0.2.0

[0.2.0] 2023-05-18

Added

• pod5 view tool to view / inspect pod5 files as tables. Gives a >200x speed improvement compared to pod5 inspect reads
• pod5 recover tool to recover data from corrupted / truncated pod5 files
• pod5 update documentation
• source distributions to pypi

Changed

• pod5 subset and pod5 filter uses polars to parse inputs
• pod5 subset and pod5 filter csv formatting requirements tightened
• pod5 tools which use multiple pod5 file inputs now accept directories which can be searched recursively with -r/--recursive
• pod5 subset --read-id-column argument abbreviateion -r change to -R to allow -r/--recursive to be consistent for all tools
• pod5 tools use hyphens in all arguments (e.g. --force-overwrite and --read-id-column)
• pod5 merge and pod5 update uses named -o/--output argument instead of positional output argument to standardise tools
• pod5 update progress bar and better detection of name conflicts
• Minimised number of open file handles in tools to prevent Too many open files error
• Logging added to view, merge, filter and subset. Enabled with POD5_DEBUG=1

Deprecated

• pod5 inspect reads deprecated in-favour of pod5 view

Fixed

• Exception raised when calling pod5 without any arguments
• Exception raised in pod5 convert fast5 where closed writers were reopened after being closed by a caught exception
• Fixed Gitlab 38, pod5_get_end_reason and pod5_get_pore_type ignoring input string length checks.

Removed

• pod5 subset --json mapping arguments
• pod5 merge --chunk-size argument
• ReadTableVersion replaced with an integer value