/*************************************************************************************
                           The MIT License

   BWA-MEM2  (Sequence alignment using Burrows-Wheeler Transform),
   Copyright (C) 2019  Intel Corporation, Heng Li.

   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.

Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
         Heng Li <hli@jimmy.harvard.edu>
*****************************************************************************************/

#ifndef BWA_H_
#define BWA_H_

#include <stdint.h>
#include <stdio.h>
#include <zlib.h>
#include "bntseq.h"
#include "bwt.h"
#include "macro.h"

#define BWA_IDX_BWT 0x1
#define BWA_IDX_BNS 0x2
#define BWA_IDX_PAC 0x4
#define BWA_IDX_ALL 0x7

#define BWA_CTL_SIZE 0x10000

typedef struct {
	// bwt2_t   *bwt2;
	bwt_t    *bwt; // FM-index
	bntseq_t *bns; // information on the reference sequences
	uint8_t  *pac; // the actual 2-bit encoded reference sequences with 'N' converted to a random base

	int    is_shm;
	int64_t l_mem;
	uint8_t  *mem;
} bwaidx_t;


typedef struct {
	int l_seq, id;
	char *name, *comment, *seq, *qual, *sam;
	/* BAM output: per-read list of bam1_t* accumulated by worker threads
	 * (used by --bam and --meth alike). Typed as void* to keep htslib out
	 * of this header. */
	void **bams;
	int    n_bams;
	int    cap_bams;
} bseq1_t;

extern int bwa_verbose;
extern char bwa_rg_id[256];

#ifdef __cplusplus
extern "C" {
#endif
    bseq1_t *bseq_read_orig(int64_t chunk_size, int *n_, void *ks1_, void *ks2_, int64_t *s);

    bseq1_t *bseq_read(int64_t chunk_size, int *n_, void *ks1_,
                       void *ks2_, FILE* fpp, int len,
                       int64_t *sz);
    
    bseq1_t *bseq_read_one_fasta_file(int64_t chunk_size, int *n_, gzFile fp, int64_t *s);
    
    void bseq_classify(int n, bseq1_t *seqs, int m[2], bseq1_t *sep[2]);
    
	void bwa_fill_scmat(int a, int b, int8_t mat[25]);
    
	uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_,
							int64_t l_pac, const uint8_t *pac, int l_query,
							uint8_t *query, int64_t rb, int64_t re,
							int *score, int *n_cigar, int *NM);
	
	uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del,
							 int o_ins, int e_ins, int w_, int64_t l_pac,
							 const uint8_t *pac, int l_query, uint8_t *query,
							 int64_t rb, int64_t re, int *score,
							 int *n_cigar, int *NM);

	int bwa_idx_build(const char *fa, const char *prefix);

	char *bwa_idx_infer_prefix(const char *hint);
	bwt_t *bwa_idx_load_bwt(const char *hint);
	bwt2_t *bwa_idx_load_bwt2(const char *hint);
	
	bwaidx_t *bwa_idx_load_from_shm(const char *hint);
	bwaidx_t *bwa_idx_load_from_disk(const char *hint, int which);
	bwaidx_t *bwa_idx_load(const char *hint, int which);
	
	void bwa_idx_destroy(bwaidx_t *idx);
	void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line, FILE *fp);
	void bwa_print_sam_hdr2(const bntseq_t *bns, const char *idx_hdr_lines,
	                        const char *hdr_line, FILE *fp);
	char *bwa_load_hdr_from_index(const char *prefix);
	char *bwa_set_rg(const char *s);
	char *bwa_insert_header(const char *s, char *hdr);
	char *bwa_insert_header_file(FILE *fp, char *hdr);
#ifdef __cplusplus
}
#endif

#endif
