# Changelog All notable changes and fixes to ont_fast5_api will be documented here The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) This project (aspires to) adhere to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). ## [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: https://github.com/nanoporetech/ont_fast5_api/issues/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