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73b5ef676947e48eb6a7890ef145b37076b44d01
hifiasm/CommandLines.cpp
chhylp123 73b5ef6769 bubble phasing
2020-11-21 20:50:31 -05:00

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#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"
#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_no_argument, 305 },
{ "max-od-final", ko_no_argument, 306 },
{ "ex-list", ko_required_argument, 307 },
{ "ex-iter", ko_required_argument, 308 },
{ "purge-cov", ko_required_argument, 309 },
{ "pri-range", ko_required_argument, 310 },
{ "high-het", ko_no_argument, 311 },
{ "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 },
{ 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, " -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, " 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, " --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, " 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, " -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, "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");
}
void init_opt(hifiasm_opt_t* asm_opt)
{
memset(asm_opt, 0, sizeof(hifiasm_opt_t));
asm_opt->flag = 0;
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_files[0] = NULL;
asm_opt->hic_files[1] = NULL;
asm_opt->hic_enzymes = NULL;
asm_opt->thread_num = 1;
asm_opt->k_mer_length = 51;
asm_opt->hic_mer_length = 31;
asm_opt->mz_win = 51;
asm_opt->bf_shift = 37;
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 = 100;
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->adapterLen = 0;
asm_opt->clean_round = 4;
asm_opt->small_pop_bubble_size = 100000;
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->min_cnt = 2;
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_overlap_len = 1;
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 = 70;
///asm_opt->bub_mer_length = 3;
asm_opt->bub_mer_length = 10;
}
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)
{
int i;
for (i = 0; i < asm_opt->hic_enzymes->n; i++)
{
free(asm_opt->hic_enzymes->a[i]);
}
free(asm_opt->hic_enzymes->a);
free(asm_opt->hic_enzymes->l);
free(asm_opt->hic_enzymes);
}
}
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);
}
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;
}
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 > 2)
{
fprintf(stderr, "[ERROR] the level of purge-dup should be [0, 2] (-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] purge duplication coverage threshold should be >= 0 (--purge-cov)\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_files[0] != NULL && check_file(asm_opt->hic_files[0], "HIC1") == 0) return 0;
if(asm_opt->hic_files[1] != NULL && check_file(asm_opt->hic_files[1], "HIC2") == 0) return 0;
if(asm_opt->hic_files[0] != NULL && asm_opt->hic_files[1] == NULL)
{
fprintf(stderr, "[ERROR] lack r2 of HiC reads (--h2)\n");
return 0;
}
if(asm_opt->hic_files[1] != NULL && asm_opt->hic_files[0] == NULL)
{
fprintf(stderr, "[ERROR] lack r1 of HiC reads (--h1)\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;
}
// 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_rate: %f\n", asm_opt->purge_simi_rate);
// fprintf(stderr, "purge_overlap_len: %d\n", asm_opt->purge_overlap_len);
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;
gzFile dfp;
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);
}
gzclose(dfp);
}
}
void get_hic_enzymes(char *argv, hifiasm_opt_t* asm_opt)
{
int i, k, pre_i, len = strlen(argv);
asm_opt->hic_enzymes = (enzyme*)calloc(1, sizeof(enzyme));
if(len == 0)
{
asm_opt->hic_enzymes->n = 0;
asm_opt->hic_enzymes->l = NULL;
asm_opt->hic_enzymes->a = NULL;
return;
}
asm_opt->hic_enzymes->n = 1;
for (i = pre_i = 0; i < len; i++)
{
if(argv[i] == ',')
{
asm_opt->hic_enzymes->n++;
continue;
}
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')
{
asm_opt->hic_enzymes->n = 0;
asm_opt->hic_enzymes->l = NULL;
asm_opt->hic_enzymes->a = NULL;
return;
}
}
asm_opt->hic_enzymes->l = (int*)calloc(asm_opt->hic_enzymes->n, sizeof(int));
asm_opt->hic_enzymes->a = (char**)calloc(asm_opt->hic_enzymes->n, sizeof(char*));
for (i = pre_i = k = 0; i < len; i++)
{
if(argv[i] == ',')
{
asm_opt->hic_enzymes->l[k] = i - pre_i;
asm_opt->hic_enzymes->a[k] = (char*)malloc(sizeof(char)*(asm_opt->hic_enzymes->l[k]+1));
memcpy(asm_opt->hic_enzymes->a[k], argv + pre_i, asm_opt->hic_enzymes->l[k]);
asm_opt->hic_enzymes->a[k][asm_opt->hic_enzymes->l[k]] = '\0';
pre_i = i + 1;
k++;
}
}
asm_opt->hic_enzymes->l[k] = i - pre_i;
asm_opt->hic_enzymes->a[k] = (char*)malloc(sizeof(char)*(asm_opt->hic_enzymes->l[k]+1));
memcpy(asm_opt->hic_enzymes->a[k], argv + pre_i, asm_opt->hic_enzymes->l[k]);
asm_opt->hic_enzymes->a[k][asm_opt->hic_enzymes->l[k]] = '\0';
}
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: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 == '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') asm_opt->flag |= HA_F_BAN_POST_JOIN;
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);
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) asm_opt->hic_files[0] = opt.arg;
else if (c == 315) asm_opt->hic_files[1] = opt.arg;
else if (c == 316) get_hic_enzymes(opt.arg, asm_opt);
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 = 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]);
return 1;
}
else if (c == '?')
{
fprintf(stderr, "[ERROR] unknown option in \"%s\"\n", argv[opt.i - 1]);
return 1;
}
}
if (argc == opt.ind)
{
Print_H(asm_opt);
return 0;
}
get_queries(argc, argv, &opt, asm_opt);
return check_option(asm_opt);
}
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