Accept multiple input libraries for slice→slicenumpy.

[lightning.git] / slice_test.go

diff --git a/slice_test.go b/slice_test.go
index c73d3d7dc0cd8496e4e02b9e93f84f41ad18a19b..532b7bb2e5b1653223faf3d20a986cb66ccd8657 100644 (file)
--- a/slice_test.go
+++ b/slice_test.go
@@ -19,8 +19,20 @@ var _ = check.Suite(&sliceSuite{})
 
 func (s *sliceSuite) TestImportAndSlice(c *check.C) {
        tmpdir := c.MkDir()
+       err := os.Mkdir(tmpdir+"/lib1", 0777)
+       c.Assert(err, check.IsNil)
+       err = os.Mkdir(tmpdir+"/lib2", 0777)
+       c.Assert(err, check.IsNil)
+       err = os.Mkdir(tmpdir+"/lib3", 0777)
+       c.Assert(err, check.IsNil)
+       cwd, err := os.Getwd()
+       c.Assert(err, check.IsNil)
+       err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1")
+       c.Assert(err, check.IsNil)
+       err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1dup")
+       c.Assert(err, check.IsNil)
 
-       err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
+       err = ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
        c.Check(err, check.IsNil)
 
        c.Log("=== import testdata/ref ===")
@@ -29,7 +41,7 @@ func (s *sliceSuite) TestImportAndSlice(c *check.C) {
                "-tag-library", "testdata/tags",
                "-output-tiles",
                "-save-incomplete-tiles",
-               "-o", tmpdir + "/library1.gob",
+               "-o", tmpdir + "/lib1/library1.gob",
                "testdata/ref.fasta",
        }, nil, os.Stderr, os.Stderr)
        c.Assert(exited, check.Equals, 0)
@@ -39,29 +51,31 @@ func (s *sliceSuite) TestImportAndSlice(c *check.C) {
                "-local=true",
                "-tag-library", "testdata/tags",
                "-output-tiles",
-               "-o", tmpdir + "/library2.gob",
-               "testdata/pipeline1",
+               "-o", tmpdir + "/lib2/library2.gob",
+               tmpdir + "/pipeline1",
        }, nil, os.Stderr, os.Stderr)
        c.Assert(exited, check.Equals, 0)
 
-       c.Log("=== merge ===")
-       exited = (&merger{}).RunCommand("merge", []string{
+       c.Log("=== import pipeline1dup ===")
+       exited = (&importer{}).RunCommand("import", []string{
                "-local=true",
-               "-o", tmpdir + "/library.gob",
-               tmpdir + "/library1.gob",
-               tmpdir + "/library2.gob",
+               "-tag-library", "testdata/tags",
+               "-output-tiles",
+               "-o", tmpdir + "/lib3/library3.gob",
+               tmpdir + "/pipeline1dup",
        }, nil, os.Stderr, os.Stderr)
        c.Assert(exited, check.Equals, 0)
 
-       input := tmpdir + "/library.gob"
        slicedir := c.MkDir()
 
        c.Log("=== slice ===")
        exited = (&slicecmd{}).RunCommand("slice", []string{
                "-local=true",
-               "-input-dir=" + input,
                "-output-dir=" + slicedir,
                "-tags-per-file=2",
+               tmpdir + "/lib1",
+               tmpdir + "/lib2",
+               tmpdir + "/lib3",
        }, nil, os.Stderr, os.Stderr)
        c.Check(exited, check.Equals, 0)
        out, _ := exec.Command("find", slicedir, "-ls").CombinedOutput()
@@ -83,9 +97,9 @@ func (s *sliceSuite) TestImportAndSlice(c *check.C) {
        defer f.Close()
        npy, err := gonpy.NewReader(f)
        c.Assert(err, check.IsNil)
-       c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
+       c.Check(npy.Shape, check.DeepEquals, []int{4, 4})
        variants, err := npy.GetInt16()
-       c.Check(variants, check.DeepEquals, []int16{3, 2, 1, 2, -1, -1, 1, 1})
+       c.Check(variants, check.DeepEquals, []int16{3, 2, 1, 2, -1, -1, 1, 1, 3, 2, 1, 2, -1, -1, 1, 1})
 
        annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
        c.Assert(err, check.IsNil)