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fix(sam): use safe conversions for CIGAR ref span and revcomp string #158

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Merged
nh13 merged 1 commit into from
Mar 4, 2026
Merged

fix(sam): use safe conversions for CIGAR ref span and revcomp string #158

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3 changes: 2 additions & 1 deletion crates/fgumi-sam/src/alignment_tags.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -294,7 +294,8 @@ pub fn regenerate_alignment_tags_raw(
let cigar_ops = fgumi_raw_bam::get_cigar_ops(record);

// Calculate reference span from CIGAR ops
let ref_span = fgumi_raw_bam::reference_length_from_cigar(&cigar_ops) as usize;
let ref_span = usize::try_from(fgumi_raw_bam::reference_length_from_cigar(&cigar_ops))
.context("CIGAR-derived reference span is negative")?;

// Handle edge case: CIGAR with no reference-consuming operations
if ref_span == 0 {
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7 changes: 1 addition & 6 deletions crates/fgumi-sam/src/lib.rs
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Expand Up @@ -310,11 +310,6 @@ pub fn reverse_buf_value(value: &BufValue) -> BufValue {
///
/// A new `BufValue` with reverse complemented sequence, or a clone if not a string
///
/// # Panics
///
/// Cannot panic in practice: the byte-level complement maps ASCII to ASCII,
/// so `String::from_utf8` always succeeds.
///
/// # Examples
///
/// ```rust,ignore
Expand All @@ -328,7 +323,7 @@ pub fn revcomp_buf_value(value: &BufValue) -> BufValue {
match value {
BufValue::String(s) => {
let revcomp = fgumi_dna::reverse_complement(s.as_bytes());
BufValue::from(String::from_utf8(revcomp).expect("complement of ASCII is ASCII"))
BufValue::from(String::from_utf8_lossy(&revcomp).into_owned())
}
_ => value.clone(),
}
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