0.2.4

[0.2.4] 2023-07-13

Changed

• Increased numpy minimum version to >= 1.21.0
• Improved performance of subset, filter and merge tools.
• Repacker.wait and Repacker.waiter parameters

Deprecated

• Repacker.wait and Repacker.waiter some parameters are deprecated and issue FutureWarning

Fixed

• Repacker.is_complete returning True when work is queued.

0.2.3

[0.2.3] 2023-06-26

Added

• Add API (pod5_open_file_options) to prevent pod5 from opening a file using mmap, instead using direct file IO.
• Default field values (empty string) when converting fast5 files with missing fields

Changed

• Corrected Oxford Nanopore Technologies company name in package metadata to use Public Limited Company (Plc) instead of Limited (Ltd)
• Limited the number of processes created when specifying --threads to the number of cpu cores available os.cpu_count()
• Reduced the default value for --threads from 8 to 4 to improve stability on resource constrained systems

0.2.2

[0.2.2] 2023-06-0

Fixed

• Add API error when adding reads with invalid end reason, pore type or run info.

Changed

• Update internal arrow lib to not export flatbuffers symbols.

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

0.1.21

[0.1.21] 2023-04-27

Fixed

• Repacker reads_completed value while copying a selection of reads.
• Fixed crash when trying to load files with a bad footer.

0.1.20

[0.1.20] 2023-04-20

Fixed

• Fixed merging many files running out the size limit of dictionary indices.

0.1.19

[0.1.19] 2023-04-14

Changed

• pod5 convert fast5 now creates logs when POD5_DEBUG=1 set
• pod5 convert fast5 checks multi-read fast5s at conversion time
• Updated internal arrow version to 8.0.0.3

Fixed

• Fixed memory usage growth over time as signal was loaded with large pod5 files.
• Fixed crash loading malicious files (found via fuzz testing)
• Fixed leaks and UB when running unit tests.
• Fixed run-away memory consumption during fast5 conversion

0.1.16

• Fixed issue where pod5 would read out of bounds memory when decompressing some reads.

0.1.15

[0.1.15] 2023-03-31

Changed

• Refactored pod5 convert fast5 to use concurrent.futures only.
• Add further info to error message when signal cannot be decompressed by zstd
• Make merge operation not generate multiple identical run infos.

Fixed

• Fixed closing uninitialised file handles.
• Fixed pod5 inspect reads repeating header
• Fixed a crash with certain pod5 search operations.

0.1.13

• Fix loading large pod5 files on virtual-memory limited systems.