fix: mismatch-filtered reads misclassified as TooShort in Log.final.out

[Psy-Fer]

fix: mismatch-filtered reads misclassified as TooShort in Log.final.out

Summary

When all transcript candidates for a read are removed by the mismatch count or mismatch-rate filter (--outFilterMismatchNmax, --outFilterMismatchNoverLmax), rustar-aligner classifies those reads as UnmappedReason::TooShort rather than UnmappedReason::TooManyMismatches. This inflates the Number of reads unmapped: too short counter and keeps Number of reads unmapped: too many mismatches at zero.

STAR reference behaviour

STAR's ReadAlign_mappedFilter.cpp distinguishes:

• lines 20–26: score/match threshold failure → unmappedShort → Log.final.out "too short"
• lines 27–30: mismatch count or rate exceeded → unmappedMismatch → Log.final.out "too many mismatches"

Location

src/align/read_align.rs, lines 636–638:

let unmapped_reason = if transcripts.is_empty() {
    Some(UnmappedReason::TooShort)   // always TooShort — wrong when mismatches fired
} else {
    None
};

The retain() closure at lines 415–522 already tracks filter reasons via a HashMap<&str, usize> (filter_reasons), but this map is only used for log::debug! output and is dropped before the catch-all above.

Fix

Replace the string-keyed filter_reasons HashMap with two booleans in the retain() closure:

let mut any_mismatch_filter = false;
let mut any_other_filter = false;

transcripts.retain(|t| {
    // score / match filters:
    if /* score or match condition */ {
        any_other_filter = true;
        return false;
    }
    // mismatch count / rate filters:
    if /* mismatch condition */ {
        any_mismatch_filter = true;
        return false;
    }
    true
});

let unmapped_reason = if transcripts.is_empty() {
    if any_mismatch_filter && !any_other_filter {
        Some(UnmappedReason::TooManyMismatches)
    } else {
        Some(UnmappedReason::TooShort)
    }
} else {
    None
};

The existing filter_reasons HashMap can be removed (the two booleans replace its only production use).

Related

• Closes residual part of Log.final.out folds all unmapped reads into too short; other bucket always 0 #48 (the "other = 0" part was fixed separately; the mismatch bucket was not).
• Will feed the correct uT:A: tag value once unmapped-record tags are implemented