hts.h

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/*  hts.h -- format-neutral I/O, indexing, and iterator API functions.

    Copyright (C) 2012-2014 Genome Research Ltd.
    Copyright (C) 2012 Broad Institute.

    Author: Heng Li <lh3@sanger.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.  */

#ifndef HTSLIB_HTS_H
#define HTSLIB_HTS_H

#include <stddef.h>
#include <stdint.h>

#ifndef HTS_BGZF_TYPEDEF
typedef struct BGZF BGZF;
#define HTS_BGZF_TYPEDEF
#endif
struct cram_fd;
struct hFILE;

#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
    size_t l, m;
    char *s;
} kstring_t;
#endif

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

#define hts_expand(type_t, n, m, ptr) if ((n) > (m)) { \
        (m) = (n); kroundup32(m); \
        (ptr) = (type_t*)realloc((ptr), (m) * sizeof(type_t)); \
    }
#define hts_expand0(type_t, n, m, ptr) if ((n) > (m)) { \
        int t = (m); (m) = (n); kroundup32(m); \
        (ptr) = (type_t*)realloc((ptr), (m) * sizeof(type_t)); \
        memset(((type_t*)ptr)+t,0,sizeof(type_t)*((m)-t)); \
    }

/************
 * File I/O *
 ************/

// Add new entries only at the end (but before the *_maximum entry)
// of these enums, as their numbering is part of the htslib ABI.

enum htsFormatCategory {
    unknown_category,
    sequence_data,    // Sequence data -- SAM, BAM, CRAM, etc
    variant_data,     // Variant calling data -- VCF, BCF, etc
    index_file,       // Index file associated with some data file
    region_list,      // Coordinate intervals or regions -- BED, etc
    category_maximum = 32767
};

enum htsExactFormat {
    unknown_format,
    binary_format, text_format,
    sam, bam, bai, cram, crai, vcf, bcfv1, bcf, csi, gzi, tbi, bed,
    format_maximum = 32767
};

enum htsCompression {
    no_compression, gzip, bgzf, custom,
    compression_maximum = 32767
};

typedef struct htsFormat {
    enum htsFormatCategory category;
    enum htsExactFormat format;
    enum htsCompression compression;
} htsFormat;

// Maintainers note htsFile cannot be an opaque structure because some of its
// fields are part of libhts.so's ABI (hence these fields must not be moved):
//  - fp is used in the public sam_itr_next()/etc macros
//  - is_bin is used directly in samtools <= 1.1 and bcftools <= 1.1
//  - is_write and is_cram are used directly in samtools <= 1.1
//  - fp is used directly in samtools (up to and including current develop)
//  - line is used directly in bcftools (up to and including current develop)
typedef struct {
    uint32_t is_bin:1, is_write:1, is_be:1, is_cram:1, dummy:28;
    int64_t lineno;
    kstring_t line;
    char *fn, *fn_aux;
    union {
        BGZF *bgzf;
        struct cram_fd *cram;
        struct hFILE *hfile;
        void *voidp;
    } fp;
    htsFormat format;
} htsFile;

// REQUIRED_FIELDS
enum sam_fields {
    SAM_QNAME = 0x00000001,
    SAM_FLAG  = 0x00000002,
    SAM_RNAME = 0x00000004,
    SAM_POS   = 0x00000008,
    SAM_MAPQ  = 0x00000010,
    SAM_CIGAR = 0x00000020,
    SAM_RNEXT = 0x00000040,
    SAM_PNEXT = 0x00000080,
    SAM_TLEN  = 0x00000100,
    SAM_SEQ   = 0x00000200,
    SAM_QUAL  = 0x00000400,
    SAM_AUX   = 0x00000800,
    SAM_RGAUX = 0x00001000,
};

enum cram_option {
    CRAM_OPT_DECODE_MD,
    CRAM_OPT_PREFIX,
    CRAM_OPT_VERBOSITY,
    CRAM_OPT_SEQS_PER_SLICE,
    CRAM_OPT_SLICES_PER_CONTAINER,
    CRAM_OPT_RANGE,
    CRAM_OPT_VERSION,
    CRAM_OPT_EMBED_REF,
    CRAM_OPT_IGNORE_MD5,
    CRAM_OPT_REFERENCE,
    CRAM_OPT_MULTI_SEQ_PER_SLICE,
    CRAM_OPT_NO_REF,
    CRAM_OPT_USE_BZIP2,
    CRAM_OPT_SHARED_REF,
    CRAM_OPT_NTHREADS,
    CRAM_OPT_THREAD_POOL,
    CRAM_OPT_USE_LZMA,
    CRAM_OPT_USE_RANS,
    CRAM_OPT_REQUIRED_FIELDS,
};

/**********************
 * Exported functions *
 **********************/

extern int hts_verbose;

extern const unsigned char seq_nt16_table[256];

extern const char seq_nt16_str[];

#ifdef __cplusplus
extern "C" {
#endif

const char *hts_version(void);

int hts_detect_format(struct hFILE *fp, htsFormat *fmt);

const char *hts_format_description(const htsFormat *format);

htsFile *hts_open(const char *fn, const char *mode);

htsFile *hts_hopen(struct hFILE *fp, const char *fn, const char *mode);

int hts_close(htsFile *fp);

const htsFormat *hts_get_format(htsFile *fp);

int hts_set_opt(htsFile *fp, enum cram_option opt, ...);

int hts_getline(htsFile *fp, int delimiter, kstring_t *str);
char **hts_readlines(const char *fn, int *_n);
char **hts_readlist(const char *fn, int is_file, int *_n);

int hts_set_threads(htsFile *fp, int n);

int hts_set_fai_filename(htsFile *fp, const char *fn_aux);

#ifdef __cplusplus
}
#endif

/************
 * Indexing *
 ************/

#define HTS_IDX_NOCOOR (-2)
#define HTS_IDX_START  (-3)
#define HTS_IDX_REST   (-4)
#define HTS_IDX_NONE   (-5)

#define HTS_FMT_CSI 0
#define HTS_FMT_BAI 1
#define HTS_FMT_TBI 2
#define HTS_FMT_CRAI 3

struct __hts_idx_t;
typedef struct __hts_idx_t hts_idx_t;

typedef struct {
    uint64_t u, v;
} hts_pair64_t;

typedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, int *beg, int *end);

typedef struct {
    uint32_t read_rest:1, finished:1, dummy:29;
    int tid, beg, end, n_off, i;
    uint64_t curr_off;
    hts_pair64_t *off;
    hts_readrec_func *readrec;
    struct {
        int n, m;
        int *a;
    } bins;
} hts_itr_t;

#ifdef __cplusplus
extern "C" {
#endif

    #define hts_bin_first(l) (((1<<(((l)<<1) + (l))) - 1) / 7)
    #define hts_bin_parent(l) (((l) - 1) >> 3)

    hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls);
    void hts_idx_destroy(hts_idx_t *idx);
    int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped);
    void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset);

    void hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt);
    hts_idx_t *hts_idx_load(const char *fn, int fmt);

    uint8_t *hts_idx_get_meta(hts_idx_t *idx, int *l_meta);
    void hts_idx_set_meta(hts_idx_t *idx, int l_meta, uint8_t *meta, int is_copy);

    int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped);
    uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx);

    const char *hts_parse_reg(const char *s, int *beg, int *end);
    hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec);
    void hts_itr_destroy(hts_itr_t *iter);

    typedef int (*hts_name2id_f)(void*, const char*);
    typedef const char *(*hts_id2name_f)(void*, int);
    typedef hts_itr_t *hts_itr_query_func(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec);

    hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec);
    int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data);
    const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values

#ifdef __cplusplus
}
#endif

static inline int hts_reg2bin(int64_t beg, int64_t end, int min_shift, int n_lvls)
{
    int l, s = min_shift, t = ((1<<((n_lvls<<1) + n_lvls)) - 1) / 7;
    for (--end, l = n_lvls; l > 0; --l, s += 3, t -= 1<<((l<<1)+l))
        if (beg>>s == end>>s) return t + (beg>>s);
    return 0;
}

static inline int hts_bin_bot(int bin, int n_lvls)
{
    int l, b;
    for (l = 0, b = bin; b; ++l, b = hts_bin_parent(b)); // compute the level of bin
    return (bin - hts_bin_first(l)) << (n_lvls - l) * 3;
}

/**************
 * Endianness *
 **************/

static inline int ed_is_big(void)
{
    long one= 1;
    return !(*((char *)(&one)));
}
static inline uint16_t ed_swap_2(uint16_t v)
{
    return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
}
static inline void *ed_swap_2p(void *x)
{
    *(uint16_t*)x = ed_swap_2(*(uint16_t*)x);
    return x;
}
static inline uint32_t ed_swap_4(uint32_t v)
{
    v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
    return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
}
static inline void *ed_swap_4p(void *x)
{
    *(uint32_t*)x = ed_swap_4(*(uint32_t*)x);
    return x;
}
static inline uint64_t ed_swap_8(uint64_t v)
{
    v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
    v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
    return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
}
static inline void *ed_swap_8p(void *x)
{
    *(uint64_t*)x = ed_swap_8(*(uint64_t*)x);
    return x;
}

#endif