Index A | B | C | E | G | H | I | L | M | P | R | S | U | V | W A add_homozygosity_to_variant_json() (in module emumadz.plot_homozygosity) B bedgraph_to_tdf() (in module emumadz.plot_homozygosity) C calculate_allele_freq() (emumadz.parse_vcf.VCFParser method) calculate_score() (emumadz.plot_homozygosity.HenkeScorer method) (emumadz.plot_homozygosity.HomozygosityScorer method) chrom (emumadz.plot_homozygosity.VariantData attribute) create_bam_subset() (emumadz.parse_vcf.VCFParser method) create_reference_bam_subsets() (emumadz.parse_vcf.VCFParser method) E emumadz.parse_vcf module emumadz.plot_homozygosity module G generate_coverage_report() (emumadz.parse_vcf.VCFParser method) get_impact_color() (emumadz.parse_vcf.VCFParser method) get_name() (emumadz.plot_homozygosity.HenkeScorer method) (emumadz.plot_homozygosity.HomozygosityScorer method) get_relative_bam_file() (emumadz.parse_vcf.VCFParser method) get_sample_data() (emumadz.plot_homozygosity.VariantData method) H HenkeScorer (class in emumadz.plot_homozygosity) homozygosity_threshold (emumadz.plot_homozygosity.HenkeScorer attribute) HomozygosityAnalyser (class in emumadz.plot_homozygosity) HomozygosityError HomozygosityScorer (class in emumadz.plot_homozygosity) I is_snp (emumadz.plot_homozygosity.VariantData attribute) L load_samplesheet() (in module emumadz.plot_homozygosity) M main() (in module emumadz.parse_vcf) (in module emumadz.plot_homozygosity) match_sample() (emumadz.parse_vcf.VCFParser method) min_coverage (emumadz.plot_homozygosity.HenkeScorer attribute) module emumadz.parse_vcf emumadz.plot_homozygosity P parse_allele_depths() (in module emumadz.plot_homozygosity) parse_ann_field() (emumadz.parse_vcf.VCFParser method) parse_csq_field() (emumadz.parse_vcf.VCFParser method) pos (emumadz.plot_homozygosity.VariantData attribute) process_sample_variants() (emumadz.parse_vcf.VCFParser method) process_vcf() (emumadz.parse_vcf.VCFParser method) (emumadz.plot_homozygosity.HomozygosityAnalyser method) R requires_references() (emumadz.plot_homozygosity.HenkeScorer method) (emumadz.plot_homozygosity.HomozygosityScorer method) S sample_info (emumadz.parse_vcf.VCFParser attribute) scorer (emumadz.plot_homozygosity.HomozygosityAnalyser attribute) step_size (emumadz.plot_homozygosity.HomozygosityAnalyser attribute) U use_snp_windows (emumadz.plot_homozygosity.HomozygosityAnalyser attribute) V validate_bam_subset() (emumadz.parse_vcf.VCFParser method) VariantData (class in emumadz.plot_homozygosity) VCFParser (class in emumadz.parse_vcf) W window_size (emumadz.plot_homozygosity.HomozygosityAnalyser attribute) write_bedgraph() (in module emumadz.plot_homozygosity)