main.cpp

#include <stdio.h>
#include <stdlib.h>
#include "CommandLines.h"
#include "Process_Read.h"
#include "Assembly.h"
#include "Levenshtein_distance.h"
#include "htab.h"
#include "meta_util_debug.h"

int main(int argc, char *argv[])
{
	int i, ret;
	yak_reset_realtime();
    init_opt(&asm_opt);
    int ret_opt = CommandLine_process(argc, argv, &asm_opt);
    if (ret_opt==0) return 1;
    else if (ret_opt==2) return 0;  // help or version

	// debug modules
	if (asm_opt.mode_read_kmer_profile){
		hamt_read_kmer_profile(&asm_opt, &R_INF);
		return 0;
	}
	else if (asm_opt.is_dump_read_mask){
		hamt_dump_read_selection_mask(&asm_opt, &R_INF);
		return 0;
	}
	else if (asm_opt.is_dump_read_names){
		hamt_dump_selected_read_names(&asm_opt, &R_INF);
		return 0;
	}
	else if (asm_opt.is_dump_ovec_error_count){
		hamt_dump_ovec_read_error_count_and_kmerinfo(&asm_opt, &R_INF);
		return 0;
	}


	time_t rawtime;
    struct tm * timeinfo;
    time (&rawtime);
    timeinfo = localtime (&rawtime);
	fprintf(stderr, "[M::%s] Start: %s\n", __func__, asctime(timeinfo));

	// main
	if (asm_opt.is_use_exp_graph_cleaning){
		ret = hamt_assemble();
		fprintf(stderr, "[M::%s] Hifiasm code base version: %s\n", __func__, HA_VERSION);
		fprintf(stderr, "[M::%s] Hifiasm_meta version: %s\n", __func__, HAMT_VERSION);
	}else{
		fprintf(stderr, "[M::%s] (only for experiment) Disabled meta; note this is not identical to stable hifiasm\n", __func__);
		ret = ha_assemble();
		fprintf(stderr, "[M::%s] Hifiasm %s\n", __func__, HA_VERSION);
	}
    // (an alternative to gfa comment lines)
	char* logname = (char*)malloc(strlen(asm_opt.output_file_name)+100);
    sprintf(logname, "%s.cmd", asm_opt.output_file_name);
	FILE *fp = fopen(logname, "w");
	fprintf(fp, "#");
    for (int i=0; i<argc; i++){
        fprintf(fp, " %s", argv[i]);
    }
    fprintf(fp, "\n");
    fprintf(fp, "# Hifiasm code base version: %s\n",  HA_VERSION);
    fprintf(fp, "# Hifiasm_meta version: %s\n", HAMT_VERSION);
	fprintf(fp, "# Real time: %.3f sec; CPU: %.3f sec; Peak RSS: %.3f GB\n", yak_realtime(), yak_cputime(), yak_peakrss_in_gb());
	fclose(fp);
	free(logname);
	
	
	destory_opt(&asm_opt);

	fprintf(stderr, "[M::%s] CMD:", __func__);
	for (i = 0; i < argc; ++i)
		fprintf(stderr, " %s", argv[i]);
	fprintf(stderr, "\n[M::%s] Real time: %.3f sec; CPU: %.3f sec; Peak RSS: %.3f GB\n", __func__, yak_realtime(), yak_cputime(), yak_peakrss_in_gb());
    return ret;
}