Features

• LOH analysis: Output LOH bedgraph for entire edit chromosome, not just cut site vicinity
• Outcome classification: Revamp on-target outcome classification with blast queries, error correction, and MSA consensus
• Schema updates: Add optional donor context outside homology arms for better annotation
• Knock-knock integration: Provide CRISPR donor extra sequence context for improved annotation
• Variant QC: Implement quality filtering for knock-knock, LOH, and annotated variants

Fixes

• Adjust consensus MSA parameters for better handling of expected insertion gaps
• Pass INFO/parent annotation inputs; reduce resource requests to avoid job saturation
• Fix PAV VCF sample names with by reheader to prevent loss of structural variant calls (non-alphanum_ sanitized, previously lost pav SVs from samples with "." in name)
• Fix knock-knock crash on short sequences with no alignment found

Performance

• Minor optimization to BAM input staging