Harden read-quality indexing and document exon-boundary insertion handling

- anchor_base_quality now returns None when the CIGAR-derived query index falls
  past the stored sequence (a malformed CIGAR whose query length exceeds SEQ),
  instead of reading a bogus quality. Well-formed reads are unaffected.
- Document why an insertion anchored at an internal exon's last base is left out
  of the spliced-CDS model: the inserted bases sit on the exon|intron boundary
  and are genomically ambiguous (end-of-exon vs spliced-out intron start), so
  they are reported intergenic rather than assigned a possibly-wrong codon. This
  is intentional; the exclusive upper bound (< segment.end) encodes it.

Author: Paururo

src/read_count/observation.rs

@@ -98,6 +98,12 @@ pub(super) fn anchor_base_quality(rec: &bam::Record, position: usize) -> Option<
         // silently failing every quality gate.
         return Some(u8::MAX);
     }
+    // Defensive: a malformed CIGAR whose query length exceeds the stored
+    // sequence could yield an index past the quality scores. Treat that as "no
+    // observation" rather than reading a bogus quality.
+    if qidx >= rec.sequence().len() {
+        return None;
+    }
     Some(qual.iter().nth(qidx).unwrap_or(0))
 }
 

src/variants/codon/transcript_model.rs

@@ -56,6 +56,14 @@ pub(super) fn transcript_offset_for_position(gene: &Gene, position: usize) -> Op
     None
 }
 
+/// Whether an insertion anchored at `position` falls strictly inside this CDS
+/// segment. The upper bound is exclusive (`< segment.end`) on purpose: a VCF
+/// insertion places the inserted bases *after* the anchor, so an anchor at the
+/// segment's last base sits on the exon|intron boundary, where the inserted
+/// sequence is genomically ambiguous between "end of this exon" and "start of
+/// the intron" (spliced out). Such boundary insertions are intentionally left
+/// out of the spliced-CDS model rather than assigned a possibly-wrong codon;
+/// they surface as intergenic instead. Anchors inside an exon are unaffected.
 pub(super) fn insertion_anchor_in_segment(segment: &CdsSegment, position: usize) -> bool {
     position >= segment.start && position < segment.end
 }