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@@ -771,6 +771,22 @@ pub fn fb_inv_from_record(
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// anyhow::bail!("No SM tag found in @RG header of {bam_path}")
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// }
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+// fn ensure_bam_sm_tag(id: &str, config: &Config) -> anyhow::Result<()> {
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+// for bam in [config.normal_bam(id), config.tumoral_bam(id)] {
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+// if read_sm_tag(&bam).is_err() {
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+// let sample = Path::new(&bam)
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+// .file_stem()
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+// .unwrap_or_default()
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+// .to_string_lossy()
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+// .to_string();
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+// info!("Injecting missing @RG SM:{sample} into {bam}");
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+// SamtoolsReheader::from_config(config, &bam, &sample).run()?;
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+// SamtoolsIndex::from_config(config, &bam).run()?;
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+// }
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+// }
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+// Ok(())
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+// }
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+
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pub fn read_sm_tag_or_inject(
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bam_path: &str,
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fallback_sample: &str,
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@@ -780,7 +796,6 @@ pub fn read_sm_tag_or_inject(
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.with_context(|| format!("Failed to open BAM: {bam_path}"))?;
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let header = bam::Header::from_template(reader.header());
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let header_text = String::from_utf8_lossy(&header.to_bytes()).to_string();
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-
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for line in header_text.lines() {
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if line.starts_with("@RG") {
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for field in line.split('\t') {
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@@ -791,9 +806,14 @@ pub fn read_sm_tag_or_inject(
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}
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}
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+ // Preserve original mtime before modifying header
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+ let original_mtime = filetime::FileTime::from_last_modification_time(
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+ &std::fs::metadata(bam_path)
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+ .with_context(|| format!("Failed to stat BAM: {bam_path}"))?,
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+ );
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+
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// SM missing (dorado/MinKNOW unclassified barcode) — inject it
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info!("No @RG SM tag in {bam_path}, injecting SM:{fallback_sample}");
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-
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let mut reheader = SamtoolsReheader::from_config(config, bam_path, fallback_sample);
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reheader
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.run()
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@@ -804,5 +824,9 @@ pub fn read_sm_tag_or_inject(
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.run()
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.with_context(|| format!("Failed to re-index {bam_path}"))?;
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+ // Restore original mtime so is_file_older() doesn't re-trigger downstream callers
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+ filetime::set_file_mtime(bam_path, original_mtime)
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+ .with_context(|| format!("Failed to restore mtime on {bam_path}"))?;
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+
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Ok(fallback_sample.to_string())
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}
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