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/* The MIT License
Copyright (c) 2010 Broad Institute
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.
*/
/* Contact: Heng Li <[email protected]> */
#ifndef BCF_H
#define BCF_H
#define BCF_VERSION "0.1.19-44428cd"
#include <stdint.h>
#include <zlib.h>
#ifndef BCF_LITE
#include "bgzf.h"
typedef BGZF *bcfFile;
#else
typedef gzFile bcfFile;
#define bgzf_open(fn, mode) gzopen(fn, mode)
#define bgzf_fdopen(fd, mode) gzdopen(fd, mode)
#define bgzf_close(fp) gzclose(fp)
#define bgzf_read(fp, buf, len) gzread(fp, buf, len)
#define bgzf_write(fp, buf, len)
#define bgzf_flush(fp)
#endif
/*
A member in the structs below is said to "primary" if its content
cannot be inferred from other members in any of structs below; a
member is said to be "derived" if its content can be derived from
other members. For example, bcf1_t::str is primary as this comes from
the input data, while bcf1_t::info is derived as it can always be
correctly set if we know bcf1_t::str. Derived members are for quick
access to the content and must be synchronized with the primary data.
*/
typedef struct {
uint32_t fmt; // format of the block, set by bcf_str2int().
int len; // length of data for each individual
void *data; // concatenated data
// derived info: fmt, len (<-bcf1_t::fmt)
} bcf_ginfo_t;
typedef struct {
int32_t tid, pos; // refID and 0-based position
int32_t l_str, m_str; // length and the allocated size of ->str
float qual; // SNP quality
char *str; // concatenated string of variable length strings in VCF (from col.2 to col.7)
char *ref, *alt, *flt, *info, *fmt; // they all point to ->str; no memory allocation
int n_gi, m_gi; // number and the allocated size of geno fields
bcf_ginfo_t *gi; // array of geno fields
int n_alleles, n_smpl; // number of alleles and samples
// derived info: ref, alt, flt, info, fmt (<-str), n_gi (<-fmt), n_alleles (<-alt), n_smpl (<-bcf_hdr_t::n_smpl)
uint8_t *ploidy; // ploidy of all samples; if NULL, ploidy of 2 is assumed.
} bcf1_t;
typedef struct {
int32_t n_ref, n_smpl; // number of reference sequences and samples
int32_t l_nm; // length of concatenated sequence names; 0 padded
int32_t l_smpl; // length of concatenated sample names; 0 padded
int32_t l_txt; // length of header text (lines started with ##)
char *name, *sname, *txt; // concatenated sequence names, sample names and header text
char **ns, **sns; // array of sequence and sample names; point to name and sname, respectively
// derived info: n_ref (<-name), n_smpl (<-sname), ns (<-name), sns (<-sname)
} bcf_hdr_t;
typedef struct {
int is_vcf; // if the file in operation is a VCF
void *v; // auxillary data structure for VCF
bcfFile fp; // file handler for BCF
} bcf_t;
struct __bcf_idx_t;
typedef struct __bcf_idx_t bcf_idx_t;
#ifdef __cplusplus
extern "C" {
#endif
// open a BCF file; for BCF file only
bcf_t *bcf_open(const char *fn, const char *mode);
// close file
int bcf_close(bcf_t *b);
// read one record from BCF; return -1 on end-of-file, and <-1 for errors
int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b);
// call this function if b->str is changed
int bcf_sync(bcf1_t *b);
// write a BCF record
int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b);
// read the BCF header; BCF only
bcf_hdr_t *bcf_hdr_read(bcf_t *b);
// write the BCF header
int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h);
// set bcf_hdr_t::ns and bcf_hdr_t::sns
int bcf_hdr_sync(bcf_hdr_t *b);
// destroy the header
void bcf_hdr_destroy(bcf_hdr_t *h);
// destroy a record
int bcf_destroy(bcf1_t *b);
// BCF->VCF conversion
char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b);
// append more info
int bcf_append_info(bcf1_t *b, const char *info, int l);
// remove tag
int remove_tag(char *string, const char *tag, char delim);
// remove info tag, string is the kstring holder of bcf1_t.str
void rm_info(kstring_t *string, const char *key);
// copy
int bcf_cpy(bcf1_t *r, const bcf1_t *b);
// open a VCF or BCF file if "b" is set in "mode"
bcf_t *vcf_open(const char *fn, const char *mode);
// close a VCF/BCF file
int vcf_close(bcf_t *bp);
// read the VCF/BCF header
bcf_hdr_t *vcf_hdr_read(bcf_t *bp);
// read the sequence dictionary from a separate file; required for VCF->BCF conversion
int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn);
// read a VCF/BCF record; return -1 on end-of-file and <-1 for errors
int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
// write the VCF header
int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h);
// write a VCF record
int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
// keep the first n alleles and discard the rest
int bcf_shrink_alt(bcf1_t *b, int n);
// keep the masked alleles and discard the rest
void bcf_fit_alt(bcf1_t *b, int mask);
// convert GL to PL
int bcf_gl2pl(bcf1_t *b);
// if the site is an indel
int bcf_is_indel(const bcf1_t *b);
bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list);
int bcf_subsam(int n_smpl, int *list, bcf1_t *b);
// move GT to the first FORMAT field
int bcf_fix_gt(bcf1_t *b);
// update PL generated by old samtools
int bcf_fix_pl(bcf1_t *b);
// convert PL to GLF-like 10-likelihood GL
int bcf_gl10(const bcf1_t *b, uint8_t *gl);
// convert up to 4 INDEL alleles to GLF-like 10-likelihood GL
int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl);
// string hash table
void *bcf_build_refhash(bcf_hdr_t *h);
void bcf_str2id_destroy(void *_hash);
void bcf_str2id_thorough_destroy(void *_hash);
int bcf_str2id_add(void *_hash, const char *str);
int bcf_str2id(void *_hash, const char *str);
void *bcf_str2id_init();
// indexing related functions
int bcf_idx_build(const char *fn);
uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg);
int bcf_parse_region(void *str2id, const char *str, int *tid, int *begin, int *end);
bcf_idx_t *bcf_idx_load(const char *fn);
void bcf_idx_destroy(bcf_idx_t *idx);
#ifdef __cplusplus
}
#endif
static inline uint32_t bcf_str2int(const char *str, int l)
{
int i;
uint32_t x = 0;
for (i = 0; i < l && i < 4; ++i) {
if (str[i] == 0) return x;
x = x<<8 | str[i];
}
return x;
}
#endif
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