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This commit is contained in:
Haoyu Cheng
2019-12-28 04:45:53 -05:00
parent 8f549c1c16
commit 1523d10291
11 changed files with 831 additions and 107 deletions
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CommandLines.cpp
+51 -14
View File
@@ -1,10 +1,12 @@
#include "CommandLines.h"
#include <zlib.h>
#include <stdlib.h>
#include <stdio.h>
#include "ketopt.h"
#include <sys/time.h>
#define VERSION "0.0.0.1"
#define DEFAULT_OUTPUT "hifiasm.asm"
hifiasm_opt_t asm_opt;
@@ -17,38 +19,39 @@ double Get_T(void)
void Print_H(hifiasm_opt_t* asm_opt)
{
fprintf(stderr, "Usage: hifiasm [options] -q <input.fa> -o <output_asm>\n");
fprintf(stderr, "Usage: hifiasm [options] <in_1.fq> <in_2.fq> <...>\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, " -q FILE input in the fastq(.gz)/fasta(.gz) formats\n");
fprintf(stderr, " -o FILE output assembly (in gfa format) and corrected reads [%s]\n", asm_opt->output_file_name);
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, " -w write all overlaps to disk, can accelerate assembly next time [%d]\n", asm_opt->write_index_to_disk);
fprintf(stderr, " -l load all overlaps from disk, can avoid overlap calculation [%d]\n", asm_opt->load_index_from_disk);
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\n");
fprintf(stderr, "Example: ./hifiasm -w -l -o NA12878.asm -k 40 -t 32 -r 2 NA12878.fq.gz\n");
}
void init_opt(hifiasm_opt_t* asm_opt)
{
asm_opt->read_file_name = NULL;
asm_opt->output_file_name = NULL;
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->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->load_index_from_disk = 1;
asm_opt->write_index_to_disk = 1;
asm_opt->number_of_round = 2;
asm_opt->adapterLen = 0;
asm_opt->clean_round = 4;
@@ -58,6 +61,14 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->max_drop_rate = 0.8;
}
void destory_opt(hifiasm_opt_t* asm_opt)
{
if(asm_opt->read_file_names != NULL)
{
free(asm_opt->read_file_names);
}
}
void clear_opt(hifiasm_opt_t* asm_opt, int last_round)
{
asm_opt->complete_threads = 0;
@@ -70,7 +81,7 @@ void clear_opt(hifiasm_opt_t* asm_opt, int last_round)
int check_option(hifiasm_opt_t* asm_opt)
{
if(asm_opt->read_file_name == NULL)
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;
@@ -141,7 +152,7 @@ int check_option(hifiasm_opt_t* asm_opt)
}
// fprintf(stderr, "input file: %s\n", asm_opt->read_file_name);
// 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);
@@ -155,6 +166,32 @@ int check_option(hifiasm_opt_t* asm_opt)
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);
}
}
int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
{
@@ -162,7 +199,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
int c;
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:q:k:lwm:n:r:a:b:z:x:y:p:", 0)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:lwm:n:r:a:b:z:x:y:p:", 0)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
@@ -175,7 +212,6 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
}
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);
@@ -206,6 +242,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
return 0;
}
get_queries(argc, argv, &opt, asm_opt);
return check_option(asm_opt);
}