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CHANGELOG.md

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Changelog

All notable changes and fixes to ont_fast5_api will be documented here

The format is based on Keep a Changelog This project (aspires to) adhere to Semantic Versioning.

[4.1.3]

Added

  • Support for python up to 3.12

[4.1.2]

Added

  • Support for h5py>=3.9

Changed

  • Renamed VBZ compression settings to make it clearer which version is used in production

Removed

  • Support for python3.6

[4.1.1]

Fixed

  • Compatibility with numpy==1.24 unicode type

Changed

  • Updated Windows VBZ Plugin dll

[4.1.0]

Added

  • Support for fast5_api on macOS-M1

[4.0.2]

Fixed

  • Fixed Fast5Read import error

[4.0.1]

Changed

  • Fixed unresolved reference in compress_fast5.py
  • Fixed issue with compress_fast5.py not retaining enumeration metadata for the end_reason attribute
  • Increased minimum h5py version to 2.10

[4.0.0]

Added

  • Script demux_fast5 for demultiplexing fast5 reads based on column in summary file, e.g. for barcoded experiments

Removed

  • Removed deb builds which are no longer supported
  • Python3.5 support

[3.3.0] 2021-02-17

Added

  • Added yield_fast5_reads to conversion_tools.

[3.2.0] 2021-01-28

Changed

  • Dropped support for older h5py/numpy versions, min now h5py>=2.8, numpy>=1.16
  • fast5_subset now displays errors (but continues processing) when it encounters input fast5 files it can't read.

Added

  • Add support for explicitly specifying file drivers when loading multi-read fast5 files.

[3.1.6] 2020-08-20

Added

  • compress_fast5 now has a --sanitize option to remove optional groups.

Fixed

  • Correctly handle the case where h5pl can be imported but doesn't have the prepend() function available.

[3.1.5] 2020-06-15

Added

  • Added explicit requirements and checks to prevent running on Python 2.

[3.1.4] 2020-06-12

Fixed

  • Compression now works in single_to_multi.

[3.1.3] 2020-05-28

Fixed

  • Compression argument in fast5_subset and single_to_multi failed if not set

[3.1.2] 2020-05-04

Fixed

  • Compression argument in fast5_subset and single_to_multi was parsed incorrectly

[3.1.1] 2020-04-03

Fixed

  • Argument list for fast5_subset and single_to_multi had a syntax error

[3.1.0] 2020-04-02

Added

  • Hardlinking of metadata to prevent duplication and reduce filesize
  • Ability to enable compression when using fast5_subset and single_to_multi

Fixed

  • fast5_subset thread pool could sometimes close before all tasks were completed
  • fast5_subset will create output directory if it doesn't exist

[3.0.2] 2020-03-17

Fixed

  • Comparison of file_versions could throw an error

[3.0.1] 2020-01-29

Fixed

  • Basecall1DTools could not load data from a Fast5Read

[3.0.0] 2020-01-20

Removed

  • python2 compatibility

Fixed

  • minor documentation errors: #28

[2.1.0] 2019-12-16

Added

  • Script to check the compression type of fast5 files in a folder
  • compress_fast5 can now be used --in_place

Fixed

  • Reading arrays with padded strings now succeeds (on h5py>2.7)
  • Compatibility bugs with h5py==2.6 now raises appropriate errors
  • Fast5File now has attribute read_id to match documentation

Changed

  • Now use standard settings for gzip compression (gzip=1, shuffle=None)
  • Inverted dependency between Fast5File and Fast5Read so Fast5Read is now the primary object

[2.0.1] 2019-11-28

Added

  • Option to --ignore_symlinks in fast5 conversion scripts
  • Explicit check to file_type for detemining single/multi-read files

Fixed

  • fast5_subset with single read fast5s was failing
  • unit test data now cleaned up properly

[2.0.0] 2019-11-19

Added

  • Compatibility for VBZ compressed reads
  • compress_fast5 script for compressing/decompressing fast5 files
  • get_reads() helper method to more easily loop through reads in a fast5 file

Changed

  • Fast5File().get_raw_data() updated interface to match Fast5Read and remove support for legacy files with multiple read numbers in a single Fast5File
  • Minimum depedency version requirements bumped. Set to Ubuntu16 apt python3-package defaults

Removed

  • Legacy Fast5Writer object. MultiReadFast5 or EmptyFast5File are preferred

[1.4.9] 2019-11-01

Added

  • Check for progressbar2 package and fail early if it's installed.

[1.4.8] 2019-10-22

Added

  • Support for h5py==2.10 string data type encoding changes

Fixed

  • Corrected some "for for" typos in argparse help text.

[1.4.7] 2019-07-29

Fixed

  • Bug in read string and read_id concatenation resulted in broken output file

[1.4.6] 2019-07-03

Added

  • Updated fast5_subset script to extract also from single-read fast5 files

Changed

  • Renamed fast5_subset source script from multi_fast5_subset.py to fast5_subset.py

[1.4.5] 2019-07-01

Fixed

  • Bug in number of processes being 0 when batch size is greater than number of reads (py2)

[1.4.4] 2019-06-18

Fixed

  • Bug in path name output from pathlib changes

[1.4.3] 2019-06-12

Fixed

  • Bug with apt-install and pathlib2

[1.4.2] 2019-06-10

Fixed

  • get_raw_data() now works with scale=True when start,end are None

[1.4.1] 2019-06-06

Added

  • Useful error message if no input files found

Fixed

  • filename_mapping output gave incorrect filenames

[1.4.0] 2019-05-29

Added

  • Script for extracting reads by id from multi_read files

[1.3.0] 2019-03-01

Fixed

  • Bug in output to filename_mapping.txt

[1.2.0] 2019-01-11

Added

  • Multi-threading support for multi<->single conversion for improved performance

Fixed

  • Removed incorrect license accidentally added to README

[1.1.1] 2019-01-10

Changed

  • Minor documentation updates
  • Follow symlinks when finding files recursively

[1.1.0] 2019-01-07

Added

  • Generic single- and multi- read interface via get_fast5_file

Fixed

  • Incorrect time estimates for single-multi conversion
  • Fixed path creation if not exist

[1.0.1] 2018-09-26

Added

  • Support for multi-read fast5 files
  • Conversion tools for single-multi read files

Fixed

  • Support for deprecated interface to Basecall2D following 0.4.0, support will end in v1.x.x

[0.4.0] 2017-07-16 (internal only)

Fixed

  • Basecall1d and Basecall2d raise consistent KeyError when fastq data missing

Changed

  • Interface to Basecall1d and Basecall2d unified for add_sequence() and get_sequence()

[0.3.3] 2017-06-23

Added

  • Fast5 file now supports logging via 'Fast5File.add_log()'

Fixed

  • Invalid component names no longer checked against LEGACY_COMPENENTS
  • Raise KeyError when fastq data missing from Basecall1d
  • median_before and start_mux populate correctly with sensible defaults

[0.3.2] 2017-03-22

Added

Major release - changes not logged before this point