v0.6.0

* 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.

---------

Co-authored-by: Mitchell R. Vollger <[email protected]>

.gitignore

@@ -18,3 +18,7 @@ tests/data/chr20*bam*
 hub.txt
 *test.bam*
 py-ft/Cargo.lock
+py-ft/test.html
+py-ft/test.py
+py-ft/test.tbl
+tests/data/shuffle.chr20.hifi.bed.gz

CHANGELOG.md

@@ -2,6 +2,19 @@
 
 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.
+
 ## [0.5.4] - 2024-09-10
 
 ### ⚙️ Miscellaneous Tasks
@@ -10,6 +23,7 @@ All notable changes to this project will be documented in this file.
 - Readme
 - Readme
 - Readme
+- Release fibertools-rs version 0.5.4
 
 ## [0.5.3] - 2024-07-31
 

Cargo.toml

@@ -57,6 +57,8 @@ rand = "0.8.5"
 
 [build-dependencies]
 burn-import = {version = "0.12"}
+vergen-git2 = { version = "1.0.1", features = ["build"] }
+
 
 [dev-dependencies]
 assert_cmd = "2.0.11"

build.rs

@@ -1,6 +1,22 @@
-use std::process::Command;
+use std::error::Error;
+use vergen_git2::*;
+
+fn vergen() -> Result<(), Box<dyn Error>> {
+    // NOTE: This will output everything, and requires all features enabled.
+    // NOTE: See the specific builder documentation for configuration options.
+    let build = BuildBuilder::all_build()?;
+    let git2 = Git2Builder::all_git()?;
+
+    Emitter::default()
+        .add_instructions(&build)?
+        .add_instructions(&git2)?
+        .emit()?;
+    Ok(())
+}
 
 fn main() {
+    /*
+    use std::process::Command;
     let output = Command::new("git")
         .args(["rev-parse", "HEAD"])
         .output()
@@ -12,6 +28,8 @@ fn main() {
         cargo:rustc-env=CARGO_LONG_VERSION={} commit:{}",
         git_hash, version, git_hash
     );
+    */
+    vergen().expect("Unable to set version and git hash");
 
     // Generate the model code and state file from the ONNX file.
     use burn_import::onnx::ModelGen;

py-ft/Cargo.toml

@@ -1,7 +1,8 @@
 [package]
 edition = "2021"
 name = "pyft"
-version = "0.2.3"
+version = "0.2.6"
+readme = "./README.md"
 
 [lib]
 crate-type = ["cdylib"]