;
}
if(asm_opt->ul_mod != 0 && asm_opt->ul_mod != 1) {
fprintf(stderr, "[ERROR] must be 0 or 1 (--ul-m)\n");
return 0;
}
if(asm_opt->telo_motif) {
uint64_t k, tlen = strlen((asm_opt->telo_motif)); char c;
if(tlen > 32) {
fprintf(stderr, "[ERROR] [--telo-m] must be no longer than 32\n");
return 0;
}
for (k = 0; k < tlen; k++) {
c = asm_opt->telo_motif[k];
if(c != 'A' && c != 'C' && c != 'G' && c != 'T' &&
c != 'a' && c != 'c' && c != 'g' && c != 't') {
fprintf(stderr, "[ERROR] [--telo-m] must be A/C/G/T\n");
return 0;
}
}
}
return 1;
}
void get_queries(int argc, char *argv[], ketopt_t* opt, hifiasm_opt_t* asm_opt)
{
if(opt->ind == argc) {
return;
}
asm_opt->num_reads = argc - opt->ind;
asm_opt->read_file_names = (char**)malloc(sizeof(char*)*asm_opt->num_reads);
long long i; int ret;
gzFile dfp; kseq_t *ks = NULL;
for (i = 0; i < asm_opt->num_reads; i++) {
asm_opt->read_file_names[i] = argv[i + opt->ind];
dfp = gzopen(asm_opt->read_file_names[i], "r");
if (dfp == 0) {
fprintf(stderr, "[ERROR] Cannot find the input read file: %s\n",
asm_opt->read_file_names[i]);
exit(0);
} else if(asm_opt->is_sc){
ks = kseq_init(dfp);
while (((ret = kseq_read(ks)) >= 0)) {
if((ks->qual.l == 0) || (ks->qual.s == NULL)) {
fprintf(stderr, "[ERROR] %s is in fasta format rather than fastq format\n", asm_opt->read_file_names[i]);
asm_opt->is_sc = 0;
exit(0);
}
break;
}
kseq_destroy(ks); ks = NULL;
}
gzclose(dfp);
}
}
void get_hic_enzymes(char *argv, enzyme** x, int check_name)
{
int i, k, pre_i, len = strlen(argv);
(*x) = (enzyme*)calloc(1, sizeof(enzyme));
if(len == 0)
{
(*x)->n = 0; (*x)->l = NULL; (*x)->a = NULL;
return;
}
(*x)->n = 1;
for (i = pre_i = 0; i < len; i++)
{
if(argv[i] == ',')
{
(*x)->n++;
continue;
}
if(check_name)
{
if(argv[i] != 'A' && argv[i] != 'C' && argv[i] != 'G' && argv[i] != 'T' &&
argv[i] != 'a' && argv[i] != 'c' && argv[i] != 'g' && argv[i] != 't' &&
argv[i] != 'N' && argv[i] != 'n')
{
(*x)->n = 0;
(*x)->l = NULL;
(*x)->a = NULL;
return;
}
}
}
(*x)->l = (int*)calloc((*x)->n, sizeof(int));
(*x)->a = (char**)calloc((*x)->n, sizeof(char*));
for (i = pre_i = k = 0; i < len; i++)
{
if(argv[i] == ',')
{
(*x)->l[k] = i - pre_i;
(*x)->a[k] = (char*)malloc(sizeof(char)*((*x)->l[k]+1));
memcpy((*x)->a[k], argv + pre_i, (*x)->l[k]);
(*x)->a[k][(*x)->l[k]] = '\0';
pre_i = i + 1;
k++;
}
}
(*x)->l[k] = i - pre_i;
(*x)->a[k] = (char*)malloc(sizeof(char)*((*x)->l[k]+1));
memcpy((*x)->a[k], argv + pre_i, (*x)->l[k]);
(*x)->a[k][(*x)->l[k]] = '\0';
}
int64_t inter_gsize(char *argv)
{
int64_t len = strlen(argv);
double s;
if(len <= 1) return -2;
char t = argv[len-1];
if(t != 'k' && t != 'K' && t != 'm' && t != 'M' && t != 'g' && t != 'G') return -2;
char *ss=(char*)malloc(len);
memcpy(ss, argv, len-1); ss[len-1] = '\0';
s = atof(ss);
free(ss);
if(t == 'k' || t == 'K') return s*1000;
if(t == 'm' || t == 'M') return s*1000000;
if(t == 'g' || t == 'G') return s*1000000000;
return s;
}
int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
{
ketopt_t opt = KETOPT_INIT;
int c;
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:3:4:5:l:s:O:eu:", long_options)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
return 0;
}
else if (c == 'v' || c == 300)
{
puts(HA_VERSION);
return 0;
}
else if (c == 'f') asm_opt->bf_shift = atoi(opt.arg);
else if (c == 't') asm_opt->thread_num = atoi(opt.arg);
else if (c == 'o') asm_opt->output_file_name = opt.arg;
else if (c == 'r') asm_opt->number_of_round = atoi(opt.arg);
else if (c == 'k') asm_opt->k_mer_length = atoi(opt.arg);
else if (c == 'i') asm_opt->load_index_from_disk = 0;
else if (c == 'w') asm_opt->mz_win = atoi(opt.arg);
else if (c == 'D') asm_opt->high_factor = atof(opt.arg);
else if (c == 'F') asm_opt->flag |= HA_F_NO_KMER_FLT;
else if (c == 'N') asm_opt->max_n_chain = atoi(opt.arg);
else if (c == 'a') asm_opt->clean_round = atoi(opt.arg);
else if (c == 'z') asm_opt->adapterLen = atoi(opt.arg);
else if (c == 'b') asm_opt->required_read_name = opt.arg;
else if (c == 'c') asm_opt->min_cnt = atoi(opt.arg);
else if (c == 'd') asm_opt->mid_cnt = atoi(opt.arg);
else if (c == '1' || c == 'P') asm_opt->fn_bin_yak[0] = opt.arg; // -P/-M reserved for backward compatibility
else if (c == '2' || c == 'M') asm_opt->fn_bin_yak[1] = opt.arg;
else if (c == '3') asm_opt->fn_bin_list[0] = opt.arg;
else if (c == '4') asm_opt->fn_bin_list[1] = opt.arg;
else if (c == '5') asm_opt->fn_bin_poy = opt.arg;
else if (c == 'x') asm_opt->max_drop_rate = atof(opt.arg);
else if (c == 'y') asm_opt->min_drop_rate = atof(opt.arg);
else if (c == 'p') asm_opt->small_pop_bubble_size = atoll(opt.arg);
else if (c == 'm') asm_opt->large_pop_bubble_size = atoll(opt.arg);
else if (c == 'n') asm_opt->max_short_tip = atoll(opt.arg);
else if (c == 'e') asm_opt->flag |= HA_F_BAN_ASSEMBLY;
else if (c == 'u') {
if(atoll(opt.arg)) {
asm_opt->hifi_pst_join = asm_opt->ul_pst_join = 1;
} else {
asm_opt->hifi_pst_join = asm_opt->ul_pst_join = 0;
}
}
else if (c == 301) asm_opt->flag |= HA_F_VERBOSE_GFA;
else if (c == 302) asm_opt->flag |= HA_F_WRITE_PAF;
else if (c == 303) asm_opt->flag |= HA_F_WRITE_EC;
else if (c == 304) asm_opt->flag |= HA_F_SKIP_TRIOBIN;
else if (c == 305) asm_opt->max_ov_diff_ec = atof(opt.arg);
else if (c == 306) asm_opt->max_ov_diff_final = atof(opt.arg);
else if (c == 307) asm_opt->extract_list = opt.arg;
else if (c == 308) asm_opt->extract_iter = atoi(opt.arg);
else if (c == 309)
{
asm_opt->hom_global_coverage = atoi(opt.arg);
asm_opt->hom_global_coverage_set = 1;
}
else if (c == 310)
{
char* s = NULL;
asm_opt->recover_atg_cov_min = strtol(opt.arg, &s, 10);
if (*s == ',') asm_opt->recover_atg_cov_max = strtol(s + 1, &s, 10);
if(asm_opt->recover_atg_cov_min == -1 || asm_opt->recover_atg_cov_max == -1)
{
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 == 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);
else if (c == 315) get_hic_enzymes(opt.arg, &(asm_opt->hic_reads[1]), 0);
else if (c == 316) get_hic_enzymes(opt.arg, &(asm_opt->hic_enzymes), 1);
else if (c == 317) asm_opt->b_low_cov = atoi(opt.arg);
else if (c == 318) asm_opt->b_high_cov = atoi(opt.arg);
else if (c == 319) asm_opt->m_rate = atof(opt.arg);
else if (c == 320) asm_opt->flag -= HA_F_PARTITION, asm_opt->is_alt = 1;
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 == 326) asm_opt->n_weight = atoi(opt.arg);
else if (c == 327) asm_opt->misjoin_len = atol(opt.arg);
else if (c == 328) asm_opt->pur_global_coverage = atoi(opt.arg);
else if (c == 329) asm_opt->flag |= HA_F_FAST;
else if (c == 330) asm_opt->dp_e = atof(opt.arg);
else if (c == 331) asm_opt->max_kmer_cnt = atol(opt.arg);
else if (c == 332) asm_opt->hg_size = inter_gsize(opt.arg);
else if (c == 333) get_hic_enzymes(opt.arg, &(asm_opt->ar), 0);
else if (c == 334) asm_opt->flag |= HA_F_USKEW;
else if (c == 335) asm_opt->kpt_rate = atof(opt.arg);
else if (c == 336) asm_opt->ul_error_rate = atof(opt.arg);
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 == 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 == 341) asm_opt->bin_only = 1;
else if (c == 342) asm_opt->ul_clean_round = atol(opt.arg);
else if (c == 343) asm_opt->prt_dbg_gfa = 1;
else if (c == 344) asm_opt->integer_correct_round = atol(opt.arg);
else if (c == 345) asm_opt->dbg_ovec_cal = 1;
else if (c == 346) asm_opt->max_path_drop_rate = atof(opt.arg);
else if (c == 347) asm_opt->min_path_drop_rate = atof(opt.arg);
else if (c == 348) asm_opt->trio_cov_het_ovlp = 1;
else if (c == 349) asm_opt->ul_min_base = atol(opt.arg);
else if (c == 350) asm_opt->self_scaf = 1;
else if (c == 351) asm_opt->self_scaf_gap_max = atol(opt.arg);
else if (c == 352) get_hic_enzymes(opt.arg, &(asm_opt->sec_in), 0);
else if (c == 353) asm_opt->somatic_cov = atol(opt.arg);
else if (c == 354) asm_opt->telo_motif = opt.arg;
else if (c == 355) asm_opt->telo_pen = atol(opt.arg);
else if (c == 356) asm_opt->telo_drop = atol(opt.arg);
else if (c == 357) asm_opt->telo_mic_sc = atol(opt.arg);
else if (c == 358) asm_opt->max_contig_tip = atol(opt.arg);
else if (c == 359) {
asm_opt->is_ont = 1; asm_opt->max_ov_diff_ec = 0.07; asm_opt->is_sc = 1; ///asm_opt->mz_win = 37; asm_opt->k_mer_length = 37;
} /**else if (c == 360) {
asm_opt->is_sc = 1;
}**/ else if (c == 361) {
asm_opt->chemical_cov = atol(opt.arg);
} else if (c == 362) {
asm_opt->chemical_flank = atol(opt.arg);
///pending for integration
/**
} else if (c == 363) {
asm_opt->ul_mod = atol(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);
}
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 == ':')
{
fprintf(stderr, "[ERROR] missing option argument in \"%s\"\n", argv[opt.i - 1]);