fix: Add error messages for missing annotations (#206)

* fix: Add error messages for missing annotations * Return anyhow error instead of Option<T>
rust-bio · Dec 6, 2021 · 6210dd2 · 6210dd2
1 parent e19b4fb
commit 6210dd2
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Showing 2 changed files with 9 additions and 10 deletions.
diff --git a/src/bcf/report/oncoprint.rs b/src/bcf/report/oncoprint.rs
@@ -64,9 +64,7 @@ pub fn oncoprint(
     for (sample, path) in sample_calls.iter().sorted() {
         let bcf_reader = bcf::Reader::from_path(path)?;
         let header_records = bcf_reader.header().header_records();
-        let ann_fields: Vec<_> = get_ann_description(header_records).unwrap_or_else(|| {
-            panic!("No ANN field found. Please only use VEP-annotated VCF-files.")
-        });
+        let ann_fields: Vec<_> = get_ann_description(header_records)?;
         clin_sig_present.insert(
             sample.to_owned(),
             ann_fields.contains(&"CLIN_SIG".to_owned()),
@@ -97,9 +95,7 @@ pub fn oncoprint(
             sample_names.push(String::from_utf8(s.to_owned())?);
         }
         let header_records = header.header_records();
-        let ann_fields: Vec<_> = get_ann_description(header_records).unwrap_or_else(|| {
-            panic!("No ANN field found. Please only use VEP-annotated VCF-files.")
-        });
+        let ann_fields: Vec<_> = get_ann_description(header_records)?;
 
         for (i, field) in ann_fields.iter().enumerate() {
             ann_indices.insert(field, i);

diff --git a/src/bcf/report/table_report/create_report_table.rs b/src/bcf/report/table_report/create_report_table.rs
@@ -1,6 +1,7 @@
 use crate::bcf::report::table_report::fasta_reader::{get_fasta_lengths, read_fasta};
 use crate::bcf::report::table_report::static_reader::{get_static_reads, Variant};
 use crate::common::Region;
+use anyhow::anyhow;
 use anyhow::Context as AnyhowContext;
 use anyhow::Result;
 use chrono::{DateTime, Local};
@@ -62,7 +63,7 @@ pub(crate) fn make_table_report(
     let mut vcf = rust_htslib::bcf::Reader::from_path(&vcf_path).unwrap();
     let header = vcf.header().clone();
     let header_records = header.header_records();
-    let ann_field_description: Vec<_> = get_ann_description(header_records).unwrap();
+    let ann_field_description: Vec<_> = get_ann_description(header_records)?;
     let samples: Vec<_> = header
         .samples()
         .iter()
@@ -441,7 +442,7 @@ fn escape_hgvsg(hgvsg: &str) -> String {
     hgvsg.replace(".", "_").replace(">", "_").replace(":", "_")
 }
 
-pub(crate) fn get_ann_description(header_records: Vec<HeaderRecord>) -> Option<Vec<String>> {
+pub(crate) fn get_ann_description(header_records: Vec<HeaderRecord>) -> Result<Vec<String>> {
     for rec in header_records {
         if let rust_htslib::bcf::HeaderRecord::Info { key: _, values } = rec {
             if values.get("ID").unwrap() == "ANN" {
@@ -457,11 +458,13 @@ pub(crate) fn get_ann_description(header_records: Vec<HeaderRecord>) -> Option<V
                     entry = entry.trim();
                     owned_fields.push(entry.to_owned());
                 }
-                return Some(owned_fields);
+                return Ok(owned_fields);
             }
         }
     }
-    None
+    Err(anyhow!(
+        "Could not find any annotations by VEP. Please only use VEP-annotated VCF-files."
+    ))
 }
 
 pub(crate) fn read_tag_entries(