Add null csv rows for ref/undiffed. Ensure 0 means ref in matrix.

[lightning.git] / export_test.go

diff --git a/export_test.go b/export_test.go
index d87b3ae51c3d9dbac364a28499921ac07b72f66a..ac7063d2fc625f28b583550d5ed06ced823a6f13 100644 (file)
--- a/export_test.go
+++ b/export_test.go
@@ -164,6 +164,7 @@ chr2        471     .       GG      AA      .       .       AC=1
                "-output-dir=" + outdir,
                "-output-format=hgvs-numpy",
                "-ref=testdata/ref.fasta",
+               "-match-genome=input[12]",
        }, nil, os.Stderr, os.Stderr)
        c.Check(exited, check.Equals, 0)
 
@@ -213,4 +214,21 @@ chr2       471     .       GG      AA      .       .       AC=1
 5,"chr2.470_472del"
 6,"chr2.471_472delinsAA"
 `)
+
+       c.Logf("export hgvs-numpy with p-value threshold")
+       outdir = c.MkDir()
+       err = ioutil.WriteFile(tmpdir+"/cases", []byte("input1\n"), 0777)
+       c.Assert(err, check.IsNil)
+       exited = (&exporter{}).RunCommand("export", []string{
+               "-local=true",
+               "-input-dir=" + input,
+               "-p-value=0.05",
+               "-cases=" + tmpdir + "/cases",
+               "-output-dir=" + outdir,
+               "-output-format=hgvs-numpy",
+               "-ref=testdata/ref.fasta",
+               "-match-genome=input[12]",
+       }, nil, os.Stderr, os.Stderr)
+       c.Check(exited, check.Equals, 0)
+
 }