├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── kcount.R └── pseudoRef.R ├── README.md ├── _config.yml ├── man ├── kcount.Rd └── pseudoRef.Rd ├── pseudoRef.Rproj └── test ├── debug.Rmd ├── debug.nb.html ├── head.txt ├── n1000_bisnp_annot.txt ├── output ├── JRIAL2A.fasta └── JRIAL2B.fasta └── sample_chr10.fa /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/kcount.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/R/kcount.R -------------------------------------------------------------------------------- /R/pseudoRef.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/R/pseudoRef.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/README.md -------------------------------------------------------------------------------- /_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/_config.yml -------------------------------------------------------------------------------- /man/kcount.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/man/kcount.Rd -------------------------------------------------------------------------------- /man/pseudoRef.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/man/pseudoRef.Rd -------------------------------------------------------------------------------- /pseudoRef.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/pseudoRef.Rproj -------------------------------------------------------------------------------- /test/debug.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/test/debug.Rmd -------------------------------------------------------------------------------- /test/debug.nb.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/test/debug.nb.html -------------------------------------------------------------------------------- /test/head.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/test/head.txt -------------------------------------------------------------------------------- /test/n1000_bisnp_annot.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/test/n1000_bisnp_annot.txt -------------------------------------------------------------------------------- /test/output/JRIAL2A.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/test/output/JRIAL2A.fasta -------------------------------------------------------------------------------- /test/output/JRIAL2B.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/test/output/JRIAL2B.fasta -------------------------------------------------------------------------------- /test/sample_chr10.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yangjl/pseudoRef/HEAD/test/sample_chr10.fa --------------------------------------------------------------------------------