dhtslib.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, tbx_conf_t* conf): build tabix index
tbx_index_build int tbx_index_build(char* fn, int min_shift, tbx_conf_t* conf)
tbx_index_build2 int tbx_index_build2(char* fn, char* fnidx, int min_shift, tbx_conf_t* conf)
tbx_index_build3 int tbx_index_build3(char* fn, char* fnidx, int min_shift, int n_threads, tbx_conf_t* conf): build tabix index
tbx_index_load tbx_t* tbx_index_load(char* fn)
tbx_index_load2 tbx_t* tbx_index_load2(char* fn, char* fnidx): load tabix index
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, int* beg, int* 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;
tbx_conf_psltbl tbx_conf_t tbx_conf_psltbl;
tbx_conf_sam tbx_conf_t tbx_conf_sam;
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;: generic flat file
TBX_MAX_SHIFT enum int TBX_MAX_SHIFT;: @file htslib/tbx.h Tabix API functions. +//// ??
TBX_SAM enum int TBX_SAM;: SAM
TBX_UCSC enum int TBX_UCSC;: ?UCSC flat file?
TBX_VCF enum int TBX_VCF;: VCF