serialize

src/variants.rs

@@ -37,7 +37,7 @@ use noodles_fasta::indexed_reader::Builder as FastaBuilder;
 use noodles_gff as gff;
 
 use rayon::prelude::*;
-use serde::{Deserialize, Serialize};
+use serde::{Deserialize, Serialize, Serializer, ser::SerializeStruct};
 use std::io::Write;
 use std::{
     env::temp_dir,
@@ -62,6 +62,23 @@ pub struct Variants {
     pub mp: MultiProgress,
 }
 
+impl Serialize for Variants {
+    fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
+    where
+        S: Serializer,
+    {
+        // 3 is the number of fields in the struct.
+        let mut state = serializer.serialize_struct("Variants", 5)?;
+        state.serialize_field("name", &self.name)?;
+        state.serialize_field("data", &self.data)?;
+        state.serialize_field("constit", &self.constit)?;
+        state.serialize_field("stats_vcf", &self.stats_vcf)?;
+        state.serialize_field("stats_bam", &self.stats_bam)?;
+        state.end()
+    }
+}
+
+
 #[derive(Debug, Clone, Serialize, Deserialize, Default)]
 pub struct StatsVCF {
     n_tumoral_init: usize,
@@ -1439,6 +1456,7 @@ pub fn run_pipe(name: &str, multi: &MultiProgress) -> Result<()> {
     variants.keep_somatics_un();
     info!("Variants retained: {}", variants.len());
 
+    // TODO check if SNP are matching
     if variants.len() > 100_000 {
         return Err(anyhow!("Too many variants, verify if somatic and tumoral samples match."));
     }