Add --variants-vcf support for alignments#3
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Support using a variants-only VCF in from-alignments mode to estimate omitted alignment thresholds and exclude non-SNP variant spans. Adds a --variants-vcf CLI flag and a variants_vcf field on AlignmentRunConfig, validation for the VCF path, and a bedtools.subtract helper. Implements VCF parsing utilities (VariantThresholdEstimates, estimate_alignment_thresholds_from_variants_vcf, write_variant_exclusion_bed and helpers) to derive min/max DP from per-sample FORMAT/DP and min MAPQ from INFO/MQ, and to emit exclusion intervals for indels, symbolic SVs, breakends and multi-nucleotide polymorphisms. Integrates threshold resolution and exclusion-bed generation into the workflow (resolve thresholds, write/merge exclusion intervals, subtract exclusions from per-sample pass BEDs). Includes unit tests for the new parsing, CLI, validation, bedtools, and workflow behaviors.
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Support using a variants-only VCF in from-alignments mode to estimate omitted alignment thresholds and exclude non-SNP variant spans. Adds a --variants-vcf CLI flag and a variants_vcf field on AlignmentRunConfig, validation for the VCF path, and a bedtools.subtract helper. Implements VCF parsing utilities (VariantThresholdEstimates, estimate_alignment_thresholds_from_variants_vcf, write_variant_exclusion_bed and helpers) to derive min/max DP from per-sample FORMAT/DP and min MAPQ from INFO/MQ, and to emit exclusion intervals for indels, symbolic SVs, breakends and multi-nucleotide polymorphisms. Integrates threshold resolution and exclusion-bed generation into the workflow (resolve thresholds, write/merge exclusion intervals, subtract exclusions from per-sample pass BEDs). Includes unit tests for the new parsing, CLI, validation, bedtools, and workflow behaviors.