Crate slow5lib_sys
source ·Expand description
§slow5lib-sys
Low level bindings to the slow5lib C library version 1.1.0
§Installation
Add the following to your Cargo.toml:
[dependencies]
slow5lib-sys = "0.9"
§License
Licensed under either of
- Apache License, Version 2.0, (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
- MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)
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§
- @struct slow5_aux_meta SLOW5 auxiliary field metadata (information available in the SLOW5 header)
- @struct slow5_file SLOW5 file structure
- @struct slow5_file SLOW5 file meta data
- @struct slow5_fmt_meta SLOW5 file meta data
- @struct slow5_hdr SLOW5 header
- @struct slow5_hdr_data SLOW5 header data (constant attributes in FAST5 files)
- @struct slow5_rec SLOW5 record data struct (represents a single SLOW5 record)
- @struct slow5_rec_aux_data SLOW5 auxiliary field data (represents a single SLOW5 auxiliary field of a particular read record)
- @struct slow5_version @brief SLOW5 file version
Constants§
- < the format is ASCII SLOW5
- < the format is binary SLOW5 (that is, BLOW5)
- < the format is unknown, usually the case before parsing the file extension
Statics§
Functions§
- Add a read entry to the SLOW5 file while updating the SLOW5 index (not thread safe).
- Adds an auxiliary field to a SLOW5 header. Return
- Get an auxiliary field in a SLOW5 record as an 8-bit signed integer.
- Get an auxiliary field in a SLOW5 record as an 8-bit signed integer array.
- Close a slow5 file and free its memory. If the file had been opened for writing or appending, EOF marker will be written
- Print the binary end of file to a file pointer.
- Get a read entry from a slow5 file corresponding to a read_id.
- 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
- Get the read entry under the current file pointer of a slow5 file.
- Adds a new header data attribute.
- Add a new header data attribute.
- Add a new header read group.
- Print the header in the specified format to a file pointer.
- Get a header data attribute for a particular read_group.
- Sets a header data attribute for a particular read_group.
- Get the header in the specified format.
- Writes the associated SLOW5 header to a SLOW5 file.
- Create the index file for slow5 file. Overwrites if already exists.
- Loads the index file for slow5 file. Creates the index if not found.
- Loads the index file for slow5 file given it’s pathname. Will not create the index if not found.
- Create the index file for slow5 file. Overrides if already exists.
- Unloads an index associted to a slow5_file_t using slow5_idx_load and free the memory.
- Ultra-Low-level API ******************************************************************************
- Open a slow5 file with a specific mode given it’s pathname.
- Open a slow5 file of a specific format with a mode given it’s pathname.
- Free a slow5 record.
- Print a read entry in the specified format to a file pointer.
- Get the read entry in the specified format.
- Remove a read entry at a read_id in a slow5 file while updating the SLOW5 index (not thread safe).
- Low-level API *******************************************************************************
- Writes a SLOW5 record to a SLOW5 file.
Type Aliases§
- @struct slow5_aux_meta SLOW5 auxiliary field metadata (information available in the SLOW5 header)
- SLOW5 record
- @struct slow5_file SLOW5 file meta data
- @struct slow5_file SLOW5 file structure
- @enum slow5_fmt File formats we are dealing with
- @struct slow5_hdr_data SLOW5 header data (constant attributes in FAST5 files)
- @struct slow5_hdr SLOW5 header
- @struct slow5_rec SLOW5 record data struct (represents a single SLOW5 record)