htslib.tbx

htslib-1.9 tbx.h as D module

Changes include: Removed if(n)defs Change numeric #defines to enum int Changed ^typedef struct {...} <name>$ to ^struct <name> {...}$ extern const to __gshared made #define function macros into inline functions (tbx_itr* -> hts_itr*) In D, const on either LHS or RHS of function declaration applies to the function, not return value, unless parents included: changed ^const <type> <fnname> to ^const(<type>) <fnname>

Members

Aliases

tbx_itr_destroy alias tbx_itr_destroy = hts_itr_destroy: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Functions

hts_get_bgzfp BGZF* hts_get_bgzfp(htsFile* fp): Internal helper function used by tbx_itr_next() defined in hts.c -- do not use directly
tbx_bgzf_itr_next auto tbx_bgzf_itr_next(BGZF* bgzfp, tbx_t* tbx, hts_itr_t* itr, void* r): advance tabix iterator
tbx_destroy void tbx_destroy(tbx_t* tbx): destroy/dealloc tabix data
tbx_index tbx_t* tbx_index(BGZF* fp, int min_shift, const(tbx_conf_t)* conf): The index struct returned by a successful call should be freed via tbx_destroy() when it is no longer needed.
tbx_index_build int tbx_index_build(const(char)* fn, int min_shift, const(tbx_conf_t)* conf): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
tbx_index_build2 int tbx_index_build2(const(char)* fn, const(char)* fnidx, int min_shift, const(tbx_conf_t)* conf)
tbx_index_build3 int tbx_index_build3(const(char)* fn, const(char)* fnidx, int min_shift, int n_threads, const(tbx_conf_t)* conf): The index struct returned by a successful call should be freed via tbx_destroy() when it is no longer needed.
tbx_index_load tbx_t* tbx_index_load(const(char)* fn): @param fn Name of the data file corresponding to the index
tbx_index_load2 tbx_t* tbx_index_load2(const(char)* fn, const(char)* fnidx): @param fn Name of the data file corresponding to the index @param fnidx Name of the indexed file @return The index, or NULL if an error occurred
tbx_index_load3 tbx_t* tbx_index_load3(const(char)* fn, const(char)* fnidx, HTS_IDX_FLAG flags): @param fn Name of the data file corresponding to the index @param fnidx Name of the indexed file @param flags Flags to alter behaviour (see description) @return The index, or NULL if an error occurred
tbx_itr_next auto tbx_itr_next(htsFile* htsfp, tbx_t* tbx, hts_itr_t* itr, void* r): advance tabix iterator
tbx_itr_queryi auto tbx_itr_queryi(tbx_t* tbx, int tid, int beg, int end): tabix query by integer based tid(contig)/start/end
tbx_itr_querys auto tbx_itr_querys(tbx_t* tbx, char* s): tabix query by string "chr:start-end"
tbx_name2id int tbx_name2id(tbx_t* tbx, char* ss): contig name to integer id
tbx_readrec int tbx_readrec(BGZF* fp, void* tbxv, void* sv, int* tid, hts_pos_t* beg, hts_pos_t* end): Called by tabix iterator to read the next record
tbx_seqnames
const(char**) tbx_seqnames(tbx_t* tbx, int* n): return C-style array of sequence names (NB: free the array but not the values)

Static variables

tbx_conf_bed tbx_conf_t tbx_conf_bed;: prebaked TABIX config data for GFF3, BED, PSL table, SAM, VCF
tbx_conf_gff tbx_conf_t tbx_conf_gff;: prebaked TABIX config data for GFF3, BED, PSL table, SAM, VCF
tbx_conf_psltbl tbx_conf_t tbx_conf_psltbl;: prebaked TABIX config data for GFF3, BED, PSL table, SAM, VCF
tbx_conf_sam tbx_conf_t tbx_conf_sam;: prebaked TABIX config data for GFF3, BED, PSL table, SAM, VCF
tbx_conf_vcf tbx_conf_t tbx_conf_vcf;: prebaked TABIX config data for GFF3, BED, PSL table, SAM, VCF

Structs

tbx_conf_t struct tbx_conf_t: tabix config
tbx_t struct tbx_t: tabix data

Variables

TBX_GENERIC enum int TBX_GENERIC;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
TBX_MAX_SHIFT enum int TBX_MAX_SHIFT;: @file htslib/tbx.h Tabix API functions.
TBX_SAM enum int TBX_SAM;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
TBX_UCSC enum int TBX_UCSC;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
TBX_VCF enum int TBX_VCF;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.