v0.2.2

[v0.2.2] - 2024-09-10

Fixed

• Faulty pod5 files (e.g. pod5: IOError: Invalid signature in file) are now catched, faulty input files are skipped.

Added

• get_truncated.sh: added a new script to easily obtain the truncated reads from the detected_boundaries*.csv files.
• command.json file is now saved in the output folder and contains the command used to run ADAPTed.
• Logging: process outputs are now logged to the adapted.log file and to stdout.
• ADAPTed now supports continuing from a previous (incomplete) run using the continue <continue_from_path> subcommand.

Changed

• Multiprocessing of reads now relies on a shared memory object to process the results of the reads. This allows for a more efficient use of system resources and prevents issues with broken pipe errors.
• The output directory is now named after the version of ADAPTed and a random UUID rather than the current date and time.

Removed

• The --create_subdir argument is removed. The output directory is now always created in the specified output folder.