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clean code

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This commit is contained in:
Haoyu Cheng
2019-12-26 02:26:24 -05:00
parent 7f9c73507d
commit 4ac9907e49
26 changed files with 1585 additions and 19325 deletions
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239
CommandLines.cpp
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@@ -4,23 +4,9 @@
#include "ketopt.h"
#include <sys/time.h>
#define VERSION "0.0.0.1"
char* read_file_name = NULL;
char* output_file_name = NULL;
int thread_num = 1;
int k_mer_length = 40;
int coverage = -1;
//int k_mer_min_freq = 9;
int k_mer_min_freq = 3;
//int k_mer_min_freq = 2;
int k_mer_max_freq = 66;
int load_index_from_disk = 0;
int write_index_to_disk = 0;
int number_of_round = 1;
int read_graph = 0;
int c_round = 4;
int adapterLen = 0;
char* required_read_name = NULL;
hifiasm_opt_t asm_opt;
double Get_T(void)
{
@@ -29,66 +15,197 @@ double Get_T(void)
return t.tv_sec+t.tv_usec/1000000.0;
}
void Print_H()
void Print_H(hifiasm_opt_t* asm_opt)
{
fprintf(stderr, "Incorrect options.\n");
fprintf(stderr, "./ccs_assembly -w -l -q NA12878_chr1_10M.fq -o output_NA12878_v11_2.fa -c 31 -k 40 -t 32 -r 2 -a 4 -z 0\n");
fprintf(stderr, "Usage: hifiasm [options] -q <input.fa> -o <output_asm>\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -q FILE input in the fastq(.gz)/fasta(.gz) formats\n");
fprintf(stderr, " -k FILE output assembly (in gfa format) and corrected reads (in fasta format)\n");
fprintf(stderr, " -t INT number of threads [%d]\n", asm_opt->thread_num);
fprintf(stderr, " -r INT round of correction [%d]\n", asm_opt->number_of_round);
fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round);
fprintf(stderr, " -k INT k-mer length [%d] (must be < 64)\n", asm_opt->k_mer_length);
fprintf(stderr, " -w write all overlaps to disk, can accelerate assembly next time\n");
fprintf(stderr, " -l load all overlaps from disk, can avoid overlap calculation\n");
fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " -p INT size of popped bubbles [%lld]\n", asm_opt->pop_bubble_size);
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, " -v show version number\n");
fprintf(stderr, " -h show help information\n");
fprintf(stderr, "Example: ./hifiasm -w -l -q NA12878.fq.gz -o NA12878.asm -k 40 -t 32 -r 2 -a 4 -z 0\n");
}
int CommandLine_process (int argc, char *argv[])
void init_opt(hifiasm_opt_t* asm_opt)
{
asm_opt->read_file_name = NULL;
asm_opt->output_file_name = NULL;
asm_opt->required_read_name = NULL;
asm_opt->thread_num = 1;
asm_opt->k_mer_length = 40;
asm_opt->k_mer_min_freq = 3;
asm_opt->k_mer_max_freq = 66;
asm_opt->load_index_from_disk = 0;
asm_opt->write_index_to_disk = 0;
asm_opt->number_of_round = 2;
asm_opt->adapterLen = 0;
asm_opt->clean_round = 4;
asm_opt->complete_threads = 0;
asm_opt->pop_bubble_size = 100000;
asm_opt->min_drop_rate = 0.2;
asm_opt->max_drop_rate = 0.8;
}
static ko_longopt_t longopts[] = {
{ "help", ko_no_argument, 100},
{ "seq", ko_required_argument, 101},
{ "output", ko_required_argument, 102},
{ "thread", ko_required_argument, 103},
{ "k_mer_min_freq", ko_required_argument, 104},
{ "k_mer_max_freq", ko_required_argument, 105},
{ "round", ko_required_argument, 106},
{ NULL, 0, 0 }
};
void clear_opt(hifiasm_opt_t* asm_opt, int last_round)
{
asm_opt->complete_threads = 0;
asm_opt->num_bases = 0;
asm_opt->num_corrected_bases = 0;
asm_opt->num_recorrected_bases = 0;
asm_opt->roundID = asm_opt->number_of_round - last_round;
}
ketopt_t opt = KETOPT_INIT;
int i, c;
while ((c = ketopt(&opt, argc, argv, 1, "ht:o:q:k:lwm:n:r:c:a:b:z:", longopts)) >= 0) {
if (c == 100 || c == 'h') Print_H();
else if (c == 103 || c == 't') thread_num = atoi(opt.arg);
else if (c == 102 || c == 'o') output_file_name = opt.arg;
else if (c == 101 || c == 'q') read_file_name = opt.arg;
else if (c == 104 || c == 'n') k_mer_min_freq = atoi(opt.arg);
else if (c == 105 || c == 'm') k_mer_max_freq = atoi(opt.arg);
else if (c == 106 || c == 'r') number_of_round = atoi(opt.arg);
else if (c == 'k') k_mer_length = atoi(opt.arg);
else if (c == 'l') load_index_from_disk = 1;
else if (c == 'w') write_index_to_disk = 1;
else if (c == 'c') coverage = atoi(opt.arg);
else if (c == 'a') c_round = atoi(opt.arg);
else if (c == 'z') adapterLen = atoi(opt.arg);
else if (c == 'b') required_read_name = opt.arg;
else if (c == '?') printf("unknown opt: -%c\n", opt.opt? opt.opt : ':');
else if (c == ':') printf("missing arg: -%c\n", opt.opt? opt.opt : ':');
int check_option(hifiasm_opt_t* asm_opt)
{
if(asm_opt->read_file_name == NULL)
{
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\n");
return 0;
}
if(asm_opt->thread_num < 1)
{
fprintf(stderr, "[ERROR] the number of threads must be > 0\n");
return 0;
}
if(asm_opt->number_of_round < 1)
{
fprintf(stderr, "[ERROR] the number of rounds for correction must be > 0\n");
return 0;
}
if(asm_opt->clean_round < 1)
{
fprintf(stderr, "[ERROR] the number of rounds for assembly cleaning must be > 0\n");
return 0;
}
if(asm_opt->adapterLen < 0)
{
fprintf(stderr, "[ERROR] the length of removed adapters must be >= 0\n");
return 0;
}
if(asm_opt->k_mer_length >= 64)
{
fprintf(stderr, "[ERROR] the length of k_mer must be < 64\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)\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)\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\n");
return 0;
}
if(asm_opt->pop_bubble_size < 0)
{
fprintf(stderr, "[ERROR] the size of popped bubbles must be >= 0\n");
return 0;
}
// fprintf(stderr, "input file: %s\n", asm_opt->read_file_name);
// 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 bubbles: %lld\n", asm_opt->pop_bubble_size);
return 1;
}
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:q:k:lwm:n:r:a:b:z:x:y:p:", 0)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
return 0;
}
else if (c == 'v')
{
fprintf(stderr, "[Version] %s\n", VERSION);
return 0;
}
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 == 'q') asm_opt->read_file_name = opt.arg;
else if (c == 'n') asm_opt->k_mer_min_freq = atoi(opt.arg);
else if (c == 'm') asm_opt->k_mer_max_freq = atoi(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 == 'l') asm_opt->load_index_from_disk = 1;
else if (c == 'w') asm_opt->write_index_to_disk = 1;
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 == '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->pop_bubble_size = atoll(opt.arg);
else if (c == ':')
{
fprintf(stderr, "[ERROR] missing option argument in \"%s\"\n", argv[opt.i - 1]);
return 0;
}
else if (c == '?')
{
fprintf(stderr, "[ERROR] unknown option in \"%s\"\n", argv[opt.i - 1]);
return 0;
}
}
if (argc == 1)
{
Print_H();
return 0;
}
if(coverage == -1)
{
fprintf(stdout, "Please set -c!\n");
Print_H();
Print_H(asm_opt);
return 0;
}
return 1;
return check_option(asm_opt);
}