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feat: add --outSAMattrRGline with @RG header and RG:Z tags #6

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Merged
Psy-Fer merged 8 commits into from
Apr 20, 2026
Merged

feat: add --outSAMattrRGline with @RG header and RG:Z tags #6

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6740954
Add --outSAMattrRGline flag and emit @RG header + RG:Z tags
ewels Apr 17, 2026
716a816
chore(simplify): drop dead rg_ids() call and redundant attrs gate
ewels Apr 17, 2026
f23e00d
chore(simplify): introduce primary_rg_id helper for writer callsites
ewels Apr 17, 2026
845398f
chore(simplify): rewrite parsed_rg_lines with Vec::split
ewels Apr 17, 2026
471518a
chore: remove dead SamWriter::write_unmapped
ewels Apr 17, 2026
8dc4262
chore: apply cargo fmt
ewels Apr 17, 2026
038c23f
Merge branch 'main' into feat/sam-rg-line
Psy-Fer Apr 20, 2026
e306046
Fix merge conflict squashing } braket
Psy-Fer Apr 20, 2026
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9 changes: 6 additions & 3 deletions src/io/bam.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -125,9 +125,10 @@ mod tests {
let read_qual = vec![30, 30, 30, 30];

// Build record using SAM builder
let record =
crate::io::sam::SamWriter::build_unmapped_record(read_name, &read_seq, &read_qual)
.unwrap();
let record = crate::io::sam::SamWriter::build_unmapped_record(
read_name, &read_seq, &read_qual, None,
)
.unwrap();

let result = writer.write_batch(&[record]);
assert!(result.is_ok(), "Writing unmapped read should succeed");
Expand Down Expand Up @@ -204,12 +205,14 @@ mod tests {
"read1",
&[0, 1, 2, 3],
&[30, 30, 30, 30],
None,
)
.unwrap(),
crate::io::sam::SamWriter::build_unmapped_record(
"read2",
&[0, 1, 2, 3],
&[30, 30, 30, 30],
None,
)
.unwrap(),
];
Expand Down
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