--- /dev/null
+/* 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 <lh3@live.co.uk> */
+
+#ifndef BCF_H
+#define BCF_H
+
+#include <stdint.h>
+#include <zlib.h>
+#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
projects / samtools.git / blobdiff