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.

0.1.12

• Fixed file handle leak in repacker
• Added readthedocs documentation links in README.md
• Updated developer installation instructions to use conan<2
• Reworked pod5 convert fast5 to tolerate runtime exceptions
• Added --output argument to pod5 convert fast5 and to_fast5 replacing positional argument of the same name
• Added --strict argument to pod5 convert fast5 to promptly stop on exceptions
• Use same type run_info_index_t for pod5_get_file_run_info_count and pod5_get_file_run_info.

0.1.11

• Python API supports python 3.11
• Changed python API dependency version pyarrow~=11.0.0 from 8.0.0 to support python 3.11
• Changed python API dependency version hdf5~=8.0.0 from v7.0.0 to support python 3.11
• Added missing python API wheels on windows

0.1.10

• Added pod5_get_read_count to find the count of all reads in file
• Added pod5_get_read_ids to retrieve all read id's in file
• Added pod5_get_file_run_info to retrieve a run info at an absolute index in the file
• Added pod5_free_run_info to free run info's (replaces pod5_release_run_info)
• Deprecated pod5_release_run_info (see pod5_free_run_info)
• Added pod5_get_file_run_info_count to find the number of run info's in a file
• Added pod5 filter tool to subset pod5 files with simple list of read ids
• Reworked pod5 subset to give better control over resources used
• Added tqdm progress bar to pod5 subset (disable with POD5_PBAR=0)
• pod5 subset can now parse csv and tsv tables / summaries
• Removed filepath header line from pod5 inspect reads
• pod5 repack now repacks all inputs one-to-one
• Versioning now controlled by VCS inspection using setuptools_scm
• Added version attributes to lib-pod5

0.1.8

• Update to zlib 1.2.13
• Update to zstd 1.5.4
• Pinned pre-commit=v2.21.0 while supporting python3.7
• Added more read_id getter methods to Reader
• Fixed pod5 inspect read
• Reworked pod5 convert to_fast5 output filenames to allow for 1-1 mapping
• Fixed pod5 convert to_fast5 creating an empty fast5 output
• Fixed pod5 convert to_fast5 ignoring the --force_overwrite argument
• Fixed issue where thread_pool.h wasn't shipped.
• Added support for python 3.8 + 3.10 on windows
• Added gcc7 linux build of pod5