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fix: skip REF-only records #576

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merged 4 commits into from
Oct 11, 2024
Merged

fix: skip REF-only records #576

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67eed24
fix: skip REF-only records
tedil Oct 11, 2024
d93246a
follow vcf spec 4.5 §5.5
tedil Oct 11, 2024
663d67c
update warning message
tedil Oct 11, 2024
2497598
remove unneeded reference
tedil Oct 11, 2024
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9 changes: 8 additions & 1 deletion src/annotate/strucvars/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -1889,7 +1889,7 @@ pub trait VcfRecordConverter {
let mut end: Option<i32> = None;
let alleles = vcf_record.alternate_bases().as_ref();
if alleles.len() != 1 {
panic!("Only one alternative allele is supported for SVs");
panic!("Only one alternative allele is supported for SVs, got {} alternative alleles ({:?})", alleles.len(), alleles);
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}
let allele = &alleles[0];
// TODO find out how to handle this properly (via noodles?)
Expand Down Expand Up @@ -2959,6 +2959,13 @@ pub async fn run_vcf_to_jsonl(
rng.fill_bytes(&mut uuid_buf);
let uuid = Uuid::from_bytes(uuid_buf);

if record.alternate_bases().is_empty()
|| record.alternate_bases().as_ref() == ["<*>".to_string()]
{
// REF-only, skip
tracing::warn!("skipping REF-only / empty ALT record {:?}", record);
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⚠️ Potential issue

Avoid logging entire records to prevent potential sensitive data exposure

Logging the full record may inadvertently expose sensitive information. Consider logging only essential details, such as the record's position and reference sequence name, to avoid potential PII leakage.

Apply this diff to address the issue:

-                tracing::warn!("skipping REF-only / empty ALT record {:?}", record);
+                tracing::warn!(
+                    "skipping REF-only / empty ALT record at {}:{}",
+                    record.reference_sequence_name(),
+                    record.position()
+                );
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
tracing::warn!("skipping REF-only / empty ALT record {:?}", record);
tracing::warn!(
"skipping REF-only / empty ALT record at {}:{}",
record.reference_sequence_name(),
record.position()
);

continue;
}
let mut record = converter.convert(pedigree, &record, uuid, GenomeRelease::Grch37)?;
annotate_cov_mq(&mut record, cov_readers)?;
if let Some(chromosome_no) = mapping.get(&record.chromosome) {
Expand Down
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