del panic

src/variants.rs

@@ -517,7 +517,7 @@ impl Variants {
         Ok(())
     }
 
-    /// 
+    ///
     pub fn merge(&mut self) {
         let pg = self.mp.add(new_pg_speed(self.len() as u64));
         pg.set_message("Merging Variants by contig, positions, ref, alt");
@@ -1320,35 +1320,36 @@ pub fn run_pipe(name: &str, multi: &MultiProgress) -> Result<()> {
         cfg.longreads_results_dir
     );
     if !std::path::Path::new(&deepvariant_diag_vcf).exists() {
-        panic!("{deepvariant_diag_vcf} is required")
+        return Err(anyhow!("{deepvariant_diag_vcf} is required"));
+        // panic!("{deepvariant_diag_vcf} is required")
     }
     let deepvariant_mrd_vcf = format!(
         "{}/{name}/mrd/DeepVariant/{name}_mrd_DeepVariant_PASSED.vcf.gz",
         cfg.longreads_results_dir
     );
     if !std::path::Path::new(&deepvariant_mrd_vcf).exists() {
-        panic!("{deepvariant_mrd_vcf} is required")
+        return Err(anyhow!("{deepvariant_mrd_vcf} is required"));
     }
     let mrd_bam = format!(
         "{}/{name}/mrd/{name}_mrd_hs1.bam",
         cfg.longreads_results_dir
     );
     if !std::path::Path::new(&mrd_bam).exists() {
-        panic!("{mrd_bam} is required")
+        return Err(anyhow!("{mrd_bam} is required"));
     }
     let clairs_vcf = format!(
         "{}/{name}/diag/ClairS/{name}_diag_clairs_PASSED.vcf.gz",
         cfg.longreads_results_dir
     );
     if !std::path::Path::new(&clairs_vcf).exists() {
-        panic!("{clairs_vcf} is required")
+        return Err(anyhow!("{clairs_vcf} is required"));
     }
     let clairs_indels_vcf = format!(
         "{}/{name}/diag/ClairS/{name}_diag_clairs_indel_PASSED.vcf.gz",
         cfg.longreads_results_dir
     );
     if !std::path::Path::new(&clairs_indels_vcf).exists() {
-        panic!("{clairs_indels_vcf} is required")
+        return Err(anyhow!("{clairs_indels_vcf} is required"));
     }
     let sniffles_vcf = format!(
         "{}/{name}/diag/Sniffles/{name}_diag_sniffles.vcf",
@@ -1359,14 +1360,14 @@ pub fn run_pipe(name: &str, multi: &MultiProgress) -> Result<()> {
         cfg.longreads_results_dir
     );
     if !std::path::Path::new(&sniffles_vcf).exists() {
-        panic!("{sniffles_vcf} is required")
+        return Err(anyhow!("{sniffles_vcf} is required"));
     }
     let nanomonsv_vcf = format!(
         "{}/{name}/diag/nanomonsv/{name}_diag_nanomonsv_PASSED.vcf.gz",
         cfg.longreads_results_dir
     );
     if !std::path::Path::new(&nanomonsv_vcf).exists() {
-        panic!("{nanomonsv_vcf} is required")
+        return Err(anyhow!("{nanomonsv_vcf} is required"));
     }
 
     // let db_path = "/data/db_results.sqlite".to_string();
@@ -1433,7 +1434,6 @@ pub fn run_pipe(name: &str, multi: &MultiProgress) -> Result<()> {
 
     let constits = variants.get_cat(&VariantCategory::Constit);
     let constits = Variants::from_vec(name.to_string(), &multi, constits);
-    // constits.save_sql(&db_constit_path)?;
     constits.save_bytes(&bytes_constit_path)?;
 
     variants.keep_somatics_un();
@@ -1445,10 +1445,11 @@ pub fn run_pipe(name: &str, multi: &MultiProgress) -> Result<()> {
     info!("Variants retained: {}", variants.len());
 
     variants.annotate_gff_feature(&cfg.gff_path)?;
+
     variants.echtvar_annotate(&deepvariant_mrd_vcf)?;
+    variants.filter_snp()?;
 
     variants.save_bytes(&bytes_path)?;
-    // variants.filter_snp()?;
     // variants.stats()?;
     //
     // if std::path::Path::new(&db_path).exists() {