skills/bioskills/bio-alternative-splicing-splicing-qc/scripts/splicing_qc.py

• run_junction_saturation · function · L15-L30 — def run_junction_saturation(bam_file, bed_file, output_prefix)
• run_junction_annotation · function · L33-L49 — def run_junction_annotation(bam_file, bed_file, output_prefix)
• count_junction_reads · function · L52-L80 — def count_junction_reads(bam_path, min_overhang=8)
• analyze_junction_coverage · function · L83-L101 — def analyze_junction_coverage(junction_counts)
• score_splice_sites · function · L104-L135 — def score_splice_sites(sequences_5ss, sequences_3ss)
• generate_qc_report · function · L138-L175 — def generate_qc_report(bam_file, bed_file, output_prefix)