#ifndef BAMLITE_H_

#define BAMLITE_H_

#include <stdint.h>

#include <zlib.h>

#include "utils.h"

typedef gzFile bamFile;

#define bam_open(fn, mode) xzopen(fn, mode)

#define bam_dopen(fd, mode) gzdopen(fd, mode)

#define bam_close(fp) err_gzclose(fp)

#define bam_read(fp, buf, size) err_gzread(fp, buf, size)

typedef struct {

int32_t n_targets;

char **target_name;

uint32_t *target_len;

size_t l_text, n_text;

char *text;

} bam_header_t;

#define BAM_FPAIRED 1

#define BAM_FPROPER_PAIR 2

#define BAM_FUNMAP 4

#define BAM_FMUNMAP 8

#define BAM_FREVERSE 16

#define BAM_FMREVERSE 32

#define BAM_FREAD1 64

#define BAM_FREAD2 128

#define BAM_FSECONDARY 256

#define BAM_FQCFAIL 512

#define BAM_FDUP 1024

#define BAM_CIGAR_SHIFT 4

#define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1)

#define BAM_CMATCH 0

#define BAM_CINS 1

#define BAM_CDEL 2

#define BAM_CREF_SKIP 3

#define BAM_CSOFT_CLIP 4

#define BAM_CHARD_CLIP 5

#define BAM_CPAD 6

typedef struct {

int32_t tid;

int32_t pos;

uint32_t bin:16, qual:8, l_qname:8;

uint32_t flag:16, n_cigar:16;

int32_t l_qseq;

int32_t mtid;

int32_t mpos;

int32_t isize;

} bam1_core_t;

typedef struct {

bam1_core_t core;

int l_aux, data_len, m_data;

uint8_t *data;

} bam1_t;

#ifndef kroundup32

#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))

#define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)

#define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)

#define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))

#define bam1_qname(b) ((char*)((b)->data))

#define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)

#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))

#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)

#define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)->core.l_qseq + 1)/2)

#define bam_init1() ((bam1_t*)xcalloc(1, sizeof(bam1_t)))

#define bam_destroy1(b) do { \

if (b) { free((b)->data); free(b); } \

} while (0)

extern int bam_is_be;

#ifdef __cplusplus

extern "C" {

bam_header_t *bam_header_init(void);

void bam_header_destroy(bam_header_t *header);

bam_header_t *bam_header_read(bamFile fp);

int bam_read1(bamFile fp, bam1_t *b);

#ifdef __cplusplus

}