Release notes

v0.14

• Added a new module allel.stats.admixture with statistical tests for admixture between populations, implementing the f2, f3 and D statistics from Patterson (2012). Functions include allel.stats.admixture.blockwise_patterson_f3() and allel.stats.admixture.blockwise_patterson_d() which compute the f3 and D statistics respectively in blocks of a given number of variants and perform a block-jackknife to estimate the standard error.

v0.12

• Added functions for principal components analysis of genotype data. Functions in the new module allel.stats.decomposition include allel.stats.decomposition.pca() to perform a PCA via full singular value decomposition, and allel.stats.decomposition.randomized_pca() which uses an approximate truncated singular value decomposition to speed up computation. In tests with real data the randomized PCA is around 5 times faster and uses half as much memory as the conventional PCA, producing highly similar results.
• Added function allel.stats.distance.pcoa() for principal coordinate analysis (a.k.a. classical multi-dimensional scaling) of a distance matrix.
• Added new utility module allel.stats.preprocessing with classes for scaling genotype data prior to use as input for PCA or PCoA. By default the scaling (i.e., normalization) of Patterson (2006) is used with principal components analysis functions in the allel.stats.decomposition module. Scaling functions can improve the ability to resolve population structure via PCA or PCoA.
• Added method allel.model.GenotypeArray.to_n_ref(). Also added dtype argument to allel.model.GenotypeArray.to_n_ref() and allel.model.GenotypeArray.to_n_alt() methods to enable direct output as float arrays, which can be convenient if these arrays are then going to be scaled for use in PCA or PCoA.
• Added allel.model.GenotypeArray.mask property which can be set with a Boolean mask to filter genotype calls from genotype and allele counting operations. A similar property is available on the allel.bcolz.GenotypeCArray class. Also added method allel.model.GenotypeArray.fill_masked() and similar method on the allel.bcolz.GenotypeCArray class to fill masked genotype calls with a value (e.g., -1).

v0.11

• Added functions for calculating Watterson’s theta (proportional to the number of segregating variants): allel.stats.diversity.watterson_theta() for calculating over a given region, and allel.stats.diversity.windowed_watterson_theta() for calculating in windows over a chromosome/contig.
• Added functions for calculating Tajima’s D statistic (balance between nucleotide diversity and number of segregating sites): allel.stats.diversity.tajima_d() for calculating over a given region and allel.stats.diversity.windowed_tajima_d() for calculating in windows over a chromosome/contig.
• Added allel.stats.diversity.windowed_df() for calculating the rate of fixed differences between two populations.
• Added function allel.model.locate_fixed_differences() for locating variants that are fixed for different alleles in two different populations.
• Added function allel.model.locate_private_alleles() for locating alleles and variants that are private to a single population.

v0.10

• Added functions implementing the Weir and Cockerham (1984) estimators for F-statistics: allel.stats.fst.weir_cockerham_fst() and allel.stats.fst.windowed_weir_cockerham_fst().
• Added functions implementing the Hudson (1992) estimator for Fst: allel.stats.fst.hudson_fst() and allel.stats.fst.windowed_hudson_fst().
• Added new module allel.stats.ld with functions for calculating linkage disequilibrium estimators, including allel.stats.ld.rogers_huff_r() for pairwise variant LD calculation, allel.stats.ld.windowed_r_squared() for windowed LD calculations, and allel.stats.ld.locate_unlinked() for locating variants in approximate linkage equilibrium.
• Added function allel.plot.pairwise_ld() for visualising a matrix of linkage disequilbrium values between pairs of variants.
• Added function allel.model.create_allele_mapping() for creating a mapping of alleles into a different index system, i.e., if you want 0 and 1 to represent something other than REF and ALT, e.g., ancestral and derived. Also added methods allel.model.GenotypeArray.map_alleles(), allel.model.HaplotypeArray.map_alleles() and allel.model.AlleleCountsArray.map_alleles() which will perform an allele transformation given an allele mapping.
• Added function allel.plot.variant_locator() ported across from anhima.
• Refactored the allel.stats module into a package with sub-modules for easier maintenance.

v0.9

• Added documentation for the functions allel.bcolz.carray_from_hdf5(), allel.bcolz.carray_to_hdf5(), allel.bcolz.ctable_from_hdf5_group(), allel.bcolz.ctable_to_hdf5_group().
• Refactoring of internals within the allel.bcolz module.

v0.8

• Added subpop argument to allel.model.GenotypeArray.count_alleles() and allel.model.HaplotypeArray.count_alleles() to enable count alleles within a sub-population without subsetting the array.
• Added functions allel.model.GenotypeArray.count_alleles_subpops() and allel.model.HaplotypeArray.count_alleles_subpops() to enable counting alleles in multiple sub-populations in a single pass over the array, without sub-setting.
• Added classes allel.model.FeatureTable and allel.bcolz.FeatureCTable for storing and querying data on genomic features (genes, etc.), with functions for parsing from a GFF3 file.
• Added convenience function allel.stats.distance.pairwise_dxy() for computing a distance matrix using Dxy as the metric.

v0.7

• Added function allel.io.write_fasta() for writing a nucleotide sequence stored as a NumPy array out to a FASTA format file.

v0.6

• Added method allel.model.VariantTable.to_vcf() for writing a variant table to a VCF format file.