Index

A

allel (module) allel.bcolz (module) allel.model (module) allel.plot (module)

allel.stats (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_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) 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.VariantTable method)

F

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) heterozygosity_observed() (in module allel.stats)

I

inbreeding_coefficient() (in module allel.stats) 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_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_range() (allel.model.SortedIndex method) (allel.model.SortedMultiIndex method) locate_ranges() (allel.model.SortedIndex method)

M

mean_pairwise_divergence() (in module allel.stats) mean_pairwise_diversity() (in module allel.stats)

moving_statistic() (in module allel.stats)

N

n_alleles (allel.model.AlleleCountsArray 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.VariantTable attribute)

P

pairwise_distance() (in module allel.plot) (in module allel.stats) per_base() (in module allel.stats)

ploidy (allel.model.GenotypeArray attribute)

Q

query() (allel.model.VariantTable method)

S

sequence_divergence() (in module allel.stats) sequence_diversity() (in module allel.stats) 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_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

VariantCTable (class in allel.bcolz)

VariantTable (class in allel.model)

W

windowed_count() (in module allel.stats) windowed_divergence() (in module allel.stats)

windowed_diversity() (in module allel.stats) windowed_statistic() (in module allel.stats)