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fix: Panic on trailing omitted FORMAT records #417

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merged 5 commits into from
Mar 27, 2024
Merged

fix: Panic on trailing omitted FORMAT records #417

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a7668cd
Handle trailing omitted FORMAT records
Feb 1, 2024
4711d1e
Remove newline
Feb 1, 2024
2479748
fix: Wrong if statement
Feb 1, 2024
d8f21f2
fmt
johanneskoester Feb 22, 2024
a8d7fb1
Merge branch 'master' into #407-trailing-omitted-format
johanneskoester Feb 23, 2024
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23 changes: 23 additions & 0 deletions src/bcf/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -1548,6 +1548,29 @@ 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();
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3 changes: 3 additions & 0 deletions src/bcf/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -1483,6 +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 {
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I'm not sure if this is the behavior we want here. Could consider returning "." but then I guess we'd need to modify the buffer

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empty seems fine

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)
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9 changes: 9 additions & 0 deletions test/test_trailing_omitted_format.vcf
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Original file line number Diff line number Diff line change
@@ -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 .
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