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fix: --skip-no-m6a skips all reads when MSP annotations are missing #102

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Merged
mrvollger merged 1 commit into from
Mar 18, 2026
Merged

fix: --skip-no-m6a skips all reads when MSP annotations are missing #102

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19 changes: 12 additions & 7 deletions src/subcommands/fire.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -72,20 +72,25 @@ pub fn add_fire_to_bam(fire_opts: &mut FireOptions) -> Result<(), anyhow::Error>
let n_msps = rec.msp.annotations.len();
if fire_opts.skip_no_m6a || fire_opts.min_msp > 0 || fire_opts.min_ave_msp_size > 0
{
// skip no calls
if rec.m6a.annotations.is_empty() || n_msps == 0 {
// skip reads with no m6a calls
if fire_opts.skip_no_m6a && rec.m6a.annotations.is_empty() {
skip_because_no_m6a += 1;
continue;
}
//let max_msp_len = *rec.msp.lengths.iter().flatten().max().unwrap_or(&0);
if n_msps < fire_opts.min_msp {
skip_because_num_msp += 1;
continue;
}
let ave_msp_size = rec.msp.lengths().iter().sum::<i64>() / n_msps as i64;
if ave_msp_size < fire_opts.min_ave_msp_size {
skip_because_ave_msp_length += 1;
continue;
if fire_opts.min_ave_msp_size > 0 {
if n_msps == 0 {
skip_because_ave_msp_length += 1;
continue;
}
let ave_msp_size = rec.msp.lengths().iter().sum::<i64>() / n_msps as i64;
if ave_msp_size < fire_opts.min_ave_msp_size {
skip_because_ave_msp_length += 1;
continue;
}
}
}
out.write(&rec.record)?;
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