Print a genotype-reference compatibility report
Usage
# S3 method for class 'hbr_compat_report'
print(x, ...)Examples
x <- structure(
list(status = "PASS",
summary = data.table::data.table(
Reference_genome = "TOY", Reference_annotation = "CUSTOM",
Declared_genotype_build = NA_character_,
Individuals = 1L, Total_variants = 1L,
Chromosomes_matched = 1L, Chromosomes_total_reference = 1L,
Chromosome_match_pct = 100, Valid_position_pct = 100,
REF_check_coverage = "genome_fasta",
REF_checked_n = 1L, REF_match_pct = 100,
Duplicate_positions = 0L, Multiallelic_variants = 0L,
Reference_mismatches = 0L, Unknown_chromosomes = 0L)),
class = "hbr_compat_report")
print(x)
#> GENOTYPE-REFERENCE COMPATIBILITY
#> ================================
#>
#> Reference genome : TOY (CUSTOM)
#> Declared genotype build: NA
#> Individuals : 1
#> Total variants : 1
#> Chromosome match : 1 / 1 (100.00%)
#> Valid positions : 100.00%
#> REF check mode : genome_fasta
#> REF match : 1 checked, 100.00%
#> Duplicate positions : 0
#> Multiallelic variants : 0
#> Reference mismatches : 0
#> Unknown chromosomes : 0
#>
#> STATUS: PASS