Changelog

All notable changes to this project will be documented in this file.

[0.6.0] - 2024-11-14

fix: do not report m6A predictions that happen within the first 7 or last 7 bp of a read. This is so the ML model only operates on real data. No changes to other calls. Will fix #65
fix: report footprint codes even if there is no spanning msp, fixes #63
feat: add a pyft utility that can take extract --all data and make it long format for plotting.
feat: Add a shuffle option to pileup to help with the FDR calculations in FIRE
feat: make nucleosomes and MSPs optional in pileup
chore: use vergen for cli version
feat: add phasing stats to QC
feat: allow strip-base mods to filter on base mod quality.

[0.5.4] - 2024-09-10

⚙️ Miscellaneous Tasks

Update changelog with release
Readme
Readme
Readme
Release fibertools-rs version 0.5.4

[0.5.3] - 2024-07-31

⚙️ Miscellaneous Tasks

Update changelog with release
Update changelog with release
Update changelog with release
Update changelog with release
Update changelog with release
Release fibertools-rs version 0.5.3

[0.5.2] - 2024-07-31

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.5.2

[0.5.1] - 2024-07-31

🐛 Bug Fixes

Remove windows target
Citation

Release

Remove windows target

[0.4.2] - 2024-03-21

⚙️ Miscellaneous Tasks

Clean
Clean
Clean cargo config
Update helps
Clean changelog
Clean docs
Clean docs

[0.4.1] - 2024-03-20

🚀 Features

Convert pytorch models to onnx to allow more backends (#46)

⚙️ Miscellaneous Tasks

Sync lock with branch
Sync lock with branch
Ignore notebook
Make test data smaller
Make cargo publish smaller
Make cargo publish smaller
Make cargo publish smaller
Make cargo publish smaller
Make cargo publish smaller
Make test data larger again since I remove the whole dir from cargo publish
Make test data larger again since I remove the whole dir from cargo publish
Make test data larger again since I remove the whole dir from cargo publish
Make test data larger again since I remove the whole dir from cargo publish

[0.3.9] - 2024-02-28

🚀 Features

Add optional min msp filter to fire output
Add optional min msp filter to fire output
Add optional min msp filter to fire output
Add optional min msp filter to fire output

🐛 Bug Fixes

Allow overwritting fire qual
Typo

⚙️ Miscellaneous Tasks

Pyft lock
Pyft lock
Pyft lock
Tch update
Tch update
Release fibertools-rs version 0.3.9

[0.3.8] - 2024-01-24

🚀 Features

Update pyft
Update pyft to have a writer function
Update pyft to have a writer function
Update pyft to have a writer function
Better fire paralization
Center and extract now include fire scores in the range of 0-255

🐛 Bug Fixes

GBDT made a semvar breaking change, fixing and locking depandancies.

⚙️ Miscellaneous Tasks

Improved error msg
Clippy
CI
CI
Simplify colos
Whitespace
Readme and help pages
Readme and help pages
Pyft lock

[0.3.7] - 2024-01-10

🚀 Features

Add hp tag to center
Add hp tag to center
Add simplify options to center
Move prediction into a feature only avalible through Cargo, since bioocnda wont let me do large installs anymore.
Add ability to print FIRE features to a text file, TODO predict FIREs in rust.
Fire progress indicator.
Add a min ML options to add-nucs and keep working on FIRE predictions
Speed up writing FIRE results
FIRE io
Start working on decorators
Start working on decorators
Use threads better, fire feats
Use threads better, fire feats
Use threads better, fire feats
Use threads better, fire feats
Update fire model
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
Adding rle information to fire feats
FIRE now works in fibertools! TODO add info to extract, etc.
Adding a fire bed+ extract for the fire pipeline.
FIRE extract update
FIRE extract update

🐛 Bug Fixes

Try and better use threads.
Try and better use threads.
Make an iterator for fiberseq records
Allow for the unaligned read start and read end
Allow for the unaligned read start and read end

⚙️ Miscellaneous Tasks

Update.
Update.
Update.
Update.
Update.
Update.
Update.
Update.
Add trace to ml mm parser

Feat

Adding code outline for footprinting tool

Chroe

Clippy
Cli

[0.3.6] - 2023-10-09

⚙️ Miscellaneous Tasks

Update

[bio-io-v0.3.2] - 2023-10-09

⚙️ Miscellaneous Tasks

Improve progress bar
Improve progress bar

[bio-io-v0.3.1] - 2023-10-08

Chrom

Add docs.

[0.3.3] - 2023-10-08

🐛 Bug Fixes

Progress bar display issues.

Chrom

Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.
Add docs.

[0.3.2] - 2023-09-27

🐛 Bug Fixes

Extra comma in ft center wide format. fixes 21

⚙️ Miscellaneous Tasks

Fix typo in cli message
Update deps

Chrom

Fix warning msg

[bio-io-v0.3.0] - 2023-08-13

🚀 Features

Better progress bar for extract.
Move progress bar into bamchunk iterator, unify progress bar.
Move progress bar into bamchunk iterator, unify progress bar.
Move progress bar into bamchunk iterator, unify progress bar.
Move progress bar into bamchunk iterator, unify progress bar.

[bio-io-v0.2.0] - 2023-07-29

⚙️ Miscellaneous Tasks

Release bio-io version 0.2.0

[bamlift-v0.2.0] - 2023-07-29

🚀 Features

Very large improvment in speed of lifting over ranges, some liftover results differ from before by 1bp but it is rare.
Adding liftover to pyft
Reorganize pyft api and docs
Adding ft center to the python module!
Add qual to ft cetner, and clean the ft center code more
Change the result of liftovers to be an Option.

🐛 Bug Fixes

Move nuc and msp logic out of extract into ranges struct and simplify. We ran on a whole genome ft extract to confirm results dont change.
Reduce number of copies for nuc and msp.
Unify api anming for liftover, optimize for inclusion in pyft

⚙️ Miscellaneous Tasks

Example py-ft
Hide more deps under features for pyft
Clippy
Clippy
Readme
Readme
Readme
Readme
Readme
Readme
Readme
Readme
Readme
Readme
Regex update
Fix docs and fetch
Drop darkmode
Improve docs
Refactor a large part of the code base to reduce redudance. TODO simplify center and basemods with this new api.
Simplifed center with new api.
Release bamlift version 0.2.0

[0.2.6] - 2023-07-21

🚀 Features

I have a minimal working python package yay!
Add cpg to python modele and make easier access in the rust basemod api

🐛 Bug Fixes

Rework fiberdata to consume bam record to avoid extra copy
Speed options

⚙️ Miscellaneous Tasks

[0.2.5] - 2023-07-18

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.2.5

[0.2.4] - 2023-07-11

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.2.4

[0.2.3] - 2023-06-24

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.2.3

[0.2.2] - 2023-06-15

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.2.2

[0.2.1] - 2023-06-14

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.2.1

[0.2.0] - 2023-06-10

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.2.0

[0.1.4] - 2023-04-19

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.1.4

[0.1.3] - 2023-03-14

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.1.3

[0.1.2] - 2023-02-13

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.1.2

[0.1.1] - 2023-02-02

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.1.1-alpha.4
Release fibertools-rs version 0.1.1

[0.1.1-alpha.3] - 2023-02-01

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.1.1-alpha.3

[0.1.1-alpha.2] - 2023-02-01

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.1.1-alpha.1
Release fibertools-rs version 0.1.1-alpha.2

[0.1.1-alpha] - 2023-02-01

⚙️ Miscellaneous Tasks

Release fibertools-rs version 0.1.1-alpha