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
On main, a single-end run with
--chimOutType WithinBAMexits 1 withread 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 Junctionsis 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_recordsinsrc/chimeric/output.rs, SE path (SEQ/QUAL vs CIGAR length of the donor/acceptor records).Tracking: #277
🤖 Generated with Claude Code