htslib.faidx

Undocumented in source.

Members

Aliases

faidx_t alias faidx_t = __faidx_t: @file

Enums

fai_format_options enum fai_format_options: File format to be dealing with.
fai_load_options enum fai_load_options: Options for fai_load functions

Functions

fai_build int fai_build(const(char)* fn): @param fn FASTA/FASTQ file name @return 0 on success; or -1 on failure
fai_build3 int fai_build3(const(char)* fn, const(char)* fnfai, const(char)* fngzi): @param fn FASTA/FASTQ file name @param fnfai Name of .fai file to build. @param fngzi Name of .gzi file to build (if fn is bgzip-compressed). @return 0 on success; or -1 on failure
fai_destroy void fai_destroy(faidx_t* fai): Destroy a faidx_t struct
fai_fetch char* fai_fetch(const(faidx_t)* fai, const(char)* reg, int* len): @param fai Pointer to the faidx_t struct @param reg Region in the format "chr2:20,000-30,000" @param len Length of the region; -2 if seq not present, -1 general error @return Pointer to the sequence; NULL on failure
fai_fetch64 char* fai_fetch64(const(faidx_t)* fai, const(char)* reg, hts_pos_t* len): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
fai_fetchqual char* fai_fetchqual(const(faidx_t)* fai, const(char)* reg, int* len): @param fai Pointer to the faidx_t struct @param reg Region in the format "chr2:20,000-30,000" @param len Length of the region; -2 if seq not present, -1 general error @return Pointer to the quality string; null on failure
fai_fetchqual64 char* fai_fetchqual64(const(faidx_t)* fai, const(char)* reg, hts_pos_t* len): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
fai_load faidx_t* fai_load(const(char)* fn): @param fn File name of the FASTA file @return Pointer to a faidx_t struct on success, NULL on failure.
fai_load3 faidx_t* fai_load3(const(char)* fn, const(char)* fnfai, const(char)* fngzi, int flags): @param fn File name of the FASTA file (can be compressed with bgzip). @param fnfai File name of the FASTA index. @param fngzi File name of the bgzip index. @param flags Option flags to control index file caching and creation. @return Pointer to a faidx_t struct on success, NULL on failure.
fai_load3_format faidx_t* fai_load3_format(const(char)* fn, const(char)* fnfai, const(char)* fngzi, int flags, fai_format_options format): @param fn File name of the FASTA/FASTQ file (can be compressed with bgzip). @param fnfai File name of the FASTA/FASTQ index. @param fngzi File name of the bgzip index. @param flags Option flags to control index file caching and creation. @param format FASTA or FASTQ file format @return Pointer to a faidx_t struct on success, NULL on failure.
fai_load_format faidx_t* fai_load_format(const(char)* fn, fai_format_options format): @param fn File name of the FASTA/FASTQ file @param format FASTA or FASTQ file format @return Pointer to a faidx_t struct on success, NULL on failure.
fai_parse_region const(char)* fai_parse_region(const(faidx_t)* fai, const(char)* s, int* tid, hts_pos_t* beg, hts_pos_t* end, int flags): @param fai Pointer to the faidx_t struct @param s Region string @param tid Returns which i-th sequence is described in the region. @param beg Returns the start of the region (0 based) @param end Returns the one past last of the region (0 based) @param flags Parsing method, see HTS_PARSE_* in hts.h. @return pointer to end of parsed s if successs, NULL if not.
fai_set_cache_size void fai_set_cache_size(faidx_t* fai, int cache_size): @param fai Pointer to the faidx_t struct @param cache_size Selected cache size in bytes
faidx_fetch_qual char* faidx_fetch_qual(const(faidx_t)* fai, const(char)* c_name, int p_beg_i, int p_end_i, int* len): @param fai Pointer to the faidx_t struct @param c_name Region name @param p_beg_i Beginning position number (zero-based) @param p_end_i End position number (zero-based) @param len Length of the region; -2 if c_name not present, -1 general error @return Pointer to the sequence; null on failure
faidx_fetch_qual64 char* faidx_fetch_qual64(const(faidx_t)* fai, const(char)* c_name, hts_pos_t p_beg_i, hts_pos_t p_end_i, hts_pos_t* len): @param fai Pointer to the faidx_t struct @param c_name Region name @param p_beg_i Beginning position number (zero-based) @param p_end_i End position number (zero-based) @param len Length of the region; -2 if c_name not present, -1 general error @return Pointer to the sequence; null on failure
faidx_fetch_seq char* faidx_fetch_seq(const(faidx_t)* fai, const(char)* c_name, int p_beg_i, int p_end_i, int* len): @param fai Pointer to the faidx_t struct @param c_name Region name @param p_beg_i Beginning position number (zero-based) @param p_end_i End position number (zero-based) @param len Length of the region; -2 if c_name not present, -1 general error @return Pointer to the sequence; null on failure
faidx_fetch_seq64 char* faidx_fetch_seq64(const(faidx_t)* fai, const(char)* c_name, hts_pos_t p_beg_i, hts_pos_t p_end_i, hts_pos_t* len): @param fai Pointer to the faidx_t struct @param c_name Region name @param p_beg_i Beginning position number (zero-based) @param p_end_i End position number (zero-based) @param len Length of the region; -2 if c_name not present, -1 general error @return Pointer to the sequence; null on failure
faidx_has_seq int faidx_has_seq(const(faidx_t)* fai, const(char)* seq): @param fai Pointer to the faidx_t struct @param seq Sequence name @return 1 if present or 0 if absent
faidx_iseq const(char)* faidx_iseq(const(faidx_t)* fai, int i): Return name of i-th sequence
faidx_nseq int faidx_nseq(const(faidx_t)* fai): Return number of sequences in fai index
faidx_seq_len int faidx_seq_len(const(faidx_t)* fai, const(char)* seq): Return sequence length, -1 if not present

Structs

__faidx_t struct __faidx_t: @file

htslib.faidx

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