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#ifndef BAMLITE_H_
#define BAMLITE_H_
#include <stdint.h>
#include <zlib.h>
typedef gzFile bamFile;
#define bam_open(fn, mode) gzopen(fn, mode)
#define bam_dopen(fd, mode) gzdopen(fd, mode)
#define bam_close(fp) gzclose(fp)
#define bam_read(fp, buf, size) 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))
#endif
#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*)calloc(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" {
#endif
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
}
#endif
#endif