minibwa/bseq.h at dist · nh13/minibwa

Repository navigation

History

#ifndef MB_BSEQ_H

#define MB_BSEQ_H

#include <stdint.h>

#include <string.h>

#include "kommon.h"

#ifdef __cplusplus

extern "C" {

#endif

struct mb_bseq_file_s;

typedef struct mb_bseq_file_s mb_bseq_file_t;

typedef struct {

uint64_t l_seq, id; // FIXME: bseq doesn't fully support 64-bit integers yet

char *name, *seq, *qual, *comment;

} mb_bseq1_t;

mb_bseq_file_t *mb_bseq_open(const char *fn);

void mb_bseq_close(mb_bseq_file_t *fp);

mb_bseq1_t *mb_bseq_read(mb_bseq_file_t *fp, int64_t chunk_size, int with_qual, int with_comment, int frag_mode, int min_cnt, int64_t max_chunk_size, int *n_);

mb_bseq1_t *mb_bseq_read_frag(int n_fp, mb_bseq_file_t **fp, int64_t chunk_size, int with_qual, int with_comment, int *n_);

int mb_bseq_eof(mb_bseq_file_t *fp);

static inline int mb_qname_len(const char *s)

{

int l;

l = strlen(s);

return l >= 3 && s[l-1] >= '0' && s[l-1] <= '9' && s[l-2] == '/'? l - 2 : l;

}

static inline int mb_qname_same(const char *s1, const char *s2)

{

int l1, l2;

l1 = mb_qname_len(s1);

l2 = mb_qname_len(s2);

return (l1 == l2 && strncmp(s1, s2, l1) == 0);

}

#ifdef __cplusplus

}

#endif

FilesExpand file tree

bseq.h

Latest commit

History

bseq.h

File metadata and controls