From 650687b083890bbb8054a16df5276bcfe9e569c8 Mon Sep 17 00:00:00 2001
From: Miguel Brown <miguel.a.brown@gmail.com>
Date: Fri, 2 Feb 2024 19:45:12 +0000
Subject: [PATCH 1/2] :hammer:

---
 src/commands/annotate_cmd.rs | 10 ++++++++++
 tests/.gitignore             |  6 ++----
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/commands/annotate_cmd.rs b/src/commands/annotate_cmd.rs
index 09884d8..9e97ee1 100644
--- a/src/commands/annotate_cmd.rs
+++ b/src/commands/annotate_cmd.rs
@@ -125,7 +125,17 @@ pub fn annotate_main(
             );
         }
         n += 1;
+        // First check if the variant is *, skip those
+        if String::from_utf8_lossy(record.alleles()[1]) == "*" {
+            eprintln!(
+                "alt has * value, skipping annotation for {:?}",
+                &record
+            );
+            ovcf.write(&record).expect("failed to write record");
+            continue;
+        }
         // this updates evalues and fills expr values
+
         for (i, e) in echts.iter_mut().enumerate() {
             e.update_expr_values(&mut record, &mut expr_values[i]);
         }
diff --git a/tests/.gitignore b/tests/.gitignore
index 8bb1f46..0162c54 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -1,6 +1,4 @@
 anno.vcf.gz
-generated-all.vcf
-generated-exclude.vcf
-test.echtvar
-test.echtvar.before
+generated-*
+test.echtvar*
 sl.zip

From 08ceffcc4b9138ba28780ba24451111a571f171f Mon Sep 17 00:00:00 2001
From: Miguel Brown <miguel.a.brown@gmail.com>
Date: Fri, 2 Feb 2024 19:59:33 +0000
Subject: [PATCH 2/2] :broom: clean up output message

---
 src/commands/annotate_cmd.rs | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/commands/annotate_cmd.rs b/src/commands/annotate_cmd.rs
index 9e97ee1..5649e85 100644
--- a/src/commands/annotate_cmd.rs
+++ b/src/commands/annotate_cmd.rs
@@ -127,9 +127,12 @@ pub fn annotate_main(
         n += 1;
         // First check if the variant is *, skip those
         if String::from_utf8_lossy(record.alleles()[1]) == "*" {
+            let rid = record.rid().unwrap();
+            let chrom = std::str::from_utf8(oheader_view.rid2name(rid).unwrap()).unwrap();
             eprintln!(
-                "alt has * value, skipping annotation for {:?}",
-                &record
+                "contig {} pos {} alt has * value, skipping annotation, outputting entry as-is",
+                &chrom,
+                record.pos() + 1
             );
             ovcf.write(&record).expect("failed to write record");
             continue;