Opaque structure representing FASTA index
File format to be dealing with.
@param fn FASTA/FASTQ file name @return 0 on success; or -1 on failure
@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
Destroy a faidx_t struct
@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
@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
@param fn File name of the FASTA file @return Pointer to a faidx_t struct on success, NULL on failure.
@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.
@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.
@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.
@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 successful, NULL if not.
@param fa String with the path to the reference file @return String with the path to the reference index file, or NULL on failure
@param fai Pointer to the faidx_t struct @param cache_size Selected cache size in bytes
@param fai Pointer to the faidx_t struct @return The number of sequences
@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
@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
@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
@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
@param fai Pointer to the faidx_t struct @param seq Sequence name @return 1 if present or 0 if absent
Return name of i-th sequence
Return number of sequences in fai index
Return sequence length, -1 if not present
@file
@file htslib/faidx.h FASTA random access.