htslib.synced_bcf_reader

@file htslib/synced_bcf_reader.h Stream through multiple VCF files.

Members

Enums

bcf_sr_error
enum bcf_sr_error
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_opt_t
enum bcf_sr_opt_t
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Functions

bcf_sr_add_reader
int bcf_sr_add_reader(bcf_srs_t* readers, const(char)* fname)

bcf_sr_add_reader() - open new reader @readers: holder of the open readers @fname: the VCF file

bcf_sr_destroy
void bcf_sr_destroy(bcf_srs_t* readers)

Destroy a bcf_srs_t struct

bcf_sr_destroy_threads
void bcf_sr_destroy_threads(bcf_srs_t* files)

Deallocates thread memory, if owned by us.

bcf_sr_get_header
auto bcf_sr_get_header(T0 _readers, T1 i)
Undocumented in source. Be warned that the author may not have intended to support it.
bcf_sr_get_line
auto bcf_sr_get_line(T0 _readers, T1 i)
Undocumented in source. Be warned that the author may not have intended to support it.
bcf_sr_get_reader
auto bcf_sr_get_reader(T0 _readers, T1 i)
Undocumented in source. Be warned that the author may not have intended to support it.
bcf_sr_has_line
auto bcf_sr_has_line(T0 readers, T1 i)
Undocumented in source. Be warned that the author may not have intended to support it.
bcf_sr_init
bcf_srs_t* bcf_sr_init()

Allocate and initialize a bcf_srs_t struct.

bcf_sr_next_line
int bcf_sr_next_line(bcf_srs_t* readers)

bcf_sr_next_line() - the iterator @readers: holder of the open readers

bcf_sr_region_done
int bcf_sr_region_done(T0 _readers, T1 i)
Undocumented in source. Be warned that the author may not have intended to support it.
bcf_sr_regions_destroy
void bcf_sr_regions_destroy(bcf_sr_regions_t* regions)
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_regions_flush
int bcf_sr_regions_flush(bcf_sr_regions_t* regs)
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_regions_init
bcf_sr_regions_t* bcf_sr_regions_init(const(char)* regions, int is_file, int chr, int from, int to)
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_regions_next
int bcf_sr_regions_next(bcf_sr_regions_t* reg)
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_regions_overlap
int bcf_sr_regions_overlap(bcf_sr_regions_t* reg, const(char)* seq, hts_pos_t start, hts_pos_t end)
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_regions_seek
int bcf_sr_regions_seek(bcf_sr_regions_t* regions, const(char)* chr)
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_remove_reader
void bcf_sr_remove_reader(bcf_srs_t* files, int i)
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_seek
int bcf_sr_seek(bcf_srs_t* readers, const(char)* seq, hts_pos_t pos)

bcf_sr_seek() - set all readers to selected position @seq: sequence name; NULL to seek to start @pos: 0-based coordinate

bcf_sr_set_opt
int bcf_sr_set_opt(bcf_srs_t* readers, bcf_sr_opt_t opt, ...)
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_set_regions
int bcf_sr_set_regions(bcf_srs_t* readers, const(char)* regions, int is_file)
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_set_samples
int bcf_sr_set_samples(bcf_srs_t* readers, const(char)* samples, int is_file)

bcf_sr_set_samples() - sets active samples @readers: holder of the open readers @samples: this can be one of: file name with one sample per line; or column-separated list of samples; or '-' for a list of samples shared by all files. If first character is the exclamation mark, all but the listed samples are included. @is_file: 0: list of samples; 1: file with sample names

bcf_sr_set_targets
int bcf_sr_set_targets(bcf_srs_t* readers, const(char)* targets, int is_file, int alleles)

bcf_sr_set_targets(), bcf_sr_set_regions() - init targets/regions @readers: holder of the open readers @targets: list of regions, one-based and inclusive. @is_fname: 0: targets is a comma-separated list of regions (chr,chr:from-to) 1: targets is a tabix indexed file with a list of regions (<chr,pos> or <chr,from,to>)

bcf_sr_set_threads
int bcf_sr_set_threads(bcf_srs_t* files, int n_threads)

bcf_sr_set_threads() - allocates a thread-pool for use by the synced reader. @n_threads: size of thread pool

bcf_sr_strerror
char* bcf_sr_strerror(int errnum)
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Manifest constants

BCF_SR_PAIR_ANY
enum BCF_SR_PAIR_ANY;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_SR_PAIR_BOTH
enum BCF_SR_PAIR_BOTH;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_SR_PAIR_BOTH_REF
enum BCF_SR_PAIR_BOTH_REF;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_SR_PAIR_EXACT
enum BCF_SR_PAIR_EXACT;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_SR_PAIR_INDELS
enum BCF_SR_PAIR_INDELS;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_SR_PAIR_INDEL_REF
enum BCF_SR_PAIR_INDEL_REF;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_SR_PAIR_SNPS
enum BCF_SR_PAIR_SNPS;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_SR_PAIR_SNP_REF
enum BCF_SR_PAIR_SNP_REF;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BCF_SR_PAIR_SOME
enum BCF_SR_PAIR_SOME;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
COLLAPSE_ANY
enum COLLAPSE_ANY;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
COLLAPSE_BOTH
enum COLLAPSE_BOTH;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
COLLAPSE_INDELS
enum COLLAPSE_INDELS;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
COLLAPSE_NONE
enum COLLAPSE_NONE;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
COLLAPSE_SNPS
enum COLLAPSE_SNPS;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
COLLAPSE_SOME
enum COLLAPSE_SOME;
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Structs

bcf_sr_region_t
struct bcf_sr_region_t
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_regions_t
struct bcf_sr_regions_t
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_sr_t
struct bcf_sr_t
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_srs_t
struct bcf_srs_t
Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

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