allel.model.ndarray
allel.GenotypeArray
n_variants
n_samples
ploidy
n_calls
n_allele_calls
count_alleles
count_alleles_subpops
to_packed
from_packed
to_sparse
from_sparse
haploidify_samples
subset
allel.GenotypeVector
n_calls
ploidy
n_allele_calls
Methods available on both GenotypeArray and GenotypeVector classes:
allel.Genotypes
mask
is_phased
fill_masked
is_called
is_missing
is_hom
is_hom_ref
is_hom_alt
is_het
is_call
count_called
count_missing
count_hom
count_hom_ref
count_hom_alt
count_het
count_call
to_n_ref
to_n_alt
to_allele_counts
to_gt
map_alleles
compress
take
concatenate
allel.HaplotypeArray
n_variants
n_haplotypes
subset
is_called
is_missing
is_ref
is_alt
is_call
count_called
count_missing
count_ref
count_alt
count_call
count_alleles
count_alleles_subpops
map_alleles
to_genotypes
to_sparse
from_sparse
prefix_argsort
distinct
distinct_counts
distinct_frequencies
compress
take
subset
concatenate
allel.AlleleCountsArray
n_variants
n_alleles
max_allele
allelism
is_variant
is_non_variant
is_segregating
is_non_segregating
is_singleton
is_doubleton
is_biallelic
is_biallelic_01
count_variant
count_non_variant
count_segregating
count_non_segregating
count_singleton
count_doubleton
to_frequencies
map_alleles
compress
take
concatenate
allel.GenotypeAlleleCountsArray
n_variants
n_samples
n_alleles
count_alleles
subset
allel.GenotypeAlleleCountsVector
n_calls
n_alleles
Methods available on both GenotypeAlleleCountsArray and GenotypeAlleleCountsVector classes:
allel.GenotypeAlleleCounts
is_called
is_missing
is_hom
is_hom_ref
is_hom_alt
is_het
compress
take
concatenate
allel.VariantTable
n_variants
names
eval
query
query_position
query_region
to_vcf
allel.FeatureTable
n_features
names
eval
query
from_gff3
to_mask
allel.SortedIndex
is_unique
locate_key
locate_keys
locate_intersection
intersect
locate_range
intersect_range
locate_ranges
locate_intersection_ranges
intersect_ranges
allel.ChromPosIndex
locate_key
locate_range
allel.SortedMultiIndex
locate_key
locate_range
allel.UniqueIndex
locate_key
locate_keys
locate_intersection
intersect