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/* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#pragma once
#include <stdint.h>
#include "bam-alignment.h"
typedef struct SAM2BAM_Parser SAM2BAM_Parser;
typedef struct RefNameLookupContext RefNameLookupContext; /**< caller defined **/
typedef bool (*RefNameLookupFunction)(RefNameLookupContext *ctx, int ch, int32_t *result, rc_t *rc);
/** implementation details **/
typedef bool (*SAM_parser_f)(SAM2BAM_Parser *, int, rc_t *, char const *, char const *);
typedef struct number_parser number_parser;
struct number_parser {
uint64_t mantissa;
int32_t exponent;
signed sgn:2;
unsigned shift:6; /**< [0 - 19] **/
unsigned state:23;
unsigned ok:1;
};
/** \brief parser state **/
struct SAM2BAM_Parser {
void *static_buffer;
size_t max_size;
bam_alignment *rslt; /**< on successful parse this is the result **/
size_t rslt_size; /**< on successful parse this is the size of the result **/
/* implementation details follow */
SAM_parser_f parser;
size_t field_out_size; /**< parsed size; only makes sense for some fields **/
size_t field_in_size; /**< input byte count for the current field (excluding delimters) **/
size_t record_chars; /**< input byte count for the whole record (including delimters but not line-feed) **/
int field;
int state; /**< each parser has its own idea of state; state is always 0 at start of field **/
bool cr;
size_t extraArrayCountPos;
number_parser numeric;
RefNameLookupFunction lookup;
RefNameLookupContext *lookup_ctx;
};
SAM2BAM_Parser *SAM2BAM_Parser_initialize(SAM2BAM_Parser *const self, void *const static_buffer, size_t const buffer_size, RefNameLookupFunction lookup, RefNameLookupContext *lookup_ctx);
SAM2BAM_Parser *SAM2BAM_Parser_parse( char const *const data
, unsigned const fields
, unsigned const *const offsets
, void *const static_buffer
, size_t const buffer_size
, RefNameLookupFunction lookup
, RefNameLookupContext *lookup_ctx
, rc_t *rc
);
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