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r211: added --write-paf/--write-ec/--skip-triobin

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Heng Li
2020-04-08 22:32:54 -04:00
parent 23dbfdef77
commit c41aae0630
8 changed files with 32 additions and 24 deletions
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CommandLines.cpp
+11 -7
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@@ -1,9 +1,9 @@
#include "CommandLines.h"
#include <zlib.h>
#include <stdlib.h>
#include <stdio.h>
#include "ketopt.h"
#include <sys/time.h>
#include "CommandLines.h"
#include "ketopt.h"
#define DEFAULT_OUTPUT "hifiasm.asm"
@@ -12,6 +12,9 @@ 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 },
{ 0, 0, 0 }
};
@@ -58,6 +61,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
void init_opt(hifiasm_opt_t* asm_opt)
{
asm_opt->flag = 0;
asm_opt->coverage = -1;
asm_opt->num_reads = 0;
asm_opt->read_file_names = NULL;
@@ -69,8 +73,6 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->k_mer_length = 51;
asm_opt->mz_win = 51;
asm_opt->bf_shift = 37;
asm_opt->no_HPC = 0;
asm_opt->no_kmer_flt = 0;
asm_opt->high_factor = 5.0f;
asm_opt->max_n_chain = 100;
asm_opt->k_mer_min_freq = 3;
@@ -92,7 +94,6 @@ 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->verbose_gfa = 0;
}
void destory_opt(hifiasm_opt_t* asm_opt)
@@ -331,7 +332,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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->no_kmer_flt = 1;
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);
@@ -345,7 +346,10 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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 == 301) asm_opt->verbose_gfa = 1;
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 == ':')
{
fprintf(stderr, "[ERROR] missing option argument in \"%s\"\n", argv[opt.i - 1]);