fix: Allow '.' genotypes (#178)

src/annotate/seqvars/mod.rs

@@ -711,14 +711,10 @@ impl VarFishSeqvarTsvWriter {
                 ..Default::default()
             };
 
-            if let Some(gt) = sample
-                .get(&GENOTYPE)
-                .map(|value| match value {
-                    Some(sample::Value::String(s)) => Ok(s.to_owned()),
-                    _ => anyhow::bail!("invalid GT value"),
-                })
-                .transpose()?
-            {
+            if let Some(gt) = sample.get(&GENOTYPE).map(|value| match value {
+                Some(sample::Value::String(s)) => s.to_owned(),
+                _ => ".".into(),
+            }) {
                 let individual = self
                     .pedigree
                     .as_ref()
@@ -1672,4 +1668,35 @@ mod test {
 
         Ok(())
     }
+
+    #[test]
+    fn test_badly_formed_vcf_entry() -> Result<(), anyhow::Error> {
+        let temp = TempDir::default();
+        let path_out = temp.join("output.tsv");
+
+        let args_common = crate::common::Args {
+            verbose: Verbosity::new(0, 1),
+        };
+        let args = Args {
+            genome_release: None,
+            path_db: String::from("tests/data/annotate/db"),
+            path_input_vcf: String::from("tests/data/db/create/badly_formed_vcf_entry.vcf"),
+            output: PathOutput {
+                path_output_vcf: None,
+                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",
+            )),
+        };
+
+        run(&args_common, &args)?;
+
+        let actual = std::fs::read_to_string(args.output.path_output_tsv.unwrap())?;
+        let expected = std::fs::read_to_string("tests/data/db/create/badly_formed_vcf_entry.tsv")?;
+        assert_eq!(&expected, &actual);
+
+        Ok(())
+    }
 }