htslib.vcf

Members

Aliases

BCF_UN_IND alias BCF_UN_IND = BCF_UN_FMT: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_clear1 alias bcf_clear1 = bcf_clear: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_close alias bcf_close = hts_close: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_destroy1 alias bcf_destroy1 = bcf_destroy: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_empty1 alias bcf_empty1 = bcf_empty: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_init1 alias bcf_init1 = bcf_init: These macros are defined only for consistency with other parts of htslib
bcf_itr_destroy alias bcf_itr_destroy = hts_itr_destroy: BCF index
bcf_open alias bcf_open = hts_open: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_read1 alias bcf_read1 = bcf_read: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_write1 alias bcf_write1 = bcf_write: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
vcfFile alias vcfFile = htsFile: bcf_open and vcf_open mode: please see hts_open() in hts.h
vcf_close alias vcf_close = hts_close: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
vcf_format1 alias vcf_format1 = vcf_format: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
vcf_open alias vcf_open = hts_open: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
vcf_parse1 alias vcf_parse1 = vcf_parse: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
vcf_read1 alias vcf_read1 = vcf_read: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
vcf_write1 alias vcf_write1 = vcf_write: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Enums

BCF_HL_FLT anonymousenum BCF_HL_FLT: Header struct *

Functions

bcf_add_filter int bcf_add_filter(const(bcf_hdr_t)* hdr, bcf1_t* line, int flt_id): 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_add_id int bcf_add_id(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* id): bcf_update_id() - sets new ID string bcf_add_id() - adds to the ID string checking for duplicates
bcf_alleles2gt auto bcf_alleles2gt(int a, int b): Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based)
bcf_clear void bcf_clear(bcf1_t* v): 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_copy bcf1_t* bcf_copy(bcf1_t* dst, bcf1_t* src): bcf_dup() - create a copy of BCF record.
bcf_destroy void bcf_destroy(bcf1_t* v): Deallocate a bcf1_t object
bcf_dup bcf1_t* bcf_dup(bcf1_t* src): bcf_dup() - create a copy of BCF record.
bcf_empty void bcf_empty(bcf1_t* v): Same as bcf_destroy() but frees only the memory allocated by bcf1_t, not the bcf1_t object itself.
bcf_enc_int1 int bcf_enc_int1(kstring_t* s, int32_t x): Undocumented Encode integer variant 1
bcf_enc_inttype int bcf_enc_inttype(long x): Undocumented Encode integer type?
bcf_enc_size int bcf_enc_size(kstring_t* s, int size, int type): ditto Undocumented Encode size?
bcf_enc_vchar int bcf_enc_vchar(kstring_t* s, int l, const(char)* a): @param s kstring to write into @param l length of input @param a input data to encode @return 0 on success; < 0 on error
bcf_enc_vfloat int bcf_enc_vfloat(kstring_t* s, int n, float* a): @param s kstring to write into @param n total number of items in @p a (<= 0 to encode BCF_BT_NULL) @param a input data to encode @return 0 on success; < 0 on error
bcf_enc_vint int bcf_enc_vint(kstring_t* s, int n, int32_t* a, int wsize): @param s kstring to write into @param n total number of items in @p a (<= 0 to encode BCF_BT_NULL) @param a input data to encode @param wsize vector length (<= 0 is equivalent to @p n) @return 0 on success; < 0 on error @note @p n should be an exact multiple of @p wsize
bcf_float_is_missing int bcf_float_is_missing(float f)
bcf_float_is_vector_end int bcf_float_is_vector_end(float f): u wot
bcf_float_set void bcf_float_set(float* ptr, uint32_t value): u wot
bcf_float_set_missing void bcf_float_set_missing(float x): float vector macros
bcf_float_set_vector_end void bcf_float_set_vector_end(float x): float vector macros
bcf_fmt_array int bcf_fmt_array(kstring_t* s, int n, int type, void* data)
bcf_fmt_sized_array uint8_t* bcf_fmt_sized_array(kstring_t* s, uint8_t* ptr): @param s kstring to write into @param n number of items in @p data @param type type of items in @p data @param data BCF format data @return 0 on success -1 if out of memory
bcf_format_gt int bcf_format_gt(bcf_fmt_t* fmt, int isample, kstring_t* str): (Undocumented) Format GT field
bcf_get_fmt bcf_fmt_t* bcf_get_fmt(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key): 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_fmt_id bcf_fmt_t* bcf_get_fmt_id(bcf1_t* line, int id): 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_char
auto bcf_get_format_char(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, void** dst, int* ndst): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_get_format_float
auto bcf_get_format_float(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, void** dst, int* ndst): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_get_format_int32
auto bcf_get_format_int32(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, void** dst, int* ndst): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_get_format_string
int bcf_get_format_string(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, char*** dst, int* ndst)
bcf_get_format_values
int bcf_get_format_values(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, void** dst, int* ndst, int type): bcf_get_format_*() - same as bcf_get_info*() above
bcf_get_genotypes
auto bcf_get_genotypes(const(bcf_hdr_t)* hdr, bcf1_t* line, void** dst, int* ndst): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_get_info bcf_info_t* bcf_get_info(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key): 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_info_flag
auto bcf_get_info_flag(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, void** dst, int* ndst): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_get_info_float
auto bcf_get_info_float(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, void** dst, int* ndst): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_get_info_id bcf_info_t* bcf_get_info_id(bcf1_t* line, int id): 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_int32
auto bcf_get_info_int32(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, void** dst, int* ndst): bcf_get_info_*() - get INFO values, integers or floats @param hdr: BCF header @param line: BCF record @param tag: INFO tag to retrieve @param dst: *dst is pointer to a memory location, can point to NULL @param ndst: pointer to the size of allocated memory @return >=0 on success -1 .. no such INFO tag defined in the header -2 .. clash between types defined in the header and encountered in the VCF record -3 .. tag is not present in the VCF record -4 .. the operation could not be completed (e.g. out of memory)
bcf_get_info_int64
auto bcf_get_info_int64(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, int64_t** dst, int* ndst): @param hdr: BCF header @param line: BCF record @param tag: INFO tag to retrieve @param dst: *dst is pointer to a memory location, can point to NULL @param ndst: pointer to the size of allocated memory @return >=0 on success -1 .. no such INFO tag defined in the header -2 .. clash between types defined in the header and encountered in the VCF record -3 .. tag is not present in the VCF record -4 .. the operation could not be completed (e.g. out of memory)
bcf_get_info_string
auto bcf_get_info_string(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, void** dst, int* ndst): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_get_info_values
int bcf_get_info_values(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* tag, void** dst, int* ndst, int type): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_get_variant_type int bcf_get_variant_type(bcf1_t* rec, int ith_allele): bcf_get_variant_types - returns one of VCF_REF, VCF_SNP, etc
bcf_get_variant_types int bcf_get_variant_types(bcf1_t* rec): bcf_get_variant_types - returns one of VCF_REF, VCF_SNP, etc
bcf_gt2alleles void bcf_gt2alleles(int igt, int* a, int* b): Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based)
bcf_gt_allele auto bcf_gt_allele(int val)
bcf_gt_is_missing auto bcf_gt_is_missing(int val)
bcf_gt_is_phased auto bcf_gt_is_phased(int idx): 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.
bcf_gt_phased auto bcf_gt_phased(int idx)
bcf_gt_unphased auto bcf_gt_unphased(int idx): 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.
bcf_has_filter int bcf_has_filter(const(bcf_hdr_t)* hdr, bcf1_t* line, char* filter): Returns 1 if present, 0 if absent, or -1 if filter does not exist. "PASS" and "." can be used interchangeably.
bcf_hdr_add_hrec int bcf_hdr_add_hrec(bcf_hdr_t* hdr, bcf_hrec_t* hrec): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_hdr_add_sample int bcf_hdr_add_sample(bcf_hdr_t* hdr, const(char)* sample): bcf_hdr_add_sample() - add a new sample. @param sample: sample name to be added
bcf_hdr_append int bcf_hdr_append(bcf_hdr_t* h, const(char)* line): Append new VCF header line, returns 0 on success
bcf_hdr_combine int bcf_hdr_combine(bcf_hdr_t* dst, const(bcf_hdr_t)* src): 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
bcf_hdr_destroy void bcf_hdr_destroy(bcf_hdr_t* h): Destroy a BCF header struct
bcf_hdr_dup bcf_hdr_t* bcf_hdr_dup(const(bcf_hdr_t)* hdr): Create a new header using the supplied template
bcf_hdr_fmt_text char* bcf_hdr_fmt_text(const(bcf_hdr_t)* hdr, int is_bcf, int* len): 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.
bcf_hdr_format int bcf_hdr_format(const(bcf_hdr_t)* hdr, int is_bcf, kstring_t* str): 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 bcf_hrec_t* bcf_hdr_get_hrec(const(bcf_hdr_t)* hdr, int type, const(char)* key, const(char)* value, const(char)* str_class): 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
bcf_hdr_get_version const(char)* bcf_hdr_get_version(const(bcf_hdr_t)* hdr): VCF version, e.g. VCFv4.2
bcf_hdr_id2coltype uint32_t bcf_hdr_id2coltype(const(bcf_hdr_t)* hdr, int type, int int_id)
bcf_hdr_id2hrc auto bcf_hdr_id2hrc(const(bcf_hdr_t)* hdr, int dict_type, int col_type, int int_id): 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 int bcf_hdr_id2int(const(bcf_hdr_t)* hdr, int type, const(char)* id): 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_id2length auto bcf_hdr_id2length(const(bcf_hdr_t)* hdr, int type, int int_id): 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_id2name const(char)* bcf_hdr_id2name(const(bcf_hdr_t)* hdr, int rid): bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID bcf_hdr_id2name() - Translates numeric ID to sequence name
bcf_hdr_id2number auto bcf_hdr_id2number(const(bcf_hdr_t)* hdr, int type, int int_id)
bcf_hdr_id2type uint32_t bcf_hdr_id2type(const(bcf_hdr_t)* hdr, int type, int int_id)
bcf_hdr_idinfo_exists auto bcf_hdr_idinfo_exists(const(bcf_hdr_t)* hdr, int type, int int_id): 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 bcf_hdr_t* bcf_hdr_init(const(char)* mode): bcf_hdr_init() - create an empty BCF header. @param mode "r" or "w"
bcf_hdr_int2id auto bcf_hdr_int2id(const(bcf_hdr_t)* hdr, int type, int int_id): 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 bcf_hdr_t* bcf_hdr_merge(bcf_hdr_t* dst, const(bcf_hdr_t)* src): 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 int bcf_hdr_name2id(const(bcf_hdr_t)* hdr, const(char)* id): bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID bcf_hdr_id2name() - Translates numeric ID to sequence name
bcf_hdr_nsamples auto bcf_hdr_nsamples(bcf_hdr_t* hdr): Get number of samples
bcf_hdr_parse int bcf_hdr_parse(bcf_hdr_t* hdr, char* htxt): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_hdr_parse_line bcf_hrec_t* bcf_hdr_parse_line(const(bcf_hdr_t)* h, const(char)* line, int* len): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_hdr_printf int bcf_hdr_printf(bcf_hdr_t* h, const(char)* format, ...): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_hdr_read bcf_hdr_t* bcf_hdr_read(htsFile* fp): @param fp The file to read the header from @return Pointer to a populated header structure on success; NULL on failure
bcf_hdr_remove void bcf_hdr_remove(bcf_hdr_t* h, int type, const(char)* key): 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
bcf_hdr_seqnames
const(char)** bcf_hdr_seqnames(const(bcf_hdr_t)* h, int* nseqs): Creates a list of sequence names. It is up to the caller to free the list (but not the sequence names)
bcf_hdr_set int bcf_hdr_set(bcf_hdr_t* hdr, const(char)* fname): Read VCF header from a file and update the header
bcf_hdr_set_samples int bcf_hdr_set_samples(bcf_hdr_t* hdr, const(char)* samples, int is_file): bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed @param 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 @param is_file @p samples is a file (1) or a comma-separated list (0)
bcf_hdr_set_version void bcf_hdr_set_version(bcf_hdr_t* hdr, const(char)* _version): @param hdr BCF header struct @param version Version to set, e.g. "VCFv4.3" @return 0 on success; < 0 on error NB: mangled second parameter to _version
bcf_hdr_subset bcf_hdr_t* bcf_hdr_subset(const(bcf_hdr_t)* h0, int n, const(char*)* samples, int* imap): 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
bcf_hdr_sync int bcf_hdr_sync(bcf_hdr_t* h): @param h Header @return 0 on success, -1 on failure
bcf_hdr_write int bcf_hdr_write(htsFile* fp, bcf_hdr_t* h): @param fp Output file @param h The header to write @return 0 on success; -1 on failure
bcf_hrec_add_key void bcf_hrec_add_key(bcf_hrec_t* hrec, const(char)* str, size_t len): @param hrec Header record @param str Key name @param len Length of @p str @return 0 on success; -1 on failure
bcf_hrec_destroy void bcf_hrec_destroy(bcf_hrec_t* hrec): @param hrec Header record
bcf_hrec_dup bcf_hrec_t* bcf_hrec_dup(bcf_hrec_t* hrec): @param hrec Header record to copy @return A new header record on success; NULL on failure
bcf_hrec_find_key int bcf_hrec_find_key(bcf_hrec_t* hrec, const(char)* key): Lookup header record by key
bcf_hrec_format int bcf_hrec_format(const(bcf_hrec_t)* hrec, kstring_t* str): @param hrec Header record @param str Destination kstring @return 0 on success; < 0 on error
bcf_hrec_set_val void bcf_hrec_set_val(bcf_hrec_t* hrec, int i, const(char)* str, size_t len, int is_quoted): @param hrec Header record @param i Index of value @param str Value to set @param len Length of @p str @param is_quoted Value should be quoted @return 0 on success; -1 on failure
bcf_idx_init int bcf_idx_init(htsFile* fp, bcf_hdr_t* h, int min_shift, const(char)* fnidx): @param fp File handle for the data file being written. @param h BCF header structured (needed for BAI and CSI). @param min_shift CSI bin size (CSI default is 14). @param fnidx Filename to write index to. This pointer must remain valid until after bcf_idx_save is called. @return 0 on success, <0 on failure. @note This must be called after the header has been written, but before any other data.
bcf_idx_save int bcf_idx_save(htsFile* fp): @param fp File handle for the data file being written. @return 0 on success, <0 on failure.
bcf_index_build int bcf_index_build(const(char)* fn, int min_shift): 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 int bcf_index_build2(const(char)* fn, const(char)* fnidx, int min_shift): 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 int bcf_index_build3(const(char)* fn, const(char)* fnidx, int min_shift, int n_threads): 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
bcf_index_load auto bcf_index_load(const(char)* fn): @param fn BCF file name @return The index, or NULL if an error occurred. @note This only works for BCF files. Consider synced_bcf_reader instead which works for both BCF and VCF.
bcf_index_load2 hts_idx_t* bcf_index_load2(const(char)* fn, const(char)* fnidx): @param fn Input BAM/BCF/etc filename @param fnidx The input index filename @return The index, or NULL if an error occurred. @note This only works for BCF files. Consider synced_bcf_reader instead which works for both BCF and VCF.
bcf_index_load3 hts_idx_t* bcf_index_load3(const(char)* fn, const(char)* fnidx, int flags): @param fn Input BAM/BCF/etc filename @param fnidx The input index filename @param flags Flags to alter behaviour (see description) @return The index, or NULL if an error occurred. @note This only works for BCF files. Consider synced_bcf_reader instead which works for both BCF and VCF.
bcf_index_seqnames auto bcf_index_seqnames(const(hts_idx_t)* idx, const(bcf_hdr_t)* hdr, int* nptr): Get a list (char **) of sequence names from the index -- free only the array, not the values
bcf_init bcf1_t* bcf_init(): Allocate and initialize a bcf1_t object.
bcf_is_snp int bcf_is_snp(bcf1_t* v): returns int as ersatz bool, but dlang bool is 8-bit
bcf_itr_next int bcf_itr_next(htsFile* htsfp, hts_itr_t* itr, void* r): 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
bcf_itr_queryi auto bcf_itr_queryi(const(hts_idx_t)* idx, int tid, int beg, int end): Generate an iterator for an integer-based range query
bcf_itr_querys auto bcf_itr_querys(const(hts_idx_t)* idx, const(bcf_hdr_t)* hdr, const(char)* s): Generate an iterator for a string-based range query
bcf_read int bcf_read(htsFile* fp, const(bcf_hdr_t)* h, bcf1_t* v): @param fp The file to read the record from @param h The header for the vcf/bcf file @param v The bcf1_t structure to populate @return 0 on success; -1 on end of file; < -1 on critical error
bcf_readrec int bcf_readrec(BGZF* fp, void* _null, void* v, int* tid, hts_pos_t* beg, hts_pos_t* end): NOTE: C API second parameter called "null", mangled here as _null
bcf_remove_filter int bcf_remove_filter(const(bcf_hdr_t)* hdr, bcf1_t* line, int flt_id, int pass): 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_seqname const(char)* bcf_seqname(const(bcf_hdr_t)* hdr, bcf1_t* rec): bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID bcf_hdr_id2name() - Translates numeric ID to sequence name
bcf_subset int bcf_subset(const(bcf_hdr_t)* h, bcf1_t* v, int n, int* imap): See the description of bcf_hdr_subset()
bcf_subset_format int bcf_subset_format(const(bcf_hdr_t)* hdr, bcf1_t* rec): bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed @param 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 @param is_file @p samples is a file (1) or a comma-separated list (0)
bcf_translate int bcf_translate(const(bcf_hdr_t)* dst_hdr, bcf_hdr_t* src_hdr, bcf1_t* src_line): 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 int bcf_unpack(bcf1_t* b, int which): bcf_unpack() - unpack/decode a BCF record (fills the bcf1_t::d field)
bcf_update_alleles
int bcf_update_alleles(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)** alleles, int nals)
bcf_update_alleles_str int bcf_update_alleles_str(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* alleles_string): 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 int bcf_update_filter(const(bcf_hdr_t)* hdr, bcf1_t* line, int* flt_ids, int n): 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 int bcf_update_format(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(void)* values, int n, int type): 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_char
auto bcf_update_format_char(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(char)** values, int n): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_update_format_float auto bcf_update_format_float(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(float)* values, int n): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_update_format_int32 auto bcf_update_format_int32(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(int)* values, int n): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_update_format_string
int bcf_update_format_string(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(char)** values, int n): 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_genotypes
auto bcf_update_genotypes(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)** gts, int n): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_update_id int bcf_update_id(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* id): bcf_update_id() - sets new ID string bcf_add_id() - adds to the ID string checking for duplicates
bcf_update_info int bcf_update_info(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(void)* values, int n, int type): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_update_info_flag auto bcf_update_info_flag(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(void)* values, int n): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_update_info_float auto bcf_update_info_float(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(void)* values, int n): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_update_info_int32 auto bcf_update_info_int32(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(void)* values, int n): bcf_update_info_*() - functions for updating INFO fields @param hdr: the BCF header @param line: VCF line to be edited @param key: the INFO tag to be updated @param values: pointer to the array of values. Pass NULL to remove the tag. @param n: number of values in the array. When set to 0, the INFO tag is removed @return 0 on success or negative value on error.
bcf_update_info_int64 auto bcf_update_info_int64(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(int64_t)* values, int n): @param hdr: the BCF header @param line: VCF line to be edited @param key: the INFO tag to be updated @param values: pointer to the array of values. Pass NULL to remove the tag. @param n: number of values in the array. When set to 0, the INFO tag is removed @return 0 on success or negative value on error.
bcf_update_info_string auto bcf_update_info_string(const(bcf_hdr_t)* hdr, bcf1_t* line, const(char)* key, const(void)* values): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_write int bcf_write(htsFile* fp, bcf_hdr_t* h, bcf1_t* v): @param fp The file to write to @param h The header for the vcf/bcf file @param v The bcf1_t structure to write @return 0 on success; -1 on error
hrec_add_idx void hrec_add_idx(bcf_hrec_t* hrec, int idx): @param hrec Header record @param idx IDX value to add @return 0 on success; -1 on failure
vcf_format int vcf_format(const(bcf_hdr_t)* h, const(bcf1_t)* v, kstring_t* s): The opposite of vcf_parse. It should rarely be called directly, see vcf_write
vcf_hdr_read bcf_hdr_t* vcf_hdr_read(htsFile* fp): @param fp The file to read the header from @return Pointer to a populated header structure on success; NULL on failure
vcf_hdr_write int vcf_hdr_write(htsFile* fp, const(bcf_hdr_t)* h): @param fp Output file @param h The header to write @return 0 on success; -1 on failure
vcf_parse int vcf_parse(kstring_t* s, const(bcf_hdr_t)* h, bcf1_t* v): Parse VCF line contained in kstring and populate the bcf1_t struct The line must not end with \n or \r characters.
vcf_read int vcf_read(htsFile* fp, const(bcf_hdr_t)* h, bcf1_t* v): @param fp The file to read the record from @param h The header for the vcf file @param v The bcf1_t structure to populate @return 0 on success; -1 on end of file; < -1 on error
vcf_write int vcf_write(htsFile* fp, const(bcf_hdr_t)* h, bcf1_t* v): @param fp The file to write to @param h The header for the vcf file @param v The bcf1_t structure to write @return 0 on success; -1 on error
vcf_write_line int vcf_write_line(htsFile* fp, kstring_t* line): @param line Line to write @param fp File to write it to @return 0 on success; -1 on failure

Static variables

bcf_float_missing uint32_t bcf_float_missing;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_float_vector_end uint32_t bcf_float_vector_end;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_type_shift uint8_t[16] bcf_type_shift;: Lookup table used in bcf_record_check MAINTAINER: in C header is []

Structs

bcf1_t struct bcf1_t: 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.
bcf_dec_t struct bcf_dec_t: Variable-length data from a VCF record
bcf_fmt_t struct bcf_fmt_t: FORMAT field data (§1.4.2 Genotype fields)
bcf_hdr_t struct bcf_hdr_t: Structured repreentation of VCF header (§1.2) Note that bcf_hdr_t structs must always be created via bcf_hdr_init()
bcf_hrec_t struct bcf_hrec_t: Structured representation of a header line (§1.2)
bcf_idinfo_t struct bcf_idinfo_t: ID Dictionary entry
bcf_idpair_t struct bcf_idpair_t: ID Dictionary k/v
bcf_info_t struct bcf_info_t: INFO field data (§1.4.1 Fixed fields, (8) INFO)
variant_t struct variant_t: variant type record embedded in bcf_dec_t variant type and the number of bases affected, negative for deletions

Variables

BCF1_DIRTY_ALS enum int BCF1_DIRTY_ALS;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF1_DIRTY_FLT enum int BCF1_DIRTY_FLT;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF1_DIRTY_ID enum int BCF1_DIRTY_ID;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF1_DIRTY_INF enum int BCF1_DIRTY_INF;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_BT_CHAR enum int BCF_BT_CHAR;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_BT_FLOAT enum int BCF_BT_FLOAT;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_BT_INT16 enum int BCF_BT_INT16;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_BT_INT32 enum int BCF_BT_INT32;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_BT_INT64 enum int BCF_BT_INT64;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_BT_INT8 enum int BCF_BT_INT8;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_BT_NULL enum int BCF_BT_NULL;: VCF record *
BCF_DT_CTG enum int BCF_DT_CTG;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_DT_ID enum int BCF_DT_ID;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_DT_SAMPLE enum int BCF_DT_SAMPLE;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_ERR_CHAR enum int BCF_ERR_CHAR;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_ERR_CTG_INVALID enum int BCF_ERR_CTG_INVALID;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_ERR_CTG_UNDEF enum int BCF_ERR_CTG_UNDEF;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_ERR_LIMITS enum int BCF_ERR_LIMITS;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_ERR_NCOLS enum int BCF_ERR_NCOLS;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_ERR_TAG_INVALID enum int BCF_ERR_TAG_INVALID;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_ERR_TAG_UNDEF enum int BCF_ERR_TAG_UNDEF;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_MAX_BT_INT16 enum int16_t BCF_MAX_BT_INT16;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_MAX_BT_INT32 enum int32_t BCF_MAX_BT_INT32;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_MAX_BT_INT8 enum int8_t BCF_MAX_BT_INT8;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_MIN_BT_INT16 enum int16_t BCF_MIN_BT_INT16;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_MIN_BT_INT32 enum int32_t BCF_MIN_BT_INT32;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_MIN_BT_INT8 enum int8_t BCF_MIN_BT_INT8;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_UN_ALL enum int BCF_UN_ALL;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_UN_FLT enum int BCF_UN_FLT;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_UN_FMT enum int BCF_UN_FMT;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_UN_INFO enum int BCF_UN_INFO;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_UN_SHR enum int BCF_UN_SHR;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_UN_STR enum int BCF_UN_STR;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
VCF_BND enum int VCF_BND;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
VCF_INDEL enum int VCF_INDEL;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
VCF_MNP enum int VCF_MNP;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
VCF_OTHER enum int VCF_OTHER;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
VCF_OVERLAP enum int VCF_OVERLAP;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
VCF_REF enum int VCF_REF;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
VCF_SNP enum int VCF_SNP;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_gt_missing enum int bcf_gt_missing;: 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.
bcf_int16_missing enum int16_t bcf_int16_missing;
bcf_int16_vector_end enum int16_t bcf_int16_vector_end;
bcf_int32_missing enum int32_t bcf_int32_missing;
bcf_int32_vector_end enum int32_t bcf_int32_vector_end;
bcf_int64_missing enum int64_t bcf_int64_missing;
bcf_int64_vector_end enum int64_t bcf_int64_vector_end;
bcf_int8_missing enum int8_t bcf_int8_missing;: 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.
bcf_int8_vector_end enum int8_t bcf_int8_vector_end;
bcf_str_missing enum char bcf_str_missing;
bcf_str_vector_end enum char bcf_str_vector_end;: 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.

htslib.vcf

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