Allow importing all-hom (reference) data from single fasta file.

[lightning.git] / cmd.go

diff --git a/cmd.go b/cmd.go
index 5e1f7fcb5896f6a7e1e6e74e6d32f39763274006..8fc3636d6c577b68ab8d439179f327dee2726f5e 100644 (file)
--- a/cmd.go
+++ b/cmd.go
@@ -16,13 +16,17 @@ var (
                "-version":  cmd.Version,
                "--version": cmd.Version,
 
+               "ref2genome":         &ref2genome{},
                "vcf2fasta":          &vcf2fasta{},
                "import":             &importer{},
                "export-numpy":       &exportNumpy{},
                "filter":             &filterer{},
                "build-docker-image": &buildDockerImage{},
-               "pca":                &pythonPCA{},
+               "pca-go":             &goPCA{},
+               "pca-py":             &pythonPCA{},
                "plot":               &pythonPlot{},
+               "diff-fasta":         &diffFasta{},
+               "stats":              &stats{},
        })
 )
 
@@ -43,7 +47,7 @@ func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Rea
 RUN DEBIAN_FRONTEND=noninteractive \
   apt-get update && \
   apt-get dist-upgrade -y && \
-  apt-get install -y --no-install-recommends bcftools samtools python3-sklearn python3-matplotlib && \
+  apt-get install -y --no-install-recommends bcftools bedtools samtools python2 python3-sklearn python3-matplotlib && \
   apt-get clean
 `), 0644)
        if err != nil {