fix!: make --path-input-ped for seqvars annotation required (#194) (#255

) Release-As: 0.17.0
varfish-org · Nov 10, 2023 · de832b2 · de832b2
1 parent 4bd5461
commit de832b2
Showing 1 changed file with 8 additions and 12 deletions.
diff --git a/src/annotate/seqvars/mod.rs b/src/annotate/seqvars/mod.rs
@@ -85,7 +85,7 @@ pub struct Args {
     pub genome_release: Option<GenomeRelease>,
     /// Path to the input PED file.
     #[arg(long)]
-    pub path_input_ped: Option<String>,
+    pub path_input_ped: String,
     /// Path to the input VCF file.
     #[arg(long)]
     pub path_input_vcf: String,
@@ -1642,7 +1642,7 @@ pub fn run(_common: &crate::common::Args, args: &Args) -> Result<(), anyhow::Err
 
         // Load the pedigree.
         tracing::info!("Loading pedigree...");
-        let pedigree = PedigreeByName::from_path(args.path_input_ped.as_ref().unwrap())?;
+        let pedigree = PedigreeByName::from_path(&args.path_input_ped)?;
         writer.set_pedigree(&pedigree);
         tracing::info!("... done loading pedigree");
 
@@ -1689,9 +1689,9 @@ mod test {
                 path_output_tsv: None,
             },
             max_var_count: None,
-            path_input_ped: Some(String::from(
+            path_input_ped: String::from(
                 "tests/data/db/create/seqvar_freqs/db-rs1263393206/input.ped",
-            )),
+            ),
         };
 
         run(&args_common, &args)?;
@@ -1727,9 +1727,9 @@ mod test {
                 path_output_tsv: Some(path_out.into_os_string().into_string().unwrap()),
             },
             max_var_count: None,
-            path_input_ped: Some(String::from(
+            path_input_ped: String::from(
                 "tests/data/db/create/seqvar_freqs/db-rs1263393206/input.ped",
-            )),
+            ),
         };
 
         run(&args_common, &args)?;
@@ -1775,9 +1775,7 @@ mod test {
                 path_output_tsv: Some(path_out.into_os_string().into_string().unwrap()),
             },
             max_var_count: None,
-            path_input_ped: Some(String::from(
-                "tests/data/db/create/badly_formed_vcf_entry.ped",
-            )),
+            path_input_ped: String::from("tests/data/db/create/badly_formed_vcf_entry.ped"),
         };
 
         run(&args_common, &args)?;
@@ -1813,9 +1811,7 @@ mod test {
                 path_output_tsv: Some(path_out.into_os_string().into_string().unwrap()),
             },
             max_var_count: None,
-            path_input_ped: Some(String::from(
-                "tests/data/db/create/mitochondrial_variants.ped",
-            )),
+            path_input_ped: String::from("tests/data/db/create/mitochondrial_variants.ped"),
         };
 
         run(&args_common, &args)?;