read-filters-qc

name	read-filters-qc
description	Reference for gbcms read-level (genomic) QC — BAM flag filters (duplicate/secondary/supplementary/qc-failed/improper-pair/indel), MAPQ and base-quality gating, heuristic BAQ near indels/splice junctions, and QC diagnostics (mq0_count, n_count, alt/ref distance-to-end). Use when changing filtering or quality gating. NOTE: this is genomic QC — for the dev lint/test sweep see the qa-check skill.

Read Filters & Quality Gating (genomic QC)

Phase 0 universal filters (shared/filters.rs)

ReadFilter::passes() checks, in order: duplicate → secondary → supplementary → qc-failed → improper-pair → indel(CIGAR I/D). Rejections are tallied in FilterCounts for debug logging.

Defaults (CLI): filter_duplicates, filter_secondary, filter_supplementary, filter_qc_failed = true; filter_improper_pair, filter_indel = false. (Nextflow nextflow.config mirrors these — keep them in sync.)

MAPQ is NOT in filters.rs. It is mode-specific and stays in the engine: RNA does NH:i:1 rescue of low-MAPQ unique reads; mq0_count tracks MAPQ==0 reads.

Base-quality gating

• min_baseq (default 20) gates discriminating bases.
• SW masks sub-min_baseq bases to N; PairHMM weights by BQ. The WFA fast-path must apply the same gate (don't make a definitive call on bases the fallback would reject).
• usable_count >= 3 high-quality bases required for a confident alignment call.

Heuristic BAQ (shared/baq.rs, Li 2011)

• Downgrades BQ within BAQ_RADIUS = 5 bp of any Ins/Del/RefSkip by BAQ_PENALTY = 20 (clamped at 0). Allocation-free when the read has no indel/N.
• For RNA, the RefSkip (N) penalty substitutes for GATK SplitNCigarReads overhang clipping.
• Default: DNA off, RNA on (--apply-baq / --no-baq). The Nextflow modules encode this asymmetry — DNA passes --apply-baq only if true; RNA passes --no-baq only if false.

QC diagnostic outputs

• mq0_count: reads with MAPQ==0 at the locus.
• n_count: reads with an N at ≥1 discriminating position (NAD) — duplex masking / failure.
• alt_dist_end_median / ref_dist_end_median: median base distance to read end.

Key Files

• rust/src/shared/filters.rs: ReadFilter, FilterCounts
• rust/src/shared/baq.rs: apply_heuristic_baq
• rust/src/counting/engine.rs: Phase 0 wiring, MAPQ/mq0, BQ gate
• tests/test_filters.py