buttery-eel v0.7.1

This patch fixes an issue when running buttery-eel with dorado-server versions older than 7.6.8

• fix namespace error on estimate_poly_a by doing a version check

Full Changelog: v0.7.0...v0.7.1

buttery-eel v0.7.0

This version has a bug when running with dorado-server versions lower than 7.6.8 - Please use v0.7.1 or newer

buttery-eel v0.7.0 significantly updates the error model.
With the new --resume option, runs that did not finish can be continued without re-basecalling reads already processed.

This release has been tested up to dorado-server-7.6.8

What's Changed

• better error handling
• --resume to resume a crashed run by providing the fastq or sam file of the crashed run
• --dorado_model_path to work like dorado model paths
• --estimate_poly_a polyA/T tail estimation
• samples per second reported at the end of a run
• qscores reported as floats instead of ints and samtag changed to qs:f: (alignment with latest dorado changes)
• update split script to handle floats and legacy ints
• updated docs

Pull request:

• Handle errors better and add new features by @Psy-Fer in #72

Full Changelog: v0.6.0...v0.7.0

buttery-eel v0.6.0

What's Changed

• RNA fixes and u2t conversion by @Psy-Fer in #61
• thread model doc update
• test updates and fixes for new test machine

Full Changelog: v0.5.1...v0.6.0

buttery-eel v0.5.1

What's Changed

• add dot try on barcode summary by @Psy-Fer in #49

Full Changelog: v0.5.0...v0.5.1

buttery-eel v0.5.0

What's Changed

• 7.4.12 dorado for v0.5.0 buttery-eel by @Psy-Fer in #47
• Added more SAM tags
• Breaking API changes accounted for - see README
• Prints total reads basecalled at the end
• Skip queue introduced and will write a skip file if skip reads are detected
• macOS changes to the queue library so it works
• read_splitting on by default for ont lib >=7.4.12

Full Changelog: v0.4.3...v0.5.0

Buttery-eel v0.4.3

What's Changed

Fixed demux parent/read ID issue
major code restructure and compatibility with lastest dorado server lib name change: ont-pybasecall-client-lib
prep for Duplex calling, but currently unavailable due to bugs/missing methods in ONT library.

• Lib change and prep for duplex by @Psy-Fer in #39

Full Changelog: v0.4.2...v0.4.3

buttery-eel v0.4.2

What's Changed

• cut off params update by @hasindu2008 in #24
• update dev from main by @Psy-Fer in #25
• Fix for old guppy API and mod calling newline bug by @Psy-Fer in #27

Full Changelog: v0.4.1...v0.4.2

buttery-eel v0.4.1

What's Changed

• pulling main to dev for fixing dorado by @Psy-Fer in #22
• Fix dorado calls by @Psy-Fer in #23
• default basecaller updated to dorado-server 7.1.4

This release fixes the problems with dorado reads not matching the output from the vanilla dorado-server.
Please use this release if you are going to use dorado server

Full Changelog: v0.4.0...v0.4.1

buttery-eel v0.4.0

What's Changed

• Dev by @Psy-Fer in #20

Barcode demultiplexing
Dorado compatibility
Updated documentation
Update format specs
Extensive testing

Feature complete basecaller for guppy v6.5.7
Tested with dorado server v7.1.4 (with differing results problem)

Full Changelog: v0.3.3...v0.4.0

buttery-eel v0.3.3

What's Changed

• Multiproc by @Psy-Fer in #19

Fix read_id in read_splitting not being written correctly to fastq

Full Changelog: v0.2.4...v0.3.3