Index

A

allel (module) allel.bcolz (module) allel.model (module) allel.plot (module) allel.stats.distance (module) allel.stats.diversity (module)

allel.stats.hw (module) allel.stats.ld (module) allel.stats.window (module) AlleleCountsArray (class in allel.model) AlleleCountsCArray (class in allel.bcolz) allelism() (allel.model.AlleleCountsArray method)

C

carray_block_compress() (in module allel.bcolz) carray_block_map() (in module allel.bcolz) carray_block_max() (in module allel.bcolz) carray_block_min() (in module allel.bcolz) carray_block_sum() (in module allel.bcolz) carray_block_take() (in module allel.bcolz) carray_from_hdf5() (in module allel.bcolz) count_alleles() (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method) count_alleles_subpops() (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method) count_alt() (allel.model.HaplotypeArray method) count_call() (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method) count_called() (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method) count_doubleton() (allel.model.AlleleCountsArray method) count_het() (allel.model.GenotypeArray method)

count_hom() (allel.model.GenotypeArray method) count_hom_alt() (allel.model.GenotypeArray method) count_hom_ref() (allel.model.GenotypeArray method) count_missing() (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method) count_non_segregating() (allel.model.AlleleCountsArray method) count_non_variant() (allel.model.AlleleCountsArray method) count_ref() (allel.model.HaplotypeArray method) count_segregating() (allel.model.AlleleCountsArray method) count_singleton() (allel.model.AlleleCountsArray method) count_variant() (allel.model.AlleleCountsArray method) create_allele_mapping() (in module allel.model) ctable_block_compress() (in module allel.bcolz) ctable_block_take() (in module allel.bcolz) ctable_from_hdf5_group() (in module allel.bcolz)

E

eval() (allel.model.FeatureTable method) (allel.model.VariantTable method)

F

FeatureCTable (class in allel.bcolz) FeatureTable (class in allel.model) from_gff3() (allel.model.FeatureTable static method)

from_packed() (allel.model.GenotypeArray static method) from_sparse() (allel.model.GenotypeArray static method) (allel.model.HaplotypeArray static method)

G

GenotypeArray (class in allel.model)

GenotypeCArray (class in allel.bcolz)

H

haploidify_samples() (allel.model.GenotypeArray method) HaplotypeArray (class in allel.model) HaplotypeCArray (class in allel.bcolz)

heterozygosity_expected() (in module allel.stats.hw) heterozygosity_observed() (in module allel.stats.hw) hudson_fst() (in module allel.stats.diversity)

I

inbreeding_coefficient() (in module allel.stats.hw) intersect() (allel.model.SortedIndex method) (allel.model.UniqueIndex method) intersect_range() (allel.model.SortedIndex method) intersect_ranges() (allel.model.SortedIndex method) is_alt() (allel.model.HaplotypeArray method) is_call() (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method) is_called() (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method) is_doubleton() (allel.model.AlleleCountsArray method) is_het() (allel.model.GenotypeArray method) is_hom() (allel.model.GenotypeArray method)

is_hom_alt() (allel.model.GenotypeArray method) is_hom_ref() (allel.model.GenotypeArray method) is_missing() (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method) is_non_segregating() (allel.model.AlleleCountsArray method) is_non_variant() (allel.model.AlleleCountsArray method) is_ref() (allel.model.HaplotypeArray method) is_segregating() (allel.model.AlleleCountsArray method) is_singleton() (allel.model.AlleleCountsArray method) is_unique (allel.model.SortedIndex attribute) is_variant() (allel.model.AlleleCountsArray method)

L

locate_fixed_differences() (in module allel.model) locate_intersection() (allel.model.SortedIndex method) (allel.model.UniqueIndex method) locate_intersection_ranges() (allel.model.SortedIndex method) locate_key() (allel.model.SortedIndex method) (allel.model.SortedMultiIndex method) (allel.model.UniqueIndex method) locate_keys() (allel.model.SortedIndex method) (allel.model.UniqueIndex method)

locate_private_alleles() (in module allel.model) locate_range() (allel.model.SortedIndex method) (allel.model.SortedMultiIndex method) locate_ranges() (allel.model.SortedIndex method) locate_unlinked() (in module allel.stats.ld)

M

map_alleles() (allel.model.AlleleCountsArray method) (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method) mean_pairwise_difference() (in module allel.stats.diversity)

mean_pairwise_difference_between() (in module allel.stats.diversity) moving_statistic() (in module allel.stats.window)

N

n_alleles (allel.model.AlleleCountsArray attribute) n_features (allel.model.FeatureTable attribute) n_haplotypes (allel.model.HaplotypeArray attribute)

n_samples (allel.model.GenotypeArray attribute) n_variants (allel.model.AlleleCountsArray attribute) (allel.model.GenotypeArray attribute) (allel.model.HaplotypeArray attribute) (allel.model.VariantTable attribute) names (allel.model.FeatureTable attribute) (allel.model.VariantTable attribute)

P

pairwise_distance() (in module allel.plot) (in module allel.stats.distance) pairwise_dxy() (in module allel.stats.distance) pairwise_ld() (in module allel.plot)

per_base() (in module allel.stats.window) ploidy (allel.model.GenotypeArray attribute)

Q

query() (allel.model.FeatureTable method) (allel.model.VariantTable method) query_position() (allel.model.VariantTable method)

query_region() (allel.model.VariantTable method)

R

rogers_huff_r() (in module allel.stats.ld)

S

sequence_divergence() (in module allel.stats.diversity) sequence_diversity() (in module allel.stats.diversity) SortedIndex (class in allel.model)

SortedMultiIndex (class in allel.model) subset() (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method)

T

to_allele_counts() (allel.model.GenotypeArray method) to_frequencies() (allel.model.AlleleCountsArray method) to_genotypes() (allel.model.HaplotypeArray method) to_gt() (allel.model.GenotypeArray method) to_haplotypes() (allel.model.GenotypeArray method)

to_mask() (allel.model.FeatureTable method) to_n_alt() (allel.model.GenotypeArray method) to_packed() (allel.model.GenotypeArray method) to_sparse() (allel.model.GenotypeArray method) (allel.model.HaplotypeArray method) to_vcf() (allel.model.VariantTable method)

U

UniqueIndex (class in allel.model)

V

variant_locator() (in module allel.plot) VariantCTable (class in allel.bcolz)

VariantTable (class in allel.model)

W

weir_cockerham_fst() (in module allel.stats.diversity) windowed_count() (in module allel.stats.window) windowed_df() (in module allel.stats.diversity) windowed_divergence() (in module allel.stats.diversity)

windowed_diversity() (in module allel.stats.diversity) windowed_hudson_fst() (in module allel.stats.diversity) windowed_statistic() (in module allel.stats.window) windowed_weir_cockerham_fst() (in module allel.stats.diversity)