Release History¶
v0.11.0 (2021-07-21)¶
Add a Region scalar with support for loading from BED files and filtering
v0.10.1 (2021-07-16)¶
Fixed an issue reporting the size of GenotypeDtype in memory
v0.10.0 (2021-07-16)¶
Change genotype scores to be a unit8 (255=missing) instead of float64, to save ~70% of memory usage
v0.9.1 (2021-07-13)¶
Fix a side-effect of to_plink that swapped allele idxs which could affect edge encoding
v0.9.0 (2021-07-12)¶
Remove fancy new pandas dtypes from edge encoding (and rename weighted encoding to edge encoding).
v0.8.0 (2021-07-09)¶
Improve randomness handling in BAMS and fix calculations to ensure they work as expected (especially quantitative)
v0.7.0 (2021-07-06)¶
Return float values for encoding instead of newer (and less compatible) pandas types
v0.6.1 (2021-06-26)¶
Specify only alternate allele frequencies when generating random genotypes, to avoid float rounding problems
v0.6.0 (2021-06-25)¶
Enhancements¶
The genomics DataFrame Accessor no longer requires that all columns in the DataFrame are backed by a GenotypeArray
v0.5.2 (2021-06-24)¶
Update numpy version requirement
v0.5.1 (2021-06-23)¶
Update dependencies to fix doc building
v0.5.0 (2021-06-23)¶
Enhancements¶
Add separate Series and DataFrame Accessors
Speed up Plink file import
Add prototype BiAllelic Model Simulator
Add random genotype simulator
Add Plink Output
v0.4.0 (2021-03-30)¶
Enhancements¶
Updates to the backing structure of the GenotypeArray
Added Variant quality scores
Added Genotype quality scores
v0.3.0 (2020-10-23)¶
Enhancements¶
Four encoding methods added to GenotypeArray: encode_additive, encode_recessive, encode_dominant, and encode_codominant
A genotype Series accessor has been added. Thus far it includes the encoding methods.
Variants now track which allele is considered the reference allele
Tests¶
I/O Tests are added for Plink and VCF. Note that VCF requires htslib, so tests are skipped on Windows
Encoding tests added
Docs¶
Improved.
v0.2.0 (2020-10-09)¶
Tests¶
Pandas ExtensionArray tests are passing. Note: a few can’t pass until it’s possible to define dtype as scalar (See Pandas #33825)
Docs¶
Some initial documentation added
v0.1.0 (2020-09-18)¶
Initial Release