LD paper accepted in Genetics

Breaking:

• switch to C++17 and above standard
• option -v/--verbose takes integer value for different verbosity level
• remove temporary files in default. only keep them when the verbose level is >=3.

Improvement:

• CLI. run PCAone --groff > pcaone.1 to generate the manual that can be read by man ./pcaone.1
• refactor the halko code
• speedup projection and prediction with multithreading

HWE accounting for population structure

• HWE test accounting for population structure via --inbreed 1
• new option --USV as the prefix of pcaone .eigvecs/.eigvals/.loadigns/.mbim files
• the output .eigvecs2 stores the eigenvectors of the covariance matrix, which also works for BEALGE file with genotype likelihood input, while the .eigvecs,.eigvals,.loadings stores the U,S,V matrix for reconstructing the PI matrix

see Full change log

Projection module

projection support via --project
1: projection by multiplying the loadings with mean imputation for missing genotypes
2: projection by solving the least squares system $Vx=g$. sites with missingness are skipped like smartPCA.

See full change log.

Small fix and CLI improvement

see full chanege log here

out-of-core LD module

see full chanege log here

LD clumping

v0.4.4

update readme

v0.4.3 new output eigvecs2

• new output eigvecs2 for plink input, which has header line
• fix ld clumping and sort snps by pvalues

v0.4.2 (speedup + LD clumping)

1. fix slowness due to the ld related stuff
2. add ld-clump functionalities

v0.4.0 (LD prune)

• celebrate PCAone is on genome research
• new feature LD prune on admixed population
• fix --maf being af not maf
• other small fix

v0.3.5

• change default behaviour to fix the warning issue
• support permuting csv input file to binary file