These macros are defined only for consistency with other parts of htslib
BCF index
bcf_open and vcf_open mode: please see hts_open() in hts.h
Header struct *
bcf_add_filter() - adds to the FILTER column @flt_id: filter ID to add, numeric ID returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS")
bcf_update_id() - sets new ID string bcf_add_id() - adds to the ID string checking for duplicates
Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based)
Make the bcf1_t object ready for next read. Intended mostly for internal use, the user should rarely need to call this function directly.
bcf_dup() - create a copy of BCF record.
Deallocate a bcf1_t object
bcf_dup() - create a copy of BCF record.
Same as bcf_destroy() but frees only the memory allocated by bcf1_t, not the bcf1_t object itself.
ditto ditto ditto
Undocumented
u wot
u wot
float vector macros
float vector macros
Undocumented
bcf_get_fmt() - returns pointer to FORMAT's field data @header: for access to BCF_DT_ID dictionary @line: VCF line obtained from vcf_parse1 @fmt: one of GT,PL,...
bcf_get_*_id() - returns pointer to FORMAT/INFO field data given the header index instead of the string ID @line: VCF line obtained from vcf_parse1 @id: The header index for the tag, obtained from bcf_hdr_id2int()
bcf_get_format_*() - same as bcf_get_info*() above
bcf_get_fmt() - returns pointer to FORMAT's field data @header: for access to BCF_DT_ID dictionary @line: VCF line obtained from vcf_parse1 @fmt: one of GT,PL,...
bcf_get_*_id() - returns pointer to FORMAT/INFO field data given the header index instead of the string ID @line: VCF line obtained from vcf_parse1 @id: The header index for the tag, obtained from bcf_hdr_id2int()
bcf_get_info_*() - get INFO values, integers or floats @hdr: BCF header @line: BCF record @tag: INFO tag to retrieve @dst: *dst is pointer to a memory location, can point to NULL @ndst: pointer to the size of allocated memory
bcf_get_variant_types - returns one of VCF_REF, VCF_SNP, etc
bcf_get_variant_types - returns one of VCF_REF, VCF_SNP, etc
Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based)
Macros for setting genotypes correctly, for use with bcf_update_genotypes only; idx corresponds to VCF's GT (1-based index to ALT or 0 for the reference allele) and val is the opposite, obtained from bcf_get_genotypes() below.
Macros for setting genotypes correctly, for use with bcf_update_genotypes only; idx corresponds to VCF's GT (1-based index to ALT or 0 for the reference allele) and val is the opposite, obtained from bcf_get_genotypes() below.
Returns 1 if present, 0 if absent, or -1 if filter does not exist. "PASS" and "." can be used interchangeably.
The following functions are for internal use and should rarely be called directly
bcf_hdr_add_sample() - add a new sample. @param sample: sample name to be added
Append new VCF header line, returns 0 on success
Copy header lines from src to dst if not already present in dst. See also bcf_translate(). Returns 0 on success or sets a bit on error: 1 .. conflicting definitions of tag length // todo
Destroy a BCF header struct
Create a new header using the supplied template
Returns formatted header (newly allocated string) and its length, excluding the terminating \0. If is_bcf parameter is unset, IDX fields are discarded. @deprecated Use bcf_hdr_format() instead as it can handle huge headers.
If _is_bcf_ is zero, IDX fields are discarded. @return 0 if successful, or negative if an error occurred @since 1.4
bcf_hdr_get_hrec() - get header line info @param type: one of the BCF_HL_* types: FLT,INFO,FMT,CTG,STR,GEN @param key: the header key for generic lines (e.g. "fileformat"), any field for structured lines, typically "ID". @param value: the value which pairs with key. Can be be NULL for BCF_HL_GEN @param str_class: the class of BCF_HL_STR line (e.g. "ALT" or "SAMPLE"), otherwise NULL
VCF version, e.g. VCFv4.2
bcf_hdr_id2*() - Macros for accessing bcf_idinfo_t @type: one of BCF_HL_FLT, BCF_HL_INFO, BCF_HL_FMT @int_id: return value of bcf_hdr_id2int, must be >=0
bcf_hdr_id2int() - Translates string into numeric ID bcf_hdr_int2id() - Translates numeric ID into string @type: one of BCF_DT_ID, BCF_DT_CTG, BCF_DT_SAMPLE @id: tag name, such as: PL, DP, GT, etc.
bcf_hdr_id2*() - Macros for accessing bcf_idinfo_t @type: one of BCF_HL_FLT, BCF_HL_INFO, BCF_HL_FMT @int_id: return value of bcf_hdr_id2int, must be >=0
bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID bcf_hdr_id2name() - Translates numeric ID to sequence name
bcf_hdr_id2*() - Macros for accessing bcf_idinfo_t @type: one of BCF_HL_FLT, BCF_HL_INFO, BCF_HL_FMT @int_id: return value of bcf_hdr_id2int, must be >=0
bcf_hdr_init() - create an empty BCF header. @param mode "r" or "w"
bcf_hdr_id2int() - Translates string into numeric ID bcf_hdr_int2id() - Translates numeric ID into string @type: one of BCF_DT_ID, BCF_DT_CTG, BCF_DT_SAMPLE @id: tag name, such as: PL, DP, GT, etc.
bcf_hdr_merge() - copy header lines from src to dst, see also bcf_translate() @param dst: the destination header to be merged into, NULL on the first pass @param src: the source header
bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID bcf_hdr_id2name() - Translates numeric ID to sequence name
Get number of samples
The following functions are for internal use and should rarely be called directly
Append new VCF header line, returns 0 on success
Reads VCF or BCF header
bcf_hdr_remove() - remove VCF header tag @param type: one of BCF_HL_* @param key: tag name or NULL to remove all tags of the given type
Creates a list of sequence names. It is up to the caller to free the list (but not the sequence names)
Read VCF header from a file and update the header
bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed @samples: samples to include or exclude from file or as a comma-separated string. LIST|FILE .. select samples in list/file ^LIST|FILE .. exclude samples from list/file - .. include all samples NULL .. exclude all samples @is_file: @samples is a file (1) or a comma-separated list (0)
Ditto NB: mangled second parameter to _version
bcf_hdr_subset() - creates a new copy of the header removing unwanted samples @param n: number of samples to keep @param samples: names of the samples to keep @param imap: mapping from index in @samples to the sample index in the original file
The following functions are for internal use and should rarely be called directly
Writes VCF or BCF header
Add key to header record
Deallocate header record
Duplicate header record
Lookup header record by key
The following functions are for internal use and should rarely be called directly
Set key's value for header record
bcf_index_build() - Generate and save an index file @fn: Input VCF(compressed)/BCF filename @min_shift: log2(width of the smallest bin), e.g. a value of 14 imposes a 16k base lower limit on the width of index bins. Positive to generate CSI, or 0 to generate TBI. However, a small value of min_shift would create a large index, which would lead to reduced performance when using the index. A recommended value is 14. For BCF files, only the CSI index can be generated.
bcf_index_build2() - Generate and save an index to a specific file @fn: Input VCF/BCF filename @fnidx: Output filename, or NULL to add .csi/.tbi to @fn @min_shift: Positive to generate CSI, or 0 to generate TBI
bcf_index_build3() - Generate and save an index to a specific file @fn: Input VCF/BCF filename @fnidx: Output filename, or NULL to add .csi/.tbi to @fn @min_shift: Positive to generate CSI, or 0 to generate TBI @n_threads: Number of VCF/BCF decoder threads
Load a BCF file's CSI index
Load BCF index with explicit fn and explicit index fn
Get a list (char **) of sequence names from the index -- free only the array, not the values
Initialize a bcf1_t object; equivalent to calloc(1, sizeof(bcf1_t))
ditto (TODO: what is this? should this be bool?)
Iterate through the range r should (probably) point to your VCF (BCF) row structure TODO: attempt to define parameter r as bcf1_t *, which is what I think it should be
Generate an iterator for an integer-based range query
Generate an iterator for a string-based range query
bcf_read() - read next VCF or BCF record
NOTE: C API second parameter called "null", mangled here as _null
bcf_remove_filter() - removes from the FILTER column @flt_id: filter ID to remove, numeric ID returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS") @pass: when set to 1 and no filters are present, set to PASS
bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID bcf_hdr_id2name() - Translates numeric ID to sequence name
See the description of bcf_hdr_subset()
bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed @samples: samples to include or exclude from file or as a comma-separated string. LIST|FILE .. select samples in list/file ^LIST|FILE .. exclude samples from list/file - .. include all samples NULL .. exclude all samples @is_file: @samples is a file (1) or a comma-separated list (0)
bcf_translate() - translate tags ids to be consistent with different header. This function is useful when lines from multiple VCF need to be combined. @dst_hdr: the destination header, to be used in bcf_write(), see also bcf_hdr_combine() @src_hdr: the source header, used in bcf_read() @src_line: line obtained by bcf_read()
bcf_unpack() - unpack/decode a BCF record (fills the bcf1_t::d field)
bcf_update_alleles() and bcf_update_alleles_str() - update REF and ALLT column @alleles: Array of alleles @nals: Number of alleles @alleles_string: Comma-separated alleles, starting with the REF allele
bcf_update_filter() - sets the FILTER column @flt_ids: The filter IDs to set, numeric IDs returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS") @n: Number of filters. If n==0, all filters are removed
bcf_update_format_*() - functions for updating FORMAT fields @values: pointer to the array of values, the same number of elements is expected for each sample. Missing values must be padded with bcf_*_missing or bcf_*_vector_end values. @n: number of values in the array. If n==0, existing tag is removed.
bcf_update_format_*() - functions for updating FORMAT fields @values: pointer to the array of values, the same number of elements is expected for each sample. Missing values must be padded with bcf_*_missing or bcf_*_vector_end values. @n: number of values in the array. If n==0, existing tag is removed.
bcf_update_id() - sets new ID string bcf_add_id() - adds to the ID string checking for duplicates
bcf_update_info_*() - functions for updating INFO fields @hdr: the BCF header @line: VCF line to be edited @key: the INFO tag to be updated @values: pointer to the array of values. Pass NULL to remove the tag. @n: number of values in the array. When set to 0, the INFO tag is removed
bcf_write() - write one VCF or BCF record. The type is determined at the open() call.
Index header record
The opposite of vcf_parse. It should rarely be called directly, see vcf_write
The following functions work only with VCFs and should rarely be called directly. Usually one wants to use their bcf_* alternatives, which work transparently with both VCFs and BCFs.
Parse VCF line contained in kstring and populate the bcf1_t struct The line must not end with \n or \r characters.
The following functions work only with VCFs and should rarely be called directly. Usually one wants to use their bcf_* alternatives, which work transparently with both VCFs and BCFs.
Note that in contrast with BCFv2.1 specification, HTSlib implementation allows missing values in vectors. For integer types, the values 0x80, 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001, 0x80000001 as end-of-vector indicators. Similarly for floats, the value of 0x7F800001 is interpreted as a missing value and 0x7F800002 as an end-of-vector indicator. Note that the end-of-vector byte is not part of the vector.
Lookup table used in bcf_record_check MAINTAINER: in C header is []
The bcf1_t structure corresponds to one VCF/BCF line. Reading from VCF file is slower because the string is first to be parsed, packed into BCF line (done in vcf_parse), then unpacked into internal bcf1_t structure. If it is known in advance that some of the fields will not be required (notably the sample columns), parsing of these can be skipped by setting max_unpack appropriately. Similarly, it is fast to output a BCF line because the columns (kept in shared.s, indiv.s, etc.) are written directly by bcf_write, whereas a VCF line must be formatted in vcf_format.
Variable-length data from a VCF record
FORMAT field data (§1.4.2 Genotype fields)
Structured repreentation of VCF header (§1.2) Note that bcf_hdr_t structs must always be created via bcf_hdr_init()
Structured representation of a header line (§1.2)
ID Dictionary entry
ID Dictionary k/v
INFO field data (§1.4.1 Fixed fields, (8) INFO)
variant type record embedded in bcf_dec_t variant type and the number of bases affected, negative for deletions
Allele(s) was edited
FILTER was edited
vptr offset, i.e., the size of the INFO key plus size+type bytes indicates that vptr-vptr_off must be freed; set only when modified and the new data block is bigger than the original +//// ID was edite
INFO was edited
char (8 bit)
float (32?)
int16
int32
int8
* VCF record * **************//// nul
dictionary type: CONTIG
dictionary type: ID
dictionary type: SAMPLE
BCF error:
BCF error:
BCF error: undefined contig
BCF error:
BCF error:
BCF error:
BCF error: undefined tag
everything
up to FILTER
unpack format and each sample
up to INFO
all shared information
up to ALT inclusive
breakend
INDEL
MNP
other (e.g. SV)
ref (e.g. in a gVCF)
SNP
Macros for setting genotypes correctly, for use with bcf_update_genotypes only; idx corresponds to VCF's GT (1-based index to ALT or 0 for the reference allele) and val is the opposite, obtained from bcf_get_genotypes() below.
Note that in contrast with BCFv2.1 specification, HTSlib implementation allows missing values in vectors. For integer types, the values 0x80, 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001, 0x80000001 as end-of-vector indicators. Similarly for floats, the value of 0x7F800001 is interpreted as a missing value and 0x7F800002 as an end-of-vector indicator. Note that the end-of-vector byte is not part of the vector.
Note that in contrast with BCFv2.1 specification, HTSlib implementation allows missing values in vectors. For integer types, the values 0x80, 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001, 0x80000001 as end-of-vector indicators. Similarly for floats, the value of 0x7F800001 is interpreted as a missing value and 0x7F800002 as an end-of-vector indicator. Note that the end-of-vector byte is not part of the vector.
D bindings to htslib-1.9 vcf Copyright 2018 James S Blachly, MD Changes are MIT licensed Section numbers refer to VCF Specification v4.2: https://samtools.github.io/hts-specs/VCFv4.2.pdf