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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 <stddef.h>
#include <stdint.h>
#include <stdbool.h>
#define HAVE_C99_FAM 1
#ifdef _MSC_VER /* && _MSC_VER < ??? newer version support this language feature */
#define HAVE_C99_FAM 0
#endif
/* this struct is packed and little-endian
* iow, multi-byte members are little-endian and not aligned
*/
struct bam_alignment_s {
uint8_t rID[4]; /* int32_t */
uint8_t pos[4]; /* int32_t */
uint8_t read_name_len;
uint8_t mapQual;
uint8_t bin[2]; /* uint16_t */
uint8_t n_cigars[2]; /* uint16_t */
uint8_t flags[2]; /* uint16_t */
uint8_t read_len[4]; /* int32_t */
uint8_t mate_rID[4]; /* int32_t */
uint8_t mate_pos[4]; /* int32_t */
uint8_t ins_size[4]; /* int32_t */
/* uint8_t read_name[read_name_len]; // nul-terminated; length includes nul
* uint8_t cigar[4 * n_cigars]; // uint32_t
* uint8_t seq[(read_len + 1) / 2]; // packed binary 4na
* uint8_t qual[read_len];
* uint8_t extra[];
*/
#if HAVE_C99_FAM
char read_name[];
#else
/* the standard says it is undefined behavior to access beyond the declared
* end of a struct, but older Microsoft compilers don't support the proper
* syntax, hence this hack
*/
char read_name[1];
#endif
};
/*#define BAM_ALIGNMENT_MIN_SIZE offsetof(struct bam_alignment_s, read_name[0])*/
#define BAM_ALIGNMENT_MIN_SIZE (sizeof(struct bam_alignment_s))
typedef union bam_alignment_u {
struct bam_alignment_s cooked;
uint8_t raw[BAM_ALIGNMENT_MIN_SIZE]; /* FAM is for structs */
} bam_alignment;
static inline uint16_t bam_alignment_get_u16(uint8_t const *const value) {
return ((uint16_t)value[0]) | (((uint16_t)value[1]) << 8);
}
static inline int16_t bam_alignment_get_i16(uint8_t const *const value) {
union { uint16_t u; int16_t i; } y;
y.u = bam_alignment_get_u16(value);
return y.i;
}
static inline uint32_t bam_alignment_get_u32(uint8_t const *const value) {
return ((uint32_t)bam_alignment_get_u16(value))
| (((uint32_t)bam_alignment_get_u16(value + 2)) << 16);
}
static inline int32_t bam_alignment_get_i32(uint8_t const *const value) {
union { uint32_t u; int32_t i; } y;
y.u = bam_alignment_get_u32(value);
return y.i;
}
static inline int32_t bam_alignment_rID(bam_alignment const *const s) {
return bam_alignment_get_i32(s->cooked.rID);
}
static inline int32_t bam_alignment_pos(bam_alignment const *const s) {
return bam_alignment_get_i32(s->cooked.pos);
}
static inline size_t bam_alignment_cigars(bam_alignment const *const s) {
return bam_alignment_get_u16(s->cooked.n_cigars);
}
static inline size_t bam_alignment_read_len(bam_alignment const *const s) {
return bam_alignment_get_i32(s->cooked.read_len);
}
static inline size_t bam_alignment_offsetof_cigars(bam_alignment const *const s) {
return BAM_ALIGNMENT_MIN_SIZE + (size_t)s->cooked.read_name_len;
}
static inline size_t bam_alignment_offsetof_sequence(bam_alignment const *const s) {
return bam_alignment_offsetof_cigars(s) + 4 * bam_alignment_cigars(s);
}
static inline size_t bam_alignment_offsetof_quality(bam_alignment const *const s) {
return bam_alignment_offsetof_sequence(s) + (bam_alignment_read_len(s) + 1) / 2;
}
static inline size_t bam_alignment_offsetof_extra(bam_alignment const *const s) {
return bam_alignment_offsetof_quality(s) + bam_alignment_read_len(s);
}
struct offset_size_s {
unsigned offset;
unsigned size; /* this is the total length of the tag; length of data is size - 3 */
};
struct BAM_Alignment {
struct BAM_File *parent;
bam_alignment const *data;
uint8_t *storage;
uint64_t keyId;
bool wasInserted;
unsigned datasize;
unsigned cigar;
unsigned seq;
unsigned qual;
unsigned numExtra;
unsigned hasColor;
unsigned platform;
#if HAVE_C99_FAM
struct offset_size_s extra[];
#else
struct offset_size_s extra[1];
#endif
};
#define BAM_ALIGNMENT_SIZE(NUM_EXTRA) offsetof(struct BAM_Alignment, extra[NUM_EXTRA])
#define BAM_ALIGNMENT_MAX_EXTRA(BYTES) ((BYTES - BAM_ALIGNMENT_SIZE(0)) / sizeof(struct offset_size_s))
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