tbx.h

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#ifndef TBX_H
#define TBX_H

#include "hts.h"

#define TBX_MAX_SHIFT 31

#define TBX_GENERIC 0
#define TBX_SAM     1
#define TBX_VCF     2
#define TBX_UCSC    0x10000

typedef struct {
        int32_t preset;
        int32_t sc, bc, ec; // seq col., beg col. and end col.
        int32_t meta_char, line_skip;
} tbx_conf_t;

typedef struct {
        tbx_conf_t conf;
        hts_idx_t *idx;
        void *dict;
} tbx_t;

extern tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sam, tbx_conf_vcf;

#ifdef __cplusplus
extern "C" {
#endif

        #define tbx_itr_destroy(iter) hts_itr_destroy(iter)
        #define tbx_itr_queryi(tbx, tid, beg, end) hts_itr_query((tbx)->idx, (tid), (beg), (end), tbx_readrec)
        #define tbx_itr_querys(tbx, s) hts_itr_querys((tbx)->idx, (s), (hts_name2id_f)(tbx_name2id), (tbx), hts_itr_query, tbx_readrec)
        #define tbx_itr_next(htsfp, tbx, itr, r) hts_itr_next(hts_get_bgzfp(htsfp), (itr), (r), (tbx))
        #define tbx_bgzf_itr_next(bgzfp, tbx, itr, r) hts_itr_next((bgzfp), (itr), (r), (tbx))

        int tbx_name2id(tbx_t *tbx, const char *ss);

        /* Internal helper function used by tbx_itr_next() */
        BGZF *hts_get_bgzfp(htsFile *fp);
        int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end);

        int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf);
        tbx_t *tbx_index_load(const char *fn);
        const char **tbx_seqnames(tbx_t *tbx, int *n);  // free the array but not the values
        void tbx_destroy(tbx_t *tbx);

#ifdef __cplusplus
}
#endif

#endif