Single-end --chimOutType WithinBAM fails with "read length-sequence length mismatch" #279

On main, a single-end run with --chimOutType WithinBAM exits 1 with read length-sequence length mismatch, raised while writing a malformed supplementary record. Paired-end WithinBAM works (8,675 supplementary records written correctly on the same test set), and single-end --chimOutType Junctions is fine.

Found while checking output identity for #278 (the partial files from main and the PR only differ in where they stop).

Likely area: build_within_bam_records in src/chimeric/output.rs, SE path (SEQ/QUAL vs CIGAR length of the donor/acceptor records).

Tracking: #277

🤖 Generated with Claude Code