+
+ c.Log("=== slice-numpy + chunked hgvs matrix ===")
+ {
+ err = ioutil.WriteFile(tmpdir+"/cases.txt", []byte("pipeline1/input1\npipeline1dup/input1\n"), 0600)
+ c.Assert(err, check.IsNil)
+ npydir := c.MkDir()
+ exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ "-local=true",
+ "-chunked-hgvs-matrix=true",
+ "-chi2-cases-file=" + tmpdir + "/cases.txt",
+ "-chi2-p-value=0.05",
+ "-min-coverage=0.75",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + npydir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
+ c.Logf("%s", out)
+
+ annotations, err := ioutil.ReadFile(npydir + "/hgvs.chr2.annotations.csv")
+ c.Assert(err, check.IsNil)
+ c.Check(string(annotations), check.Equals, `0,chr2:g.470_472del
+1,chr2:g.471G>A
+2,chr2:g.472G>A
+`)
+ }