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+ "windows_aarch64_msvc",
+ "windows_i686_gnu",
+ "windows_i686_gnullvm",
+ "windows_i686_msvc",
+ "windows_x86_64_gnu",
+ "windows_x86_64_gnullvm",
+ "windows_x86_64_msvc",
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+ "synstructure",
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+dependencies = [
+ "displaydoc",
+ "litemap",
+ "serde",
+ "zerovec",
+]
+
+[[package]]
+name = "zerovec"
+version = "0.10.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "aa2b893d79df23bfb12d5461018d408ea19dfafe76c2c7ef6d4eba614f8ff079"
+dependencies = [
+ "serde",
+ "yoke",
+ "zerofrom",
+ "zerovec-derive",
+]
+
+[[package]]
+name = "zerovec-derive"
+version = "0.10.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
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+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]

Cargo.toml

@@ -4,3 +4,9 @@ version = "0.1.0"
 edition = "2021"
 
 [dependencies]
+anyhow = "1.0.89"
+typst = "0.11.1"
+typst-as-lib = { version = "0.8.0", features = ["packages"] }
+typst-pdf = "0.11.1"
+ureq = "2.10.1"
+usvg = "0.44.0"

src/cytoband.rs

@@ -1,10 +1,12 @@
+use std::any::Any;
+use std::f64::consts::PI;
 use std::fs::File;
 use std::io::{BufRead, BufReader, Write};
 
-struct Range {
-    start: u32,
-    end: u32,
-    category: String,
+pub struct Range {
+    pub start: u32,
+    pub end: u32,
+    pub category: String,
 }
 
 struct SvgConfig {
@@ -17,7 +19,7 @@ struct SvgConfig {
     rect_height: u32,
 }
 
-fn read_ranges(filename: &str, contig: &str) -> std::io::Result<Vec<Range>> {
+pub fn read_ranges(filename: &str, contig: &str) -> std::io::Result<Vec<Range>> {
     let file = File::open(filename)?;
     let reader = BufReader::new(file);
     let mut ranges = Vec::new();
@@ -37,11 +39,7 @@ fn read_ranges(filename: &str, contig: &str) -> std::io::Result<Vec<Range>> {
     Ok(ranges)
 }
 
-fn calculate_svg_config(
-    width: u32,
-    height: u32,
-    additional_rects: &[AdditionalRect],
-) -> SvgConfig {
+fn calculate_svg_config(width: u32, height: u32, additional_rects: &[AdditionalRect]) -> SvgConfig {
     let max_above_level = additional_rects
         .iter()
         .filter_map(|r| {
@@ -83,6 +81,12 @@ fn calculate_svg_config(
     }
 }
 fn generate_svg_header(config: &SvgConfig) -> String {
+    let svg_width = config.width + 100;
+    let svg_height = config.height + 100;
+    let circle_radius = (config.height as f64) / 2.0;
+    let rect_height = config.rect_height as f64;
+    let path_radius = circle_radius + rect_height / 2.0;
+
     format!(
         r#"<svg width="{}" height="{}" xmlns="http://www.w3.org/2000/svg">
         <defs>
@@ -97,6 +101,7 @@ fn generate_svg_header(config: &SvgConfig) -> String {
         </defs>"#,
         config.width,
         config.height,
+        // path,
         config.width,
         config.tube_height,
         config.tube_height / 2,
@@ -107,7 +112,6 @@ fn generate_svg_header(config: &SvgConfig) -> String {
 fn generate_tube_base(config: &SvgConfig) -> String {
     format!(
         r#"<rect x="0" y="0" width="{}" height="{}" fill="url(#tubeGradient)" rx="{}" ry="{}"/>"#,
-        // r#"<rect x="0" y="0" width="{}" height="{}" fill="url(#tubeGradient)" stroke="black" stroke-width="1" rx="{}" ry="{}"/>"#,
         config.width,
         config.tube_height + 1,
         config.tube_height / 2,
@@ -223,7 +227,6 @@ fn generate_tube_highlights(config: &SvgConfig) -> String {
     )
 }
 
-
 fn generate_additional_rects<'a, I>(rects: I, config: &SvgConfig, scale_factor: f64) -> String
 where
     I: IntoIterator<Item = &'a AdditionalRect>,
@@ -300,6 +303,7 @@ fn create_chromosome_svg(
     svg_content.push_str("</svg>");
     svg_content
 }
+
 pub fn svg_chromosome(
     contig: &str,
     width: u32,
@@ -313,7 +317,10 @@ pub fn svg_chromosome(
     let total_range = ranges.iter().map(|r| r.end).max().unwrap_or(0);
     let config = calculate_svg_config(width, height, additional_rects);
 
-    let svg_content = create_chromosome_svg(&ranges, &config, total_range, additional_rects, lollipops);
+    let svg_content =
+        create_chromosome_svg(&ranges, &config, total_range, additional_rects, lollipops);
+
+    // let svg_content = bend_chromosome_svg(&svg_content, 0.2);
 
     let mut output_file = File::create(svg_path)?;
     output_file.write_all(svg_content.as_bytes())?;
@@ -322,3 +329,78 @@ pub fn svg_chromosome(
 
     Ok(())
 }
+
+pub fn generate_chromosome_svg(
+    ranges: Vec<Range>,
+    cx: f64,
+    cy: f64,
+    r: f64,
+    start_angle: f64,
+    end_angle: f64,
+) -> String {
+    let mut svg = String::new();
+    svg.push_str(&format!(
+        r#"<svg xmlns="http://www.w3.org/2000/svg" width="{}" height="{}">"#,
+        (2.0 * r) as u32,
+        (2.0 * r) as u32
+    ));
+
+    let angle_range = end_angle - start_angle;
+    let total_length = ranges
+        .iter()
+        .map(|range| range.end - range.start)
+        .sum::<u32>() as f64;
+
+    let mut current_angle = start_angle;
+
+    for range in ranges {
+        let start = range.start as f64;
+        let end = range.end as f64;
+        let category = &range.category;
+
+        let start_angle_rad = current_angle + (start / total_length) * angle_range;
+        let end_angle_rad = current_angle + (end / total_length) * angle_range;
+
+        let start_outer_x = cx + r * start_angle_rad.cos();
+        let start_outer_y = cy + r * start_angle_rad.sin();
+        let end_outer_x = cx + r * end_angle_rad.cos();
+        let end_outer_y = cy + r * end_angle_rad.sin();
+
+        let inner_r = r * 0.8; // Adjust this value to change the thickness of the chromosome
+        let start_inner_x = cx + inner_r * start_angle_rad.cos();
+        let start_inner_y = cy + inner_r * start_angle_rad.sin();
+        let end_inner_x = cx + inner_r * end_angle_rad.cos();
+        let end_inner_y = cy + inner_r * end_angle_rad.sin();
+
+        let large_arc_flag = if (end_angle_rad - start_angle_rad).abs() > PI {
+            1
+        } else {
+            0
+        };
+
+        let path_data = format!(
+            "M {:.2} {:.2} A {:.2} {:.2} 0 {} 1 {:.2} {:.2} L {:.2} {:.2} A {:.2} {:.2} 0 {} 0 {:.2} {:.2} Z",
+            start_outer_x, start_outer_y, r, r, large_arc_flag, end_outer_x, end_outer_y,
+            end_inner_x, end_inner_y, inner_r, inner_r, large_arc_flag, start_inner_x, start_inner_y
+        );
+
+        let color = match category.as_str() {
+            "gneg" => "rgb(255,255,255)",
+            "gpos25" => "rgb(192,192,192)",
+            "gpos50" => "rgb(128,128,128)",
+            "gpos75" => "rgb(64,64,64)",
+            "gpos100" => "rgb(0,0,0)",
+            _ => "rgb(162, 210, 255)",
+        };
+
+        svg.push_str(&format!(
+            r#"<path d="{}" fill="{}" stroke="black" stroke-width="1" />"#,
+            path_data, color
+        ));
+
+        current_angle = end_angle_rad;
+    }
+
+    svg.push_str("</svg>");
+    svg
+}

src/lib.rs

@@ -1,9 +1,16 @@
 pub mod cytoband;
 pub mod theme;
+pub mod report;
 
 #[cfg(test)]
 mod tests {
-    use cytoband::{svg_chromosome, AdditionalRect, Lollipop, RectPosition};
+    use std::{fs::File, io::Write};
+
+    use cytoband::{
+        generate_chromosome_svg, read_ranges, svg_chromosome, AdditionalRect, Lollipop,
+        RectPosition,
+    };
+    use report::write_report;
 
     use super::*;
 
@@ -60,8 +67,28 @@ mod tests {
             "/data/ref/hs1/cytoBandMapped.bed",
             "/data/chr1.svg",
             &additional_rects,
-            &lollipops
+            &lollipops,
         )
         .unwrap()
     }
+
+    #[test]
+    fn bend() -> anyhow::Result<()> {
+        let svg_path = "/data/bent.svg";
+        let ranges = read_ranges("/data/ref/hs1/cytoBandMapped.bed", "chr1")?;
+
+        let svg_content =
+            generate_chromosome_svg(ranges, 200.0, 200.0, 150.0, 0.0, 2.0 * std::f64::consts::PI);
+
+        let mut output_file = File::create(svg_path)?;
+        output_file.write_all(svg_content.as_bytes())?;
+
+        println!("SVG file created: {svg_path}");
+        Ok(())
+    }
+
+    #[test]
+    fn pdf() {
+        write_report("/data/test.pdf");
+    }
 }

src/report.rs

@@ -0,0 +1,25 @@
+use typst::eval::Tracer;
+use typst::foundations::{Bytes, Dict, Smart};
+use typst::text::Font;
+use typst_as_lib::TypstTemplate;
+
+pub fn write_report(path: &str) {
+    let font = include_bytes!("../typst_template/fonts/unicode.futurab.ttf");
+    let font = Font::new(Bytes::from_static(font), 0).expect("Could not parse font!");
+
+    let template = include_str!("../typst_template/template.typ");
+
+    let template = TypstTemplate::new(vec![font], template)
+        .with_static_source_file_resolver(vec!["/"])
+        .with_package_file_resolver(Default::default(), Some(ureq::AgentBuilder::new().build()));
+
+    let mut tracer = Default::default();
+
+    let doc = template
+        .compile_with_input(&mut tracer, Dict::new())
+        .expect("typst::compile() returned an error!");
+
+    // Create pdf
+    let pdf = typst_pdf::pdf(&doc, Smart::Auto, None);
+    std::fs::write(path, pdf).expect("Could not write pdf.");
+}

typst_template/fonts/sharefonts.net.txt

@@ -0,0 +1 @@
+Free download fonts at http://sharefonts.net

typst_template/template.typ

@@ -0,0 +1,269 @@
+#import sys: inputs
+#let cr_colors = (
+  dark_grey: rgb("#333333"), beige: rgb("#fdf0d5"), light_grey: rgb("#eeeeee"), dark_red: rgb("#780000"), red: rgb("#c1121f"), blue: rgb("#669bbc"), dark_blue: rgb("#003049"), green: rgb("#29bf12"),
+)
+
+#import "@preview/fletcher:0.5.1" as fletcher: diagram, node, edge
+// #import "@preview/metro:0.3.0": *
+// #import "@preview/cetz:0.2.2"
+
+#set page(paper: "a4", fill: cr_colors.light_grey, footer: locate(loc => [
+  #set text(10pt)
+  #if loc.page() != 1 {
+    align(right, counter(page).display("1 / 1", both: true))
+  }
+]))
+
+#show heading.where(level: 1): it => [
+  #set align(center)
+  #set text(fill: cr_colors.dark_blue)
+  #it.body
+  #v(18pt)
+]
+// #show image: set text(font: "FreeSans")
+
+#set text(size: 16pt, font: "Futura", fill: cr_colors.dark_blue)
+#let contigs = (
+  "chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY",
+)
+
+#let parseCustomDate(dateString) = {
+  let parts = dateString.split("T")
+  let datePart = parts.at(0).replace("-", "/")
+  let timePart = parts.at(1).split(":")
+  let hour = timePart.at(0)
+  let minute = timePart.at(1)
+
+  return datePart + " " + hour + "h" + minute
+}
+
+#let formatString(input) = {
+  let words = input.split("_")
+  let capitalizedWords = words.map(word => {
+    if word.len() > 0 {
+      upper(word.first()) + word.slice(1)
+    } else {
+      word
+    }
+  })
+  capitalizedWords.join(" ")
+}
+#let si-fmt(val, precision: 1, sep: "\u{202F}", binary: false) = {
+  let factor = if binary { 1024 } else { 1000 }
+  let gt1_suffixes = ("k", "M", "G", "T", "P", "E", "Z", "Y")
+  let lt1_suffixes = ("m", "μ", "n", "p", "f", "a", "z", "y")
+  let scale = ""
+  let unit = ""
+
+  if type(val) == content {
+    if val.has("text") {
+      val = val.text
+    } else if val.has("children") {
+      val = val.children.map(content => content.text).join()
+    } else {
+      panic(val.children.map(content => content.text).join())
+    }
+  }
+  // if val contains a unit, split it off
+  if type(val) == str {
+    unit = val.find(regex("(\D+)$"))
+    val = float(val.split(unit).at(0))
+  }
+
+  if calc.abs(val) > 1 {
+    for suffix in gt1_suffixes {
+      if calc.abs(val) < factor {
+        break
+      }
+      val /= factor
+      scale += " " + suffix
+    }
+  } else if val != 0 and calc.abs(val) < 1 {
+    for suffix in lt1_suffixes {
+      if calc.abs(val) > 1 {
+        break
+      }
+      val *= factor
+      scale += " " + suffix
+    }
+  }
+
+  let formatted = str(calc.round(val, digits: precision))
+
+  formatted + sep + scale.split().at(-1, default: "") + unit
+}
+
+#let reportCoverage(prefix) = {
+  image(prefix + "_global.svg", width: 100%)
+  for contig in contigs {
+    heading(level: 4, contig)
+    let path = prefix + "_" + contig
+    image(path + "_chromosome.svg")
+    let data = json(path + "_stats.json")
+    grid(
+      columns: (1fr, 2fr), gutter: 3pt, align(
+        left + horizon,
+      )[
+        #set text(size: 12pt)
+        #table(
+          stroke: none, columns: (auto, 1fr), gutter: 3pt, [Mean], [#calc.round(data.mean, digits: 2)], [Standard dev.], [#calc.round(data.std_dev, digits: 2)], ..data.breaks_values.map(r => ([#r.at(0)], [#calc.round(r.at(1) * 100, digits: 1)%])).flatten(),
+        )
+      ], align(right, image(path + "_distrib.svg", width: 100%)),
+    )
+
+    parbreak()
+  }
+}
+
+#let reportBam(path) = {
+  let data = json(path)
+  table(
+    gutter: 3pt, stroke: none, columns: (auto, 1fr), ..for (key, value) in data {
+      if key != "cramino" and key != "composition" and key != "path" and key != "modified" {
+        ([ #formatString(key) ], [ #value ])
+      } else if key == "modified" {
+        ([ Modified Date (UTC) ], [ #parseCustomDate(value) ])
+      } else if key == "composition" {
+        ([ Run(s) ], [
+          #for (i, v) in value.enumerate() {
+            if i > 0 [ \ ]
+            [#v.at(0).slice(0, 5): #calc.round(v.at(1), digits: 0)%]
+          }
+        ])
+      } else if key == "cramino" {
+        for (k, v) in value {
+          if k == "normalized_read_count_per_chromosome" {} else if k != "path" and k != "checksum" and k != "creation_time" and k != "file_name" {
+            let k = formatString(k)
+            let v = if type(v) == "integer" { si-fmt(v) } else { v }
+            ([ #k ], [ #v ])
+          } else {
+            ()
+          }
+        }.flatten()
+      } else {
+        ()
+      }
+    }.flatten(),
+  )
+}
+
+#let formatedReadCount(path) = {
+  let data = json(path)
+  let data = data.cramino.normalized_read_count_per_chromosome
+  let res = ()
+  for contig in contigs {
+    res.push(data.at(contig))
+  }
+  res.push(data.at("chrM"))
+  return res
+}
+
+#let printReadCount(diag_path, mrd_path) = {
+  let index = 14;
+  let c = contigs
+  c.push("chrM")
+  let diag = formatedReadCount(diag_path)
+  let mrd = formatedReadCount(mrd_path)
+  c.insert(0, "")
+  diag.insert(0, "diag")
+  mrd.insert(0, "mrd")
+  let arrays1 = (c.slice(0, index), diag.slice(0, index), mrd.slice(0, index))
+  table(
+    columns: arrays1.at(0).len(), ..arrays1.map(arr => arr.map(item => [#item])).flatten(),
+  )
+
+  let arrays2 = (c.slice(index), diag.slice(index), mrd.slice(index))
+  arrays2.at(0).insert(0, "")
+  arrays2.at(1).insert(0, "diag")
+  arrays2.at(2).insert(0, "mrd")
+
+  table(
+    columns: arrays2.at(0).len(), ..arrays2.map(arr => arr.map(item => [#item])).flatten(),
+  )
+}
+
+#let variantsFlow(path) = {
+  import fletcher.shapes: diamond, parallelogram, chevron
+  let data = json(path)
+  set text(8pt)
+  diagram(
+    spacing: (8pt, 25pt), node-fill: gradient.radial(cr_colors.light_grey, cr_colors.blue, radius: 300%), node-stroke: cr_colors.dark_blue + 1pt, edge-stroke: 1pt, node-inset: 8pt, node(
+      (0.2, 0), [Variants MRD: #num(data.vcf_stats.n_tumoral_init)], corner-radius: 2pt, extrude: (0, 3), name: <input_mrd>,
+    ), node(
+      (1.8, 0), [Variants Diag: #num(data.vcf_stats.n_constit_init)], corner-radius: 2pt, extrude: (0, 3), name: <input_diag>,
+    ), node(
+      (1, 1), align(center)[Variant in MRD ?], shape: diamond, name: <is_in_mrd>,
+    ), edge(<input_mrd>, "s", <is_in_mrd>, "-|>"), edge(<input_diag>, "s", <is_in_mrd>, "-|>"), edge(<is_in_mrd>, <is_low_mrd>, "-|>", [Yes], label-pos: 0.8), node(
+      (0.25, 2), [MRD variant depth \ < 4 ?], shape: diamond, name: <is_low_mrd>,
+    ), edge(<is_low_mrd>, <low_mrd>, "-|>"), node(
+      (0, 3), [Low MRD depth: #num(data.vcf_stats.n_low_mrd_depth)], shape: parallelogram, name: <low_mrd>,
+    ), edge(<is_in_mrd>, <next>, "-|>", [No], label-pos: 0.8), node(
+      (1.85, 2), [To BAM filters: #num(data.bam_stats.n_lasting)], shape: chevron, extrude: (-3, 0), name: <next>, stroke: cr_colors.green,
+    ), edge(<is_low_mrd>, <homo>, "-|>"), node((1.5, 3), [VAF = 100% ?], shape: diamond, name: <homo>), edge(<homo>, <constit>, "-|>", [Yes], label-pos: 0.5, bend: -80deg), edge(<homo>, <chi>, "-|>", [No], label-pos: 0.6), node(
+      (1.5, 4), [$#sym.chi^2$ VAF MRD vs Diag ?], shape: diamond, name: <chi>,
+    ), edge(<chi>, <constit>, "-|>", label-pos: 0.8), node(
+      (1, 5), [Constit: #num(data.vcf_stats.n_constit)], shape: parallelogram, name: <constit>,
+    ), edge(<chi>, <loh>, "-|>", [p < 0.01], label-pos: 0.8), node(
+      (2, 5), [LOH: #num(data.vcf_stats.n_loh)], shape: parallelogram, name: <loh>,
+    ),
+  )
+}
+
+#let bamFilter(path) = {
+  import fletcher.shapes: diamond, parallelogram, hexagon
+  let data = json(path)
+    set text(8pt)
+
+  diagram(
+    spacing: (8pt, 25pt), node-fill: gradient.radial(cr_colors.light_grey, cr_colors.blue, radius: 300%), node-inset: 8pt, node-stroke: cr_colors.dark_blue + 1pt, edge-stroke: 1pt, node(
+      (0.75, 0), [Variants not in MRD VCF: #num(data.bam_stats.n_lasting)], corner-radius: 2pt, extrude: (0, 3), name: <input_mrd>,
+    ), edge(<input_mrd>, <depth>, "-|>"), node((0.75, 1), [MRD alignement depth ?], shape: diamond, name: <depth>), edge(<depth>, <low_depth>, "-|>", [< 4]), node(
+      (0, 2), [Low MRD depth: #num(data.bam_stats.n_low_mrd_depth)], shape: parallelogram, name: <low_depth>,
+    ), edge(<depth>, <seen>, "-|>"), node(
+      (0.75, 3), [Alt. base seen in MRD pileup ?], shape: diamond, name: <seen>,
+    ), edge(<seen>, <constit>, "-|>", [Yes]), node(
+      (0, 4), [Constit: #num(data.bam_stats.n_constit)], shape: parallelogram, name: <constit>,
+    ), edge(<seen>, <is_div>, "-|>", [No]), node(
+      (1.1, 4), [Sequence #sym.plus.minus 20nt \ diversity ?], shape: diamond, name: <is_div>,
+    ), edge(<is_div>, <low_div>, "-|>", [entropy < 1.8]), node(
+      (0.25, 5), [Low diversity, artefact: #num(data.bam_stats.n_low_diversity)], shape: parallelogram, name: <low_div>,
+    ), edge(<is_div>, <somatic>, "-|>"), node(
+      (1.75, 5), [Somatic: #num(data.bam_stats.n_somatic)], shape: hexagon, extrude: (-3, 0), name: <somatic>, stroke: cr_colors.green,
+    ),
+  )
+}
+
+#let barCallers(path) = {
+  import cetz.draw: *
+  import cetz.chart
+  
+  let json_data = json(path).variants_stats
+  let data = json_data.find(item => item.name == "callers_cat")
+  let chart_data = data.counts.pairs().sorted(key: x => -x.at(1))
+
+  set text(11pt)
+  cetz.canvas(
+    length: 80%,
+    {
+      set-style(axes: (bottom: (tick: (label: (angle: 45deg, anchor: "north-east")))))
+      chart.columnchart(
+        chart_data,
+        size: (1, 0.5),
+      )
+  })
+}
+
+#set heading(numbering: (..numbers) => {
+  if numbers.pos().len() >= 2 and numbers.pos().len() <= 3 {
+    numbering("1.1", ..numbers.pos().slice(1))
+  }
+})
+
+#heading(level: 1, outlined: false)[Whole Genome Sequencing Report]
+
+#outline(title: "Table of Contents", depth: 3)
+#pagebreak()
+
+== Identity
+
+Camara