From a7668cd8952d313ddc4585fd6dc2d6442137e2c8 Mon Sep 17 00:00:00 2001
From: Fenner Macrae <fmacrae@illumina.com>
Date: Thu, 1 Feb 2024 11:17:58 -0800
Subject: [PATCH 1/4] Handle trailing omitted FORMAT records

---
 src/bcf/mod.rs                        | 24 ++++++++++++++++++++++++
 src/bcf/record.rs                     |  3 +++
 test/test_trailing_omitted_format.vcf |  9 +++++++++
 3 files changed, 36 insertions(+)
 create mode 100644 test/test_trailing_omitted_format.vcf

diff --git a/src/bcf/mod.rs b/src/bcf/mod.rs
index 7669911be..f781cddce 100644
--- a/src/bcf/mod.rs
+++ b/src/bcf/mod.rs
@@ -1548,6 +1548,30 @@ mod tests {
         );
     }
 
+    #[test]
+    fn test_trailing_omitted_format_fields() {
+        let mut reader = Reader::from_path("test/test_trailing_omitted_format.vcf").unwrap();
+        let first_record = reader
+            .records()
+            .next()
+            .unwrap()
+            .expect("Fail to read record");
+
+        let expected: Vec<&[u8]> = Vec::new();
+        assert_eq!(
+            *first_record.format(b"STR").string().unwrap(),
+            expected,
+        );
+        assert_eq!(
+            *first_record.format(b"INT").integer().unwrap(),
+            vec![&[i32::missing()]],
+        );
+        assert!(
+            first_record.format(b"FLT").float().unwrap()[0][0].is_nan(),
+        );
+    }
+
+
     // #[test]
     // fn test_buffer_lifetime() {
     //     let mut reader = Reader::from_path("test/obs-cornercase.vcf").unwrap();
diff --git a/src/bcf/record.rs b/src/bcf/record.rs
index b8f18871a..4ac478a92 100644
--- a/src/bcf/record.rs
+++ b/src/bcf/record.rs
@@ -1329,6 +1329,9 @@ impl<'a, 'b, B: BorrowMut<Buffer> + Borrow<Buffer> + 'b> Info<'a, B> {
     pub fn string(mut self) -> Result<Option<BufferBacked<'b, Vec<&'b [u8]>, B>>> {
         self.data(htslib::BCF_HT_STR).map(|data| {
             data.map(|ret| {
+                if ret == 0 {
+                    return BufferBacked::new(Vec::new(), self.buffer);
+                }
                 BufferBacked::new(
                     unsafe {
                         slice::from_raw_parts(self.buffer.borrow().inner as *const u8, ret as usize)
diff --git a/test/test_trailing_omitted_format.vcf b/test/test_trailing_omitted_format.vcf
new file mode 100644
index 000000000..68892198b
--- /dev/null
+++ b/test/test_trailing_omitted_format.vcf
@@ -0,0 +1,9 @@
+##fileformat=VCFv4.3
+##contig=<ID=chr1,length=10000>
+##INFO=<ID=FOO,Number=1,Type=Integer,Description="Some field">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=STR,Number=1,Type=String,Description="Some string field">
+##FORMAT=<ID=INT,Number=1,Type=Integer,Description="Some integer field">
+##FORMAT=<ID=FLT,Number=1,Type=Float,Description="Some float field">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE1
+chr1	1234	.	t	a	.	.	FOO=1	GT:STR:FLT:INT	.

From 4711d1ec90033a41797f4aa5b2e06ae4038eb8ef Mon Sep 17 00:00:00 2001
From: Fenner Macrae <fmacrae@illumina.com>
Date: Thu, 1 Feb 2024 11:20:05 -0800
Subject: [PATCH 2/4] Remove newline

---
 src/bcf/mod.rs | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/bcf/mod.rs b/src/bcf/mod.rs
index f781cddce..92cc3efb3 100644
--- a/src/bcf/mod.rs
+++ b/src/bcf/mod.rs
@@ -1571,7 +1571,6 @@ mod tests {
         );
     }
 
-
     // #[test]
     // fn test_buffer_lifetime() {
     //     let mut reader = Reader::from_path("test/obs-cornercase.vcf").unwrap();

From 247974871f56c3d150e64bc0212a46362a1b26e2 Mon Sep 17 00:00:00 2001
From: Fenner Macrae <fmacrae@illumina.com>
Date: Thu, 1 Feb 2024 12:23:41 -0800
Subject: [PATCH 3/4] fix: Wrong if statement

---
 src/bcf/record.rs | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/bcf/record.rs b/src/bcf/record.rs
index 4ac478a92..a5778d1ac 100644
--- a/src/bcf/record.rs
+++ b/src/bcf/record.rs
@@ -1329,9 +1329,6 @@ impl<'a, 'b, B: BorrowMut<Buffer> + Borrow<Buffer> + 'b> Info<'a, B> {
     pub fn string(mut self) -> Result<Option<BufferBacked<'b, Vec<&'b [u8]>, B>>> {
         self.data(htslib::BCF_HT_STR).map(|data| {
             data.map(|ret| {
-                if ret == 0 {
-                    return BufferBacked::new(Vec::new(), self.buffer);
-                }
                 BufferBacked::new(
                     unsafe {
                         slice::from_raw_parts(self.buffer.borrow().inner as *const u8, ret as usize)
@@ -1486,6 +1483,9 @@ impl<'a, 'b, B: BorrowMut<Buffer> + Borrow<Buffer> + 'b> Format<'a, B> {
     /// memory.
     pub fn string(mut self) -> Result<BufferBacked<'b, Vec<&'b [u8]>, B>> {
         self.data(htslib::BCF_HT_STR).map(|ret| {
+            if ret == 0 {
+                return BufferBacked::new(Vec::new(), self.buffer);
+            }
             BufferBacked::new(
                 unsafe {
                     slice::from_raw_parts(self.buffer.borrow_mut().inner as *const u8, ret as usize)

From d8f21f299d3bfda73d6668508bf5b8f64ee642f7 Mon Sep 17 00:00:00 2001
From: Johannes Koester <johannes.koester@uni-due.de>
Date: Thu, 22 Feb 2024 11:30:45 +0100
Subject: [PATCH 4/4] fmt

---
 src/bcf/mod.rs | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/src/bcf/mod.rs b/src/bcf/mod.rs
index 92cc3efb3..e09521599 100644
--- a/src/bcf/mod.rs
+++ b/src/bcf/mod.rs
@@ -1558,17 +1558,12 @@ mod tests {
             .expect("Fail to read record");
 
         let expected: Vec<&[u8]> = Vec::new();
-        assert_eq!(
-            *first_record.format(b"STR").string().unwrap(),
-            expected,
-        );
+        assert_eq!(*first_record.format(b"STR").string().unwrap(), expected,);
         assert_eq!(
             *first_record.format(b"INT").integer().unwrap(),
             vec![&[i32::missing()]],
         );
-        assert!(
-            first_record.format(b"FLT").float().unwrap()[0][0].is_nan(),
-        );
+        assert!(first_record.format(b"FLT").float().unwrap()[0][0].is_nan(),);
     }
 
     // #[test]