Write hgvs-based numpy matrix.

[lightning.git] / exportnumpy_test.go

diff --git a/exportnumpy_test.go b/exportnumpy_test.go
index 5011df01b44fd72b19125f4dbc6186bcb77e8291..44b0c6609d6cd334f6a0aad94cddb8b95c1bb3a1 100644 (file)
--- a/exportnumpy_test.go
+++ b/exportnumpy_test.go
@@ -22,10 +22,12 @@ func (s *exportNumpySuite) TestFastaToNumpy(c *check.C) {
        var buffer bytes.Buffer
        exited := (&importer{}).RunCommand("import", []string{"-local=true", "-tag-library", "testdata/tags", "-output-tiles", "-save-incomplete-tiles", "testdata/a.1.fasta", "testdata/tinyref.fasta"}, &bytes.Buffer{}, &buffer, os.Stderr)
        c.Assert(exited, check.Equals, 0)
-       var output bytes.Buffer
-       exited = (&exportNumpy{}).RunCommand("export-numpy", []string{"-local=true", "-output-annotations", tmpdir + "/annotations.csv", "-regions", tmpdir + "/chr1-12-100.bed"}, &buffer, &output, os.Stderr)
+       exited = (&exportNumpy{}).RunCommand("export-numpy", []string{"-local=true", "-output-dir", tmpdir, "-output-annotations", tmpdir + "/annotations.csv", "-regions", tmpdir + "/chr1-12-100.bed"}, &buffer, os.Stderr, os.Stderr)
        c.Check(exited, check.Equals, 0)
-       npy, err := gonpy.NewReader(&output)
+       f, err := os.Open(tmpdir + "/matrix.npy")
+       c.Assert(err, check.IsNil)
+       defer f.Close()
+       npy, err := gonpy.NewReader(f)
        c.Assert(err, check.IsNil)
        variants, err := npy.GetInt16()
        c.Assert(err, check.IsNil)