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@@ -38,6 +38,7 @@ use noodles_gff as gff;
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use rayon::prelude::*;
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use serde::{ser::SerializeStruct, Deserialize, Serialize, Serializer};
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+use utoipa::ToSchema;
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use std::io::Write;
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use std::{
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env::temp_dir,
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@@ -913,13 +914,16 @@ impl Variants {
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}
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pub fn filter_category(&self, and_categories: &Vec<Category>) -> Vec<&Variant> {
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- self.data.par_iter().flat_map(|v| {
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- if v.is_from_category(and_categories) {
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- vec![v]
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- } else {
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- vec![]
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- }
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- }).collect()
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+ self.data
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+ .par_iter()
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+ .flat_map(|v| {
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+ if v.is_from_category(and_categories) {
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+ vec![v]
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+ } else {
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+ vec![]
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+ }
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+ })
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+ .collect()
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}
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}
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@@ -1010,8 +1014,6 @@ impl CallerData {
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return false;
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}
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}
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-
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-
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}
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#[derive(Debug, Clone, Serialize, Eq, PartialEq, Deserialize)]
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@@ -1020,7 +1022,7 @@ pub enum VariantType {
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Constitutionnal,
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}
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-#[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
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+#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, ToSchema)]
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pub enum VCFSource {
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DeepVariant,
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ClairS,
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@@ -1247,7 +1249,7 @@ impl Variant {
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}
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vec_bools.push(bools.iter().any(|&b| b));
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}
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- Category::VAF{ min, max } => {
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+ Category::VAF { min, max } => {
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let v = if self.vaf.is_none() {
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let mut s = self.clone();
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s.vaf()
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@@ -1255,7 +1257,7 @@ impl Variant {
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self.vaf.unwrap()
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};
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vec_bools.push(v >= *min && v <= *max);
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- },
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+ }
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}
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}
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vec_bools.iter().all(|&x| x)
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@@ -1270,7 +1272,7 @@ enum AlterationCategory {
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Other,
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}
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-#[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
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+#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, ToSchema)]
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pub enum AnnotationType {
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VariantCategory(VariantCategory),
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VEP(Vec<VEP>),
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@@ -1280,7 +1282,7 @@ pub enum AnnotationType {
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NCBIGFF(NCBIGFF),
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}
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-#[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
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+#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, ToSchema)]
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pub enum VariantCategory {
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Somatic,
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LowMRDDepth,
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@@ -1462,7 +1464,10 @@ pub enum Category {
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VCFSource(VCFSource),
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NCosmic(u64),
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NCBIFeature(String),
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- VAF{min: f32, max: f32},
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+ VAF {
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+ min: f32,
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+ max: f32,
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+ },
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}
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pub fn run_pipe(name: &str, multi: &MultiProgress) -> Result<()> {
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