buttery-eel v0.2.0

Release v0.2.0 of buttery-eel

Changes:

• added multithreading in slow5 reading and associated flags --slow5_threads
• increased minimum required python3 to 3.8
• added process throttling
• added --quiet mode to suppress read progress output
• fixed some arg types
• increased tries to handle slower model loading on different systems
• added split_qscore.py to split fastq/uSAM by custom mean phread quality score after basecalling
• added --moves_out to emit the move table in uSAM output
• added read splitting with --do_read_splitting
• moved some specific controls back to regular guppy args and handled them a bit better
• bumped the default version of guppy to 3.6.8
• updated README to reflect changes

As well as a few bugs squashed and formatting changes.

NOTE: This release is the last release of the main branch of single processing. Releases after this will have the multiproc branch modified into the main branch, and the current single process main branch will be maintained on the singleproc branch

buttery-eel v0.1.0

Many use options have changed. Please see README for new examples.

Many guppy args can now be parsed directly adding them to the cmd line of buttery-eel. Not all options were tested. Many things that modify output, like demuxing, aligning, won't work. If there is something missing that you need, please open an issue and let me know and I'll see what I can do.

unaligned sam writing method heavily borrowed from bonito and dorado code from ONT. This is why I love open-source code. Thanks guys!

Overview of changes:

• Restructure server control code e235213
• add generic options for guppy_server e235213
• changed UI and args, see --help and examples in README e235213
• add -g for --guppy_bin a2b0652
• add modification calling and unaligned sam format c468ad6
• bump default guppy version to 6.3.7 f8b197c
• update README 8a68530 0660ba0
• add pass/fail threshold and output pass/fail sam/fastq with --qscore

The buttery-eel v0.0.1

Initial alpha pre-release

Please let me know if you have feedback to go into future releases