# Changelog All notable changes to this project will be documented in this file. ## [0.6.1] - 2024-12-11 - Fix: the cli version string. ## [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 - Add to changelog - Add to changelog - Readme - Python docs - Python docs - Python docs - Python docs - Python docs - Python docs - Python docs - Python docs - Python docs - Python docs - Python docs - Python docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Docs - Rename iterator - Rename iterator - Rename iterator - Rename iterator ## [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