Crate slow5lib_sys

Crate slow5lib_sys 

Source
Expand description

§slow5lib-sys

License Crates.io docs.rs

Low level bindings to the slow5lib C library version 1.3.0

§Installation

Add the following to your Cargo.toml:

[dependencies]
slow5lib-sys = "0.10"

§License

Licensed under either of

at your option.

§Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.

Structs§

__slow5_press
__va_list_tag
kh_slow5_s2a_s
kh_slow5_s2i_s
kh_slow5_s2s_s
kh_slow5_s2ui32_s
kh_slow5_s_s
ks_isort_stack_t
slow5_aux_meta
@struct slow5_aux_meta SLOW5 auxiliary field metadata (information available in the SLOW5 header)
slow5_aux_type_meta
slow5_file
@struct slow5_file SLOW5 file structure
slow5_file_meta
@struct slow5_file SLOW5 file meta data
slow5_fmt_meta
@struct slow5_fmt_meta SLOW5 file meta data
slow5_hdr
@struct slow5_hdr SLOW5 header
slow5_hdr_data
@struct slow5_hdr_data SLOW5 header data (constant attributes in FAST5 files)
slow5_hdr_data__bindgen_ty_1
slow5_idx
slow5_press
slow5_press_method_t
slow5_rec
@struct slow5_rec SLOW5 record data struct (represents a single SLOW5 record)
slow5_rec_aux_data
@struct slow5_rec_aux_data SLOW5 auxiliary field data (represents a single SLOW5 auxiliary field of a particular read record)
slow5_rec_idx
slow5_version
@struct slow5_version @brief SLOW5 file version
slow5_zlib_stream

Constants§

SLOW5_ASCII_EXTENSION
SLOW5_ASCII_MISSING
SLOW5_ASCII_MISSING_CHAR
SLOW5_ASCII_NAME
SLOW5_ASCII_NUM_GROUPS_FORMAT
SLOW5_BINARY_EXTENSION
SLOW5_BINARY_HDR_SIZE_OFFSET
SLOW5_BINARY_NAME
SLOW5_CHAR_NULL
SLOW5_COLUMN_HDR_PREFIX
SLOW5_DEBUG_PREFIX
SLOW5_ENUM_NULL
SLOW5_ERROR_PREFIX
SLOW5_ERR_ARG
SLOW5_ERR_EOF
SLOW5_ERR_HDRPARSE
SLOW5_ERR_IO
SLOW5_ERR_MAGIC
SLOW5_ERR_MEM
SLOW5_ERR_NOAUX
SLOW5_ERR_NOFLD
SLOW5_ERR_NOIDX
SLOW5_ERR_NOTFOUND
SLOW5_ERR_OTH
SLOW5_ERR_PRESS
SLOW5_ERR_RECPARSE
SLOW5_ERR_TRUNC
SLOW5_ERR_TYPE
SLOW5_ERR_UNK
SLOW5_ERR_VERSION
SLOW5_FORMAT_STRING_RAW_SIGNAL
SLOW5_HDR_DATA_PREFIX
SLOW5_HDR_DATA_PREFIX_CHAR
SLOW5_HDR_ENUM_LABELS_BEGIN
SLOW5_HDR_ENUM_LABELS_END
SLOW5_HDR_FILE_VERSION
SLOW5_HDR_FILE_VERSION_SEP
SLOW5_HDR_NUM_GROUPS
SLOW5_HDR_NUM_GROUPS_INIT
SLOW5_HDR_PREFIX
SLOW5_INDEX_EXTENSION
SLOW5_INDEX_HEADER_SIZE_OFFSET
SLOW5_INFO_PREFIX
SLOW5_INT8_T_NULL
SLOW5_INT16_T_NULL
SLOW5_INT32_T_NULL
SLOW5_LIB_VERSION
SLOW5_NO_COLOUR
SLOW5_SEP_ARRAY
SLOW5_SEP_ARRAY_CHAR
SLOW5_SEP_COL
SLOW5_SEP_COL_CHAR
SLOW5_SEP_COL_NAME
SLOW5_UINT8_T_NULL
SLOW5_UINT16_T_NULL
SLOW5_UINT32_T_NULL
SLOW5_VERBOSE_PREFIX
SLOW5_VERSION_MAJOR
SLOW5_VERSION_MINOR
SLOW5_VERSION_PATCH
SLOW5_VERSION_STRING
SLOW5_WARNING_PREFIX
SLOW5_ZLIB_COMPRESS_CHUNK
SLOW5_ZLIB_DEPRESS_CHUNK
SLOW5_ZLIB_MEM_DEFAULT
SLOW5_ZSTD_COMPRESS_LEVEL
slow5_aux_type_SLOW5_CHAR
slow5_aux_type_SLOW5_DOUBLE
slow5_aux_type_SLOW5_DOUBLE_ARRAY
slow5_aux_type_SLOW5_ENUM
slow5_aux_type_SLOW5_ENUM_ARRAY
slow5_aux_type_SLOW5_FLOAT
slow5_aux_type_SLOW5_FLOAT_ARRAY
slow5_aux_type_SLOW5_INT8_T
slow5_aux_type_SLOW5_INT8_T_ARRAY
slow5_aux_type_SLOW5_INT16_T
slow5_aux_type_SLOW5_INT16_T_ARRAY
slow5_aux_type_SLOW5_INT32_T
slow5_aux_type_SLOW5_INT32_T_ARRAY
slow5_aux_type_SLOW5_INT64_T
slow5_aux_type_SLOW5_INT64_T_ARRAY
slow5_aux_type_SLOW5_STRING
slow5_aux_type_SLOW5_UINT8_T
slow5_aux_type_SLOW5_UINT8_T_ARRAY
slow5_aux_type_SLOW5_UINT16_T
slow5_aux_type_SLOW5_UINT16_T_ARRAY
slow5_aux_type_SLOW5_UINT32_T
slow5_aux_type_SLOW5_UINT32_T_ARRAY
slow5_aux_type_SLOW5_UINT64_T
slow5_aux_type_SLOW5_UINT64_T_ARRAY
slow5_cols_COL_digitisation
slow5_cols_COL_len_raw_signal
slow5_cols_COL_offset
slow5_cols_COL_range
slow5_cols_COL_raw_signal
slow5_cols_COL_read_group
slow5_cols_COL_read_id
slow5_cols_COL_sampling_rate
slow5_cols_SLOW5_COLS_NUM
slow5_exit_condition_opt_SLOW5_EXIT_OFF
slow5_exit_condition_opt_SLOW5_EXIT_ON_ERR
slow5_exit_condition_opt_SLOW5_EXIT_ON_WARN
slow5_fmt_SLOW5_FORMAT_ASCII
< the format is ASCII SLOW5
slow5_fmt_SLOW5_FORMAT_BINARY
< the format is binary SLOW5 (that is, BLOW5)
slow5_fmt_SLOW5_FORMAT_UNKNOWN
< the format is unknown, usually the case before parsing the file extension
slow5_log_level_opt_SLOW5_LOG_DBUG
slow5_log_level_opt_SLOW5_LOG_ERR
slow5_log_level_opt_SLOW5_LOG_INFO
slow5_log_level_opt_SLOW5_LOG_OFF
slow5_log_level_opt_SLOW5_LOG_VERB
slow5_log_level_opt_SLOW5_LOG_WARN
slow5_press_method_SLOW5_COMPRESS_EX_ZD
slow5_press_method_SLOW5_COMPRESS_NONE
slow5_press_method_SLOW5_COMPRESS_SVB_ZD
slow5_press_method_SLOW5_COMPRESS_ZLIB
slow5_press_method_SLOW5_COMPRESS_ZSTD

Statics§

SLOW5_AUX_TYPE_META⚠
SLOW5_FORMAT_META⚠
SLOW5_VERSION_STRUCT⚠

Functions§

slow5_add_rec⚠
Add a read entry to the SLOW5 file while updating the SLOW5 index (not thread safe).
slow5_arr_qts_round⚠
slow5_asprintf⚠
slow5_ato_int8⚠
slow5_ato_int16⚠
slow5_ato_int32⚠
slow5_ato_int64⚠
slow5_ato_uint8⚠
slow5_ato_uint16⚠
slow5_ato_uint32⚠
slow5_ato_uint64⚠
slow5_aux_add⚠
Adds an auxiliary field to a SLOW5 header. Return
slow5_aux_add_enum⚠
slow5_aux_get_char⚠
slow5_aux_get_double⚠
slow5_aux_get_double_array⚠
slow5_aux_get_enum⚠
slow5_aux_get_enum_array⚠
slow5_aux_get_float⚠
slow5_aux_get_float_array⚠
slow5_aux_get_int8⚠
Get an auxiliary field in a SLOW5 record as an 8-bit signed integer.
slow5_aux_get_int8_array⚠
Get an auxiliary field in a SLOW5 record as an 8-bit signed integer array.
slow5_aux_get_int16⚠
slow5_aux_get_int32⚠
slow5_aux_get_int64⚠
slow5_aux_get_int16_array⚠
slow5_aux_get_int32_array⚠
slow5_aux_get_int64_array⚠
slow5_aux_get_string⚠
slow5_aux_get_uint8⚠
slow5_aux_get_uint8_array⚠
slow5_aux_get_uint16⚠
slow5_aux_get_uint32⚠
slow5_aux_get_uint64⚠
slow5_aux_get_uint16_array⚠
slow5_aux_get_uint32_array⚠
slow5_aux_get_uint64_array⚠
slow5_aux_meta_add⚠
slow5_aux_meta_add_enum⚠
slow5_aux_meta_enum_parse⚠
slow5_aux_meta_free⚠
slow5_aux_meta_init⚠
slow5_aux_meta_init_empty⚠
slow5_aux_set⚠
slow5_aux_set_string⚠
slow5_aux_type_to_str⚠
slow5_close⚠
Close a slow5 file and free its memory. If the file had been opened for writing or appending, EOF marker will be written
slow5_compress_footer_next⚠
slow5_convert⚠
slow5_data_to_str⚠
slow5_decode⚠
slow5_decode_record_press⚠
slow5_decode_signal_press⚠
slow5_double_to_str⚠
slow5_encode⚠
slow5_encode_record_press⚠
slow5_encode_signal_press⚠
slow5_eof_fwrite⚠
Print the binary end of file to a file pointer.
slow5_errno_location⚠
slow5_filestamps_cmp⚠
slow5_float_check⚠
slow5_fmt_get_name⚠
slow5_fprintf_compress⚠
slow5_fread_depress⚠
slow5_fwrite_compress⚠
slow5_fwrite_depress⚠
slow5_get⚠
Get a read entry from a slow5 file corresponding to a read_id.
slow5_get_aux_enum_labels⚠
get the enum labels for a specific auxiliary field and set the number of labels in *n return NULL on error and slow5_errno set to SLOW5_ERR_ARG if header, field NULL, n can be NULL SLOW5_ERR_NOAUX if auxiliary header is NULL SLOW5_ERR_TYPE if the enum labels or num_labels array is NULL, or the field type is not an enum type SLOW5_ERR_NOFLD if the auxiliary field was not found SLOW5_ERR_MEM memory allocation error
slow5_get_aux_names⚠
slow5_get_aux_types⚠
slow5_get_hdr_keys⚠
slow5_get_idx_path⚠
slow5_get_mem⚠
slow5_get_next⚠
Get the read entry under the current file pointer of a slow5 file.
slow5_get_next_bytes⚠
slow5_get_next_mem⚠
slow5_get_rids⚠
slow5_hdr_add⚠
Adds a new header data attribute.
slow5_hdr_add_attr⚠
Add a new header data attribute.
slow5_hdr_add_rg⚠
Add a new header read group.
slow5_hdr_add_rg_data⚠
slow5_hdr_attrs_to_str⚠
slow5_hdr_data_free⚠
slow5_hdr_data_init⚠
slow5_hdr_free⚠
slow5_hdr_fwrite⚠
Print the header in the specified format to a file pointer.
slow5_hdr_get⚠
Get a header data attribute for a particular read_group.
slow5_hdr_get_data⚠
slow5_hdr_init⚠
slow5_hdr_init_empty⚠
slow5_hdr_set⚠
Sets a header data attribute for a particular read_group.
slow5_hdr_to_mem⚠
Get the header in the specified format.
slow5_hdr_types_to_str⚠
slow5_hdr_write⚠
Writes the associated SLOW5 header to a SLOW5 file.
slow5_idx_create⚠
Create the index file for slow5 file. Overwrites if already exists.
slow5_idx_free⚠
slow5_idx_get⚠
slow5_idx_init⚠
slow5_idx_init_empty⚠
slow5_idx_init_with⚠
slow5_idx_insert⚠
slow5_idx_load⚠
Loads the index file for slow5 file. Creates the index if not found.
slow5_idx_load_with⚠
Loads the index file for slow5 file given it’s pathname. Will not create the index if not found.
slow5_idx_read⚠
slow5_idx_to⚠
Create the index file for slow5 file. Overrides if already exists.
slow5_idx_unload⚠
Unloads an index associted to a slow5_file_t using slow5_idx_load and free the memory.
slow5_idx_write⚠
slow5_init⚠
Ultra-Low-level API ******************************************************************************
slow5_init_empty⚠
slow5_int_check⚠
slow5_is_c_label⚠
slow5_is_eof⚠
slow5_memcpy_null_type⚠
slow5_memcpy_type_from_str⚠
slow5_name_get_fmt⚠
slow5_open⚠
Open a slow5 file with a specific mode given it’s pathname.
slow5_open_with⚠
Open a slow5 file of a specific format with a mode given it’s pathname.
slow5_path_get_fmt⚠
slow5_pread_depress⚠
slow5_pread_depress_solo⚠
slow5_press_free⚠
slow5_press_init⚠
slow5_printf_compress⚠
slow5_ptr_compress⚠
slow5_ptr_compress_solo⚠
slow5_ptr_depress⚠
slow5_ptr_depress_solo⚠
slow5_rec_aux_free⚠
slow5_rec_depress_parse⚠
slow5_rec_free⚠
Free a slow5 record.
slow5_rec_fwrite⚠
Print a read entry in the specified format to a file pointer.
slow5_rec_idx_print⚠
slow5_rec_parse⚠
slow5_rec_qts_round⚠
slow5_rec_set⚠
slow5_rec_set_array⚠
slow5_rec_to_mem⚠
Get the read entry in the specified format.
slow5_rm_rec⚠
Remove a read entry at a read_id in a slow5 file while updating the SLOW5 index (not thread safe).
slow5_set_exit_condition⚠
slow5_set_log_level⚠
Low-level API *******************************************************************************
slow5_set_press⚠
slow5_set_skip_rid⚠
slow5_signal_press_version_cmp⚠
slow5_str_to_aux_type⚠
slow5_strsep⚠
slow5_strtod_check⚠
slow5_strtof_check⚠
slow5_type_to_str⚠
slow5_vasprintf⚠
slow5_version_cmp⚠
slow5_write⚠
Writes a SLOW5 record to a SLOW5 file.
slow5_write_bytes⚠

Type Aliases§

__builtin_va_list
__gnuc_va_list
__int32_t
__key_t
key_t
kh_cstr_t
kh_slow5_s2a_t
kh_slow5_s2i_t
kh_slow5_s2s_t
kh_slow5_s2ui32_t
kh_slow5_s_t
khint32_t
khint64_t
khint_t
khiter_t
ksstr_t
slow5_aux_data_t
slow5_aux_meta_t
@struct slow5_aux_meta SLOW5 auxiliary field metadata (information available in the SLOW5 header)
slow5_aux_type
slow5_cols
SLOW5 record
slow5_exit_condition_opt
slow5_file_meta_t
@struct slow5_file SLOW5 file meta data
slow5_file_t
@struct slow5_file SLOW5 file structure
slow5_fmt
@enum slow5_fmt File formats we are dealing with
slow5_hdr_data_t
@struct slow5_hdr_data SLOW5 header data (constant attributes in FAST5 files)
slow5_hdr_t
@struct slow5_hdr SLOW5 header
slow5_idx_t
slow5_log_level_opt
slow5_press_method
slow5_press_t
slow5_rec_size_t
slow5_rec_t
@struct slow5_rec SLOW5 record data struct (represents a single SLOW5 record)
slow5_rid_len_t
va_list

Unions§

slow5_press_stream