ok

typst_template/template.typ

@@ -1,10 +1,18 @@
 #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"),
+  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"
+#import "@preview/badgery:0.1.1": *
 
 #set page(paper: "a4",
   // fill: cr_colors.light_grey,
@@ -27,7 +35,30 @@
 #set text(size: 16pt, 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",
+  "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) = {
@@ -52,7 +83,11 @@
   capitalizedWords.join(" ")
 }
 #let si-fmt(val, precision: 1, sep: "\u{202F}", binary: false) = {
-  let factor = if binary { 1024 } else { 1000 }
+  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 = ""
@@ -104,14 +139,24 @@
     image(path + "_chromosome.svg")
     let data = json(path + "_stats.json")
     grid(
-      columns: (1fr, 2fr), gutter: 3pt, align(
-        left + horizon,
-      )[
+      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(),
+          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%)),
+      ],
+      align(right, image(path + "_distrib.svg", width: 100%)),
     )
 
     parbreak()
@@ -121,23 +166,32 @@
 #let reportBam(path) = {
   let data = json(path)
   table(
-    gutter: 3pt, stroke: none, columns: (auto, 1fr), ..for (key, value) in data {
+    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)%]
-          }
-        ])
+        (
+          [ 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" {
+          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 }
+            let v = if type(v) == "integer" {
+              si-fmt(v)
+            } else {
+              v
+            }
             ([ #k ], [ #v ])
           } else {
             ()
@@ -162,7 +216,7 @@
 }
 
 #let printReadCount(diag_path, mrd_path) = {
-  let index = 14;
+  let index = 14
   let c = contigs
   c.push("chrM")
   let diag = formatedReadCount(diag_path)
@@ -172,7 +226,9 @@
   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(),
+    columns: arrays1.at(0).len(), ..arrays1
+      .map(arr => arr.map(item => [#item]))
+      .flatten(),
   )
 
   let arrays2 = (c.slice(index), diag.slice(index), mrd.slice(index))
@@ -181,7 +237,9 @@
   arrays2.at(2).insert(0, "mrd")
 
   table(
-    columns: arrays2.at(0).len(), ..arrays2.map(arr => arr.map(item => [#item])).flatten(),
+    columns: arrays2.at(0).len(), ..arrays2
+      .map(arr => arr.map(item => [#item]))
+      .flatten(),
   )
 }
 
@@ -190,24 +248,84 @@
   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, mark-scale: 70%, 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>,
+    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,
+    mark-scale: 70%,
+    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>,
     ),
   )
 }
@@ -215,23 +333,71 @@
 #let bamFilter(path) = {
   import fletcher.shapes: diamond, parallelogram, hexagon
   let data = json(path)
-    set text(8pt)
+  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, mark-scale: 70%, 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,
+    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,
+    mark-scale: 70%,
+    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,
     ),
   )
 }
@@ -239,7 +405,7 @@
 #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))
@@ -248,12 +414,15 @@
   cetz.canvas(
     length: 80%,
     {
-      set-style(axes: (bottom: (tick: (label: (angle: 45deg, anchor: "north-east")))))
+      set-style(axes: (
+        bottom: (tick: (label: (angle: 45deg, anchor: "north-east"))),
+      ))
       chart.columnchart(
         chart_data,
         size: (1, 0.5),
       )
-  })
+    },
+  )
 }
 #let truncate(text, max-length) = {
   if text.len() <= max-length {
@@ -262,6 +431,114 @@
     text.slice(0, max-length - 3) + "..."
   }
 }
+
+// #let add_newlines(text, n) = {
+//   let result = ""
+//   let chars = text.clusters()
+//   for (i, char) in chars.enumerate() {
+//     result += char
+//     if calc.rem((i + 1), n == 0 and i < chars.len() - 1 {
+//       result += "\n"
+//     }
+//   }
+//   result
+// }
+
+#let break_long_words(text, max_length: 20, hyphen: "") = {
+  let words = text.split(" ")
+  let result = ()
+
+  for word in words {
+    if word.len() <= max_length {
+      result.push(word)
+    } else {
+      let segments = ()
+      let current_segment = ""
+      for char in word.clusters() {
+        if current_segment.len() + 1 > max_length {
+          segments.push(current_segment + hyphen)
+          current_segment = ""
+        }
+        current_segment += char
+      }
+      if current_segment != "" {
+        segments.push(current_segment)
+      }
+      result += segments
+    }
+  }
+
+  result.join(" ")
+}
+
+#let format_sequence(text, max_length: 40, hyphen: [#linebreak()]) = {
+  let words = text.split(" ")
+  let result = ()
+  // result.push("\n")
+
+  for word in words {
+    if word.len() <= max_length {
+      result.push(word)
+    } else {
+      let segments = ()
+      let current_segment = ""
+      for char in word.clusters() {
+        if current_segment.len() + 1 > max_length {
+          segments.push(current_segment + hyphen)
+          current_segment = ""
+        }
+        current_segment += char
+      }
+      if current_segment != "" {
+        segments.push(current_segment)
+      }
+      result += segments
+    }
+  }
+  result.push("")
+  let sequence = result.join(" ")
+
+  box(width: 100%, par(leading: 0.2em, sequence))
+}
+
+#let dna(sequence, line_length: 60) = {
+  let formatted = sequence.clusters().map(c => {
+    if c == "A" {
+      text(fill: red)[A]
+    } else if c == "T" {
+      text(fill: green)[T]
+    } else if c == "C" {
+      text(fill: blue)[C]
+    } else if c == "G" {
+      text(fill: orange)[G]
+    } else {
+      c
+    }
+  })
+
+  let lines = formatted.chunks(line_length).map(line => line.join())
+  let n_lines = lines.len()
+
+  let lines = lines.join("\n")
+
+  if n_lines > 1 {
+    parbreak()
+  }
+  align(left, box(
+    fill: luma(240),
+    inset: (x: 0.5em, y: 0.5em),
+    radius: 4pt,
+      align(left, text(
+        font: "Fira Code",
+        size: 10pt,
+        lines,
+      )),
+  ))
+  if n_lines > 1 {
+    parbreak()
+  }
+}
+
 #let to-string(content) = {
   if content.has("text") {
     content.text
@@ -273,6 +550,7 @@
     " "
   }
 }
+
 #let format-number(num) = {
   let s = str(num).split("").filter(item => item != "")
   let result = ""
@@ -286,45 +564,156 @@
   result
 }
 
+#let format_json(json_data) = {
+  let format_value(value) = {
+    if value == none {
+      ""
+    } else if type(value) == "string" {
+      if value != "." {
+        value.replace(";", ", ").replace("=", ": ")
+      } else {
+        ""
+      }
+    } else if type(value) == "array" {
+      let items = value.map(v => format_value(v))
+      "[" + items.join(", ") + "]"
+    } else if type(value) == "dictionary" {
+      "{" + format_json(value) + "}"
+    } else {
+      str(value)
+    }
+  }
+
+  if type(json_data) == "dictionary" {
+    let result = ()
+    for (key, value) in json_data {
+      let formatted_value = format_value(value)
+      if formatted_value != "" {
+        if key == "svinsseq" {
+          formatted_value = dna(formatted_value)
+        }
+        result.push(upper(key) + ": " + formatted_value)
+      }
+    }
+    result.join(", ")
+  } else {
+    format_value(json_data)
+  }
+}
+
 #let card(d) = {
+  set text(12pt)
   let position_fmt = format-number(d.position)
   let title_bg_color = rgb("#f9fafb00")
-  rect(
-    width: 100%,
-    fill: cr_colors.light_grey,
-    stroke: cr_colors.dark_grey,
-    inset: 0em,
-    
-    radius: 12pt, 
-    [
-      #pad(top: 0.5em, bottom: -0.5em, box(
-        width: 100%,
-        fill: title_bg_color,
-        align(center,
-          text(weight: "bold")[
-            #d.contig:#position_fmt #d.reference#sym.quote.angle.r.single#truncate(d.alternative, 25)
-          ]
-        )
-      ))
-      #line(length: 100%)
-      
 
-      #lorem(50)
-    ]
+  let grid_content = ()
+
+  let callers_data = json.decode(d.callers_data)
+
+  // Title
+  let alt = d.alternative
+
+  // TODO: add that in pandora_lib_variants
+  if d.callers == "Nanomonsv" and alt == "<INS>" {
+    alt = d.reference + callers_data.at(0).info.Nanomonsv.svinsseq
+  }
+
+  let title = d.contig + ":" + position_fmt + " " + d.reference + sym
+    .quote
+    .angle
+    .r
+    .single + truncate(alt, 30)
+
+  grid_content.push(
+    grid.cell(
+      fill: cr_colors.light_grey,
+      align: center,
+      block(width: 100%, title),
+    ),
+  )
+
+  // Consequences
+  let consequences = d.consequence.replace(",", ", ").replace(
+    "_",
+    " ",
+  ) + " " + emph(strong(d.gene))
+  grid_content.push(
+    grid.cell(fill: cr_colors.light_grey, align: center, consequences),
+  )
+
+  // hgvs_c
+  if d.hgvs_c != none {
+    grid_content.push(
+      grid.cell(fill: rgb("#fef08a"), align: center, truncate(d.hgvs_c, 50)),
+    )
+  }
+
+  // hgvs_c
+  if d.hgvs_p != none {
+    grid_content.push(
+      grid.cell(fill: rgb("#fecaca"), align: center, truncate(d.hgvs_p, 50)),
+    )
+  }
+
+  // Content
+  let content = ()
+  content.push(
+    badge-red("VAF: " + str(calc.round(d.m_vaf * 100, digits: 2)) + "%"),
+  )
+  // content.push(" ")
+
+  if d.cosmic_n != none {
+    content.push(badge-red("Cosmic: " + str(d.cosmic_n)))
+  }
+
+  if d.gnomad_af != none {
+    content.push(badge-blue("GnomAD: " + str(d.gnomad_af)))
+  }
+
+  let callers_contents = ()
+  for caller_data in callers_data {
+    let caller = ""
+    for (k, v) in caller_data.format {
+      caller = k
+    }
+    callers_contents.push(underline(caller) + ":")
+    callers_contents.push([
+      Qual: #caller_data.qual,
+      #(format_json(caller_data.format.at(caller)), format_json(caller_data.info.at(caller))).filter(v => v != "").join(", ")
+    ])
+  }
+
+  content.push(
+    grid(
+      columns: 1,
+      inset: 0.5em,
+      ..callers_contents
+    ),
+  )
+
+  grid_content.push(grid.cell(fill: white, content.join(" ")))
+
+
+  block(
+    breakable: false,
+    width: 100%,
+    grid(
+      columns: 1,
+      inset: 0.5em,
+      stroke: cr_colors.dark_grey,
+      ..grid_content
+    ),
   )
 }
-// #let variant(d) = {
-//   card(d)
-// }
 
-#let variants(path) = {
+#let variants(path, interpretation: "PATHO") = {
   let data = json(path)
-  for var in data {
+  let patho = data.filter(d => d.interpretation == interpretation)
+  for var in patho {
     card(var)
   }
 }
 
-
 #set heading(numbering: (..numbers) => {
   if numbers.pos().len() >= 2 and numbers.pos().len() <= 3 {
     numbering("1.1", ..numbers.pos().slice(1))
@@ -340,19 +729,20 @@
 
 == Alignement
 #grid(
-  columns: (1fr, 1fr), gutter: 3pt, [
+  columns: (1fr, 1fr),
+  gutter: 3pt,
+  [
     ==== Diagnostic sample
     #set text(size: 11pt)
-    #reportBam(
-      sys.inputs.base + "/diag/" + sys.inputs.id + "_diag_hs1_info.json",
-    )
-  ], [
+    #reportBam(sys.inputs.base + "/diag/" + sys.inputs.id + "_diag_hs1_info.json")
+  ],
+  [
     ==== MRD sample
     #set text(size: 11pt)
-    #reportBam(
-      sys.inputs.base + "/mrd/" + sys.inputs.id + "_mrd_hs1_info.json",
-    )
-    #set footnote(numbering: n => { " " })
+    #reportBam(sys.inputs.base + "/mrd/" + sys.inputs.id + "_mrd_hs1_info.json")
+    #set footnote(numbering: n => {
+      " "
+    })
     #footnote[Values computed by #link("https://github.com/wdecoster/cramino")[cramino] v0.14.5
     ]
   ],
@@ -363,14 +753,17 @@
 #[
   #set text(size: 10pt)
   #printReadCount(
-    sys.inputs.base + "/diag/" + sys.inputs.id + "_diag_hs1_info.json", sys.inputs.base + "/mrd/" + sys.inputs.id + "_mrd_hs1_info.json",
+    sys.inputs.base + "/diag/" + sys.inputs.id + "_diag_hs1_info.json",
+    sys.inputs.base + "/mrd/" + sys.inputs.id + "_mrd_hs1_info.json",
   )
 ]
 
 === Coverage by chromosome
 ==== Proportion at given depth by chromosome
 #reportCoverage(sys.inputs.base + "/diag/report/data/scan/" + sys.inputs.id)
-#set footnote(numbering: n => { " " })
+#set footnote(numbering: n => {
+  " "
+})
 #footnote[Values computed by Pandora development version]
 
 == Variants
@@ -378,15 +771,29 @@
 #pagebreak()
 ==== VCF filters
 #pad(
-  top: 0.8cm, align(center, scale(x: 100%, y: 100%, reflow: true, variantsFlow(
-    sys.inputs.base + "/diag/report/data/" + sys.inputs.id + "_variants_stats.json",
-  ))),
+  top: 0.8cm,
+  align(
+    center,
+    scale(
+      x: 100%,
+      y: 100%,
+      reflow: true,
+      variantsFlow(sys.inputs.base + "/diag/report/data/" + sys.inputs.id + "_variants_stats.json"),
+    ),
+  ),
 )
 ==== BAM filters
-#pad(top: 0.8cm,
-  align(center, scale(x: 100%, y: 100%, reflow: true, bamFilter(
-    sys.inputs.base + "/diag/report/data/" + sys.inputs.id + "_variants_stats.json",
-  ))),
+#pad(
+  top: 0.8cm,
+  align(
+    center,
+    scale(
+      x: 100%,
+      y: 100%,
+      reflow: true,
+      bamFilter(sys.inputs.base + "/diag/report/data/" + sys.inputs.id + "_variants_stats.json"),
+    ),
+  ),
 )
 #pagebreak()
 
@@ -403,7 +810,23 @@
 #pagebreak()
 
 === Selected Variants
-#variants(sys.inputs.base + "/diag/report/data/" + sys.inputs.id + "_annot_variants.json")
+==== Pathogenics
+#variants(
+  sys.inputs.base + "/diag/report/data/" + sys.inputs.id + "_annot_variants.json",
+  interpretation: "PATHO",
+)
+
+==== Likely Pathogenics
+#variants(
+  sys.inputs.base + "/diag/report/data/" + sys.inputs.id + "_annot_variants.json",
+  interpretation: "PROBPATHO",
+)
+
+==== Variants of uncertain significance
+#variants(
+  sys.inputs.base + "/diag/report/data/" + sys.inputs.id + "_annot_variants.json",
+  interpretation: "US",
+)
 
 #pagebreak()
 == Conclusion