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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 @@
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 @@
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()]

Check warning on line 2963 in src/annotate/strucvars/mod.rs

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GitHub Actions / clippy

taken reference of right operand 

warning: taken reference of right operand
    --> src/annotate/strucvars/mod.rs:2963:16
     |
2963 |             || record.alternate_bases().as_ref() == &["<*>".to_string()]
     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^--------------------
     |                                                     |
     |                                                     help: use the right value directly: `["<*>".to_string()]`
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#op_ref
     = note: `#[warn(clippy::op_ref)]` on by default
{
// REF-only, skip
tracing::warn!("skipping REF-only record {:?}", record);
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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