Update to version 1.3.0

Author: egor-dolzhenko

Cargo.lock

@@ -1,9 +1,12 @@
 [package]
 name = "trgt"
-version = "1.2.0"
+version = "1.3.0"
 edition = "2021"
 build = "build.rs"
 
+[workspace]
+members = ["crates/pipeplot"]
+
 [build-dependencies]
 vergen = { version = "8.2", features = ["git", "gitcl"] }
 
@@ -20,11 +23,8 @@ kodama = "0.3"
 rand = "0.8"
 once_cell = "1.18"
 flate2 = "1.0"
-resvg = "0.36"
-usvg = "0.36"
-tiny-skia = "0.11"
-svg2pdf = "0.9"
-tempfile = "3"
 rayon = "1.10"
 crossbeam-channel = "0.5"
-semver = "1.0"
+pipeplot = { path = "crates/pipeplot" }
+semver = "1.0"
+tempfile = "3"

Cargo.toml

@@ -136,8 +136,12 @@ tandem repeats at genome scale. 2024](https://www.nature.com/articles/s41587-023
     - Merging now skips and logs problematic loci by default. Use the `--quit-on-errors` flag to terminate on errors. Statistics are logged post-merge, including counts of failed and skipped TRs.
   - `trgt validate`
     - Always outputs statistics directly to stdout and stderr instead of logging them.
-  - Bug fix: 
+  - Bug fix:
     - Resolved issue with handling bgzip-compressed BED files.
+- 1.3.0
+  - Plotting code has been refactored as we prepare to revamp repeat visualizations
+  - The maximum number of reads per allele to plot can now be specified by `--max-allele-reads`
+  - bugfix: repeat identifiers are now permitted to contain commas
 
 ### DISCLAIMER
 

README.md

@@ -0,0 +1,13 @@
+[package]
+name = "pipeplot"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+resvg = "0.36"
+usvg = "0.36"
+tiny-skia = "0.11"
+svg2pdf = "0.9"
+tempfile = "3"

crates/pipeplot/Cargo.toml

@@ -0,0 +1,46 @@
+use crate::{pdf, png, svg, PipePlot};
+use std::path::{Path, PathBuf};
+use tempfile::NamedTempFile;
+
+pub fn generate(plot: &PipePlot, path: &PathBuf) -> Result<(), String> {
+    let extension = Path::new(path)
+        .extension()
+        .and_then(|ext| ext.to_str())
+        .ok_or_else(|| format!("Failed to get extension from path: {path:?}"))?;
+    let file_type = FileType::from_extension(extension)
+        .ok_or_else(|| format!("Unsupported file extension: {extension:?}"))?;
+
+    let temp_dir = PathBuf::from(&path);
+    let temp_dir = temp_dir
+        .parent()
+        .ok_or_else(|| format!("Invalid path: {path:?}"))?;
+    let svg_temp_path = NamedTempFile::new_in(temp_dir)
+        .map_err(|e| format!("Failed to create temporary file: {e}"))?
+        .into_temp_path();
+
+    svg::generate(plot, &svg_temp_path.to_path_buf());
+    match file_type {
+        FileType::Svg => svg_temp_path.persist(path).map_err(|e| e.to_string())?,
+        FileType::Png => png::render(&svg_temp_path.to_path_buf(), path)?,
+        FileType::Pdf => pdf::render(&svg_temp_path.to_path_buf(), path)?,
+    }
+    Ok(())
+}
+
+#[derive(Debug, PartialEq)]
+enum FileType {
+    Svg,
+    Png,
+    Pdf,
+}
+
+impl FileType {
+    fn from_extension(extension: &str) -> Option<Self> {
+        match extension.to_lowercase().as_str() {
+            "svg" => Some(FileType::Svg),
+            "png" => Some(FileType::Png),
+            "pdf" => Some(FileType::Pdf),
+            _ => None,
+        }
+    }
+}

crates/pipeplot/src/image.rs

@@ -0,0 +1,18 @@
+/*!
+This crate provides functionality to generate the so-called "pipe plots"
+consisting of stacked horizontal pipes (bars). Each pipe consists of segments of
+specified width, shape, and color. Pipe plots can be annotated with scales,
+labels, and legends. The crate supports rendering of pipe plots as SVG, PNG, and
+PDF images.
+
+Pipe plots are useful for representing pileups of sequenced reads.
+*/
+
+mod image;
+mod pdf;
+mod pipeplot;
+mod png;
+mod svg;
+
+pub use image::generate as generate_image;
+pub use pipeplot::{Band, Color, Legend, Pipe, PipePlot, Seg, Shape};

crates/pipeplot/src/lib.rs

@@ -1,12 +1,14 @@
+use std::path::PathBuf;
 use usvg::{TreeParsing, TreeTextToPath};
 
-pub fn render(svg_path: &str, pdf_path: &str) {
-    let svg = std::fs::read_to_string(svg_path).unwrap();
+pub fn render(svg_path: &PathBuf, pdf_path: &PathBuf) -> Result<(), String> {
+    let svg = std::fs::read_to_string(svg_path).map_err(|e| e.to_string())?;
     let options = usvg::Options::default();
     let mut tree = usvg::Tree::from_str(&svg, &options).expect("Error parsing SVG");
     let mut db = usvg::fontdb::Database::new();
     db.load_system_fonts();
     tree.convert_text(&db);
     let pdf = svg2pdf::convert_tree(&tree, svg2pdf::Options::default());
-    std::fs::write(pdf_path, pdf).unwrap();
+    std::fs::write(pdf_path, pdf).map_err(|e| e.to_string())?;
+    Ok(())
 }

src/trvz/pdf.rs renamed to crates/pipeplot/src/pdf.rs

@@ -0,0 +1,48 @@
+#[derive(Debug, PartialEq)]
+pub enum Shape {
+    Rect,
+    HLine,
+    VLine,
+    None,
+    Tick(Option<u32>),
+}
+
+pub type Color = String;
+
+#[derive(Debug, PartialEq)]
+pub struct Seg {
+    pub width: u32,
+    pub color: Color,
+    pub shape: Shape,
+}
+
+#[derive(Debug)]
+pub struct Band {
+    pub pos: u32, // Position relative to pipe's start
+    pub width: u32,
+    pub color: Color,
+}
+
+#[derive(Debug)]
+pub struct Pipe {
+    pub xpos: u32,
+    pub ypos: u32,
+    pub height: u32,
+    pub segs: Vec<Seg>,
+    pub bands: Vec<Band>,
+    pub outline: bool,
+}
+
+#[derive(Debug)]
+pub struct Legend {
+    pub xpos: u32,
+    pub ypos: u32,
+    pub height: u32,
+    pub labels: Vec<(String, String)>,
+}
+
+#[derive(Debug)]
+pub struct PipePlot {
+    pub pipes: Vec<Pipe>,
+    pub legend: Legend,
+}

crates/pipeplot/src/pipeplot.rs

@@ -1,15 +1,18 @@
+use std::path::PathBuf;
 use usvg::{TreeParsing, TreeTextToPath};
 
-pub fn render(svg_path: &str, png_path: &str) {
-    let svg = std::fs::read(svg_path).unwrap();
+pub fn render(svg_path: &PathBuf, png_path: &PathBuf) -> Result<(), String> {
+    let svg = std::fs::read(svg_path).map_err(|e| e.to_string())?;
     let options = usvg::Options::default();
-    let mut tree = usvg::Tree::from_data(&svg, &options).unwrap();
+    let mut tree = usvg::Tree::from_data(&svg, &options).map_err(|e| e.to_string())?;
     let mut db = usvg::fontdb::Database::new();
     db.load_system_fonts();
     tree.convert_text(&db);
     let pixmap_size = tree.size.to_int_size();
-    let mut pixmap = tiny_skia::Pixmap::new(pixmap_size.width(), pixmap_size.height()).unwrap();
+    let mut pixmap = tiny_skia::Pixmap::new(pixmap_size.width(), pixmap_size.height())
+        .ok_or("Unable to init image".to_string())?;
     let tree = resvg::Tree::from_usvg(&tree);
     tree.render(resvg::usvg::Transform::identity(), &mut pixmap.as_mut());
-    pixmap.save_png(png_path).unwrap();
+    pixmap.save_png(png_path).map_err(|e| e.to_string())?;
+    Ok(())
 }