fix order of snp loadings for plink input

this is a fix for v0.3.3 version. thanks @KristJán for reporting this bug.

cli breaking change with new option --svd

• breaking change option --svd for choosing different SVD methods. default is PCAone algorithm2.
• add permuting BGEN file with multithreading.
• add Full SVD support by --svd 3
• add log transformation support for bulk RNA-seq data by --scale 1
• add binary file support
• recover the original order for SNP loadings.
• recover the eigenvalues for diploid genotype (0,1,2) data.

tab as separator in output file

• use tab "\t" as separator in output file instead of multiple spaces
• add --center option

third version manuscript

• fix bioconda can't find zlib.h
• corresponding to the third version manuscript on biorxiv after revision
• fix algorithm2 to use one more omega updates between epoch.
• option --bands changed to --windows with default 64.
• support CXXSTD compiling option to use c++17 standard. default CXXSTD=c++11
• add PCAoneR, which implement the idea of PCAone in R but without out-of-core
• colorful warning and error message. more checks and warnings.

third version manuscript

• corresponding to the third version manuscript on biorxiv after revision
• fix algorithm2 to use one more omega updates between epoch.
• option --bands changed to --windows with default 64.
• support CXXSTD compiling option to use c++17 standard. default CXXSTD=c++11
• add PCAoneR, which implement the idea of PCAone in R but without out-of-core
• colorful warning and error message. more checks and warnings.

v0.2.1

fix a bug for PCAngsd

v0.2.0

• add --maf option for SNPs filtering
• faster parser for beagle file
• optimization for PCAngsd, less RAM
• fix printing loadings for PCAoneA blockwise mode

v0.1.9

• command line options are re-designed but be compatible
• upgrade to zstd v1.5.2
• recover the original order of SNPs loading for fancy batch mode when outputting
• add --no-shuffle option, remove --shuffle option
• default PCAoneF (fancy RSVD) algorithm is chose.
• makefile fix

v0.1.8

Manuscript is on BioRxiv! See CHANGELOG.

v0.1.7

• two releases for Linux x64 and avx2
• add conda install -c bioconda pcaone
• upgrade Spectra to v1.0.1
• add logger and quickstart