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