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Mitchell R. Vollger committed Nov 14, 2024
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Expand Up @@ -4,16 +4,14 @@ All notable changes to this project will be documented in this file.

## [0.6.0] - 2024-11-14

### 🚀 Features

- Add ability to drop mods below an ML score
- Add shuffle option to pileup that produces a shuffled track in addition to the real one
- Nuc and msp optional

### 🐛 Bug Fixes

- Report footprint codes even if there is no spanning msp, will fix #63
- 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.
- 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

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