X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fbcf.h;fp=bcftools%2Fbcf.h;h=36578956bbae06d4c216c121a2ddb3a94cad94d8;hp=0000000000000000000000000000000000000000;hb=8d2494d1fb7cd0fa7c63be5ffba8dd1a11457522;hpb=cb12a866906ec4ac644de0e658679261c82ab098 diff --git a/bcftools/bcf.h b/bcftools/bcf.h new file mode 100644 index 0000000..3657895 --- /dev/null +++ b/bcftools/bcf.h @@ -0,0 +1,161 @@ +/* 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 */ + +#ifndef BCF_H +#define BCF_H + +#include +#include +#include "bgzf.h" + +/* + 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) +} 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 + BGZF *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); + // 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 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); + // convert GL to PL + int bcf_gl2pl(bcf1_t *b); + + // string hash table + void *bcf_build_refhash(bcf_hdr_t *h); + void bcf_str2id_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