/* The MIT License

   Copyright (c) 2018-     Dana-Farber Cancer Institute
                 2009-2018 Broad Institute, Inc.
                 2008-2009 Genome Research Ltd. (GRL)

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/
#include <stdio.h>
#include <string.h>
#include "kstring.h"
#include "utils.h"

#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.19-r1273"
#endif

int bwa_fa2pac(int argc, char *argv[]);
int bwa_pac2bwt(int argc, char *argv[]);
int bwa_bwtupdate(int argc, char *argv[]);
int bwa_bwt2sa(int argc, char *argv[]);
int bwa_index(int argc, char *argv[]);
int bwt_bwtgen_main(int argc, char *argv[]);

int bwa_aln(int argc, char *argv[]);
int bwa_sai2sam_se(int argc, char *argv[]);
int bwa_sai2sam_pe(int argc, char *argv[]);

int bwa_bwtsw2(int argc, char *argv[]);

int main_fastmap(int argc, char *argv[]);
int main_mem(int argc, char *argv[]);
int main_shm(int argc, char *argv[]);

int main_pemerge(int argc, char *argv[]);
int main_maxk(int argc, char *argv[]);

int bwa_bwt2kmer(int argc, char* argv[]);  // create kmer-index from bwt
int bwa_bwt2fullbytesa(int argc, char* argv[]);  // create full byte-based Suffix-Array
int bwa_bwt2hyb(int argc, char* argv[]); // create hybrid-index
int bwa_pac2hybpac(int argc, char* argv[]);  // convert pac to hyb.pac
int bwa_extract_sa(int argc, char* argv[]);  // extract suffix array from non-sampled suffix array
int bwa_extract_byte_sa(int argc, char* argv[]);  // extract suffix array from non-sampled suffix array
int main_shm_hyb(int argc, char* argv[]); // manage hybrid index in shared memory

int hyb_test(int argc, char* argv[]);  // for test

static int usage()
{
	fprintf(stderr, "\n");
	fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
	fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
	fprintf(stderr, "Contact: Heng Li <hli@ds.dfci.harvard.edu>\n\n");
	fprintf(stderr, "Usage:   bwa <command> [options]\n\n");
	fprintf(stderr, "Command: index          index sequences in the FASTA format\n");
	fprintf(stderr, "         mem            BWA-MEM algorithm\n");
	fprintf(stderr, "         fastmap        identify super-maximal exact matches\n");
	fprintf(stderr, "         pemerge        merge overlapping paired ends (EXPERIMENTAL)\n");
	fprintf(stderr, "         aln            gapped/ungapped alignment\n");
	fprintf(stderr, "         samse          generate alignment (single ended)\n");
	fprintf(stderr, "         sampe          generate alignment (paired ended)\n");
	fprintf(stderr, "         bwasw          BWA-SW for long queries (DEPRECATED)\n");
	fprintf(stderr, "\n");
	fprintf(stderr, "         shm            manage indices in shared memory\n");
	fprintf(stderr, "         fa2pac         convert FASTA to PAC format\n");
	fprintf(stderr, "         pac2bwt        generate BWT from PAC\n");
	fprintf(stderr, "         pac2bwtgen     alternative algorithm for generating BWT\n");
	fprintf(stderr, "         bwtupdate      update .bwt to the new format\n");
	fprintf(stderr, "         bwt2sa         generate SA from BWT and Occ\n");
    fprintf(stderr, "         bwt2fullbytesa generate SA(using byte array) from BWT and Occ\n");
    fprintf(stderr, "         bwt2kmer       generate kmer hash index from bwt to accelarate the first 14 bases in seeding process.\n");
    fprintf(stderr, "         bwt2hyb        generate hybrid index from BWT\n");
    fprintf(stderr, "         pac2hybpac     convert pac to hyb.pac\n");
    fprintf(stderr, "         extractsa      generate sa from full byte suffix array\n");
    fprintf(stderr, "         extractbytesa  generate byte sa from full byte suffix array\n");
    fprintf(stderr, "         hybshm         manage hybrid index in shared memory\n");
    fprintf(stderr, "\n");
	fprintf(stderr,
"Note: To use BWA, you need to first index the genome with `bwa index'.\n"
"      There are three alignment algorithms in BWA: `mem', `bwasw', and\n"
"      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'\n"
"      first. Please `man ./bwa.1' for the manual.\n\n");
	return 1;
}

int main(int argc, char *argv[])
{
	extern char *bwa_pg;
	int i, ret;
	double t_real;
	kstring_t pg = {0,0,0};
	t_real = realtime();
	ksprintf(&pg, "@PG\tID:bwa\tPN:bwa\tVN:%s\tCL:%s", PACKAGE_VERSION, argv[0]);
	for (i = 1; i < argc; ++i) ksprintf(&pg, " %s", argv[i]);
	bwa_pg = pg.s;
	if (argc < 2) return usage();
	if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1);
	else if (strcmp(argv[1], "pac2bwt") == 0) ret = bwa_pac2bwt(argc-1, argv+1);
	else if (strcmp(argv[1], "pac2bwtgen") == 0) ret = bwt_bwtgen_main(argc-1, argv+1);
	else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1);
	else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1);
	else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1);
	else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1);
	else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1);
	else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1);
	else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
	else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
	else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
	else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
	else if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1);
	else if (strcmp(argv[1], "shm") == 0) ret = main_shm(argc-1, argv+1);
	else if (strcmp(argv[1], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
	else if (strcmp(argv[1], "maxk") == 0) ret = main_maxk(argc-1, argv+1);
    else if (strcmp(argv[1], "bwt2fullbytesa") == 0) ret = bwa_bwt2fullbytesa(argc - 1, argv + 1);
	else if (strcmp(argv[1], "bwt2kmer") == 0) ret = bwa_bwt2kmer(argc - 1, argv + 1);
	else if (strcmp(argv[1], "bwt2hyb") == 0) ret = bwa_bwt2hyb(argc - 1, argv + 1);
	else if (strcmp(argv[1], "pac2hybpac") == 0) ret = bwa_pac2hybpac(argc - 1, argv + 1);
	else if (strcmp(argv[1], "extractsa") == 0) ret = bwa_extract_sa(argc - 1, argv + 1);
	else if (strcmp(argv[1], "extractbytesa") == 0) ret = bwa_extract_byte_sa(argc - 1, argv + 1);
    else if (strcmp(argv[1], "hybshm") == 0) ret = main_shm_hyb(argc - 1, argv + 1);
    else if (strcmp(argv[1], "hybtest") == 0) ret = hyb_test(argc - 1, argv + 1);
    else {
		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
		return 1;
	}
	err_fflush(stdout);
	err_fclose(stdout);
	if (ret == 0) {
		fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION);
		fprintf(stderr, "[%s] CMD:", __func__);
		for (i = 0; i < argc; ++i)
			fprintf(stderr, " %s", argv[i]);
		fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
	}
	free(bwa_pg);
	return ret;
}