fix(stats): route no-seeds-no-clusters reads to UnmappedReason::Other

The UnmappedReason enum had all four STAR-compatible variants
(Other, TooShort, TooManyMismatches, TooManyLoci), but reads that
failed before any transcript was generated were being recorded as
TooShort. Log.final.out's "Reads unmapped: other" therefore always
read 0 even when STAR would have classified the read in that bucket,
inflating "too short" by the same count.

Fix the routing at the no-seeds / no-clusters call site so reads
without alignments are recorded as Other. Totals are unchanged;
only the bucketing changes.

Fixes #48

Co-Authored-By: Claude <noreply@anthropic.com>

Author: pinin4fjords

src/align/read_align.rs

@@ -289,6 +289,7 @@ pub fn align_read(
     // Step 3: Stitch seeds within each cluster
     let scorer = AlignmentScorer::from_params(params);
     let mut transcripts = Vec::new();
+    let mut any_transcript_generated = false;
     // Collect all raw (pre-dedup) transcripts for chimericDetectionOld (Tier 1).
     let mut all_raw_transcripts: Vec<crate::align::transcript::Transcript> = Vec::new();
 
@@ -338,6 +339,9 @@ pub fn align_read(
                 );
             }
         }
+        if !cluster_transcripts.is_empty() {
+            any_transcript_generated = true;
+        }
         if params.chim_segment_min > 0 {
             all_raw_transcripts.extend(cluster_transcripts.iter().cloned());
         }
@@ -650,8 +654,11 @@ pub fn align_read(
     }
 
     let unmapped_reason = if transcripts.is_empty() {
-        // Transcripts were generated by DP but all filtered out
-        Some(UnmappedReason::TooShort)
+        if any_transcript_generated {
+            Some(UnmappedReason::TooShort)
+        } else {
+            Some(UnmappedReason::Other)
+        }
     } else {
         None
     };
@@ -814,6 +821,7 @@ pub fn align_paired_read(
     // as the search pool for chimericDetectionOld (Tier 1) on each mate independently.
     let mut all_m1_transcripts: Vec<Transcript> = Vec::new();
     let mut all_m2_transcripts: Vec<Transcript> = Vec::new();
+    let mut any_transcript_generated = false;
 
     // Stitch combined clusters, split WTs by mate_id, finalize each half
     for cluster in clusters.iter().take(params.align_windows_per_read_nmax) {
@@ -828,6 +836,10 @@ pub fn align_paired_read(
             debug_name,
         )?;
 
+        if !wts.is_empty() {
+            any_transcript_generated = true;
+        }
+
         for wt in &wts {
             let split_result =
                 split_combined_wt(wt, len1, len2, stitch_is_reverse, scorer.align_intron_min);
@@ -1233,7 +1245,14 @@ pub fn align_paired_read(
                 ))
             }
         }
-        (None, None) => Ok((Vec::new(), pe_chimeric, 0, Some(UnmappedReason::TooShort))),
+        (None, None) => {
+            let reason = if any_transcript_generated {
+                UnmappedReason::TooShort
+            } else {
+                UnmappedReason::Other
+            };
+            Ok((Vec::new(), pe_chimeric, 0, Some(reason)))
+        }
     }
 }
 
@@ -1652,7 +1671,7 @@ mod tests {
         let (paired_alns, _chimeric, n_for_mapq, unmapped_reason) = result.unwrap();
         assert_eq!(paired_alns.len(), 0);
         assert_eq!(n_for_mapq, 0);
-        assert!(unmapped_reason.is_some());
+        assert_eq!(unmapped_reason, Some(UnmappedReason::Other));
     }
 
     #[test]
@@ -2065,7 +2084,7 @@ mod tests {
             align_paired_read(&mate1, &mate2, "test", &index, &params).unwrap();
         assert!(results.is_empty(), "Both unmapped should return empty Vec");
         assert_eq!(n_for_mapq, 0);
-        assert!(unmapped_reason.is_some(), "Should have unmapped reason");
+        assert_eq!(unmapped_reason, Some(UnmappedReason::Other));
     }
 
     #[test]

src/stats.rs

@@ -827,6 +827,35 @@ mod tests {
         assert_eq!(stats.unmapped_mismatches.load(Ordering::Relaxed), 1);
     }
 
+    #[test]
+    fn test_unmapped_other_routed_and_totals_conserved() {
+        let stats = AlignmentStats::new();
+
+        let n_other = 7;
+        let n_short = 3;
+        let n_mismatches = 2;
+        for _ in 0..n_other {
+            stats.record_unmapped_reason(UnmappedReason::Other);
+        }
+        for _ in 0..n_short {
+            stats.record_unmapped_reason(UnmappedReason::TooShort);
+        }
+        for _ in 0..n_mismatches {
+            stats.record_unmapped_reason(UnmappedReason::TooManyMismatches);
+        }
+        stats.record_unmapped_reason(UnmappedReason::TooManyLoci);
+
+        let unmapped_other = stats.unmapped_other.load(Ordering::Relaxed);
+        let unmapped_short = stats.unmapped_short.load(Ordering::Relaxed);
+        let unmapped_mismatches = stats.unmapped_mismatches.load(Ordering::Relaxed);
+
+        assert!(unmapped_other > 0, "Other bucket must be populated");
+        assert_eq!(unmapped_other, n_other);
+        assert_eq!(unmapped_short, n_short);
+        assert_eq!(unmapped_mismatches, n_mismatches);
+        assert_eq!(unmapped_other + unmapped_short, (n_other + n_short));
+    }
+
     #[test]
     fn test_splice_motif_aggregation() {
         use crate::align::score::SpliceMotif;