News and Changes

v0.3.1

add phaseless R package

v0.2.6

add LA utilts

v0.2.5

add first joint model

v0.2.4

update admixture with collapsed and normalized gamma ae

v0.2.3

fix input for admixture
add new collapsing strategy

v0.2.2

add B option for collapsing. currently only works with -S option
switch float to double type for testing accuracy

v0.2.1

fix stupid cli

v0.2.0

add recombination rate in fastphase
use collapsed gamma in cluster likelihoods for admixture
estimate AF from GL

v0.1.8

fix optimal version
output big vcf, pi and info files

v0.1.7

add optimal version of O(CC+CK) complexity and reduce number errors
fix serialization
discard small chunks in phaseless

v0.1.6

change initial F and PI for phasing model
change PI storage layout to speedup forwards backwards
add both low and high RAM implementation of imputation
try using matrix form but not ideal

v0.1.5

add SqS3 EM acceleration

v0.1.4

add -P option
optimize imputation get posteriors

v0.1.3

output INFO score and EAF
add thinning by INFO score
update genotype likelihoods layout

v0.1.2

optimize forward backwards to get cluster likelihoods fast (0.4x)

v0.1.1

speedup phaseless with O(c*c/2) complexity
update fastphasek2 interface

v0.1.0

first test version