X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/30299451e290f999306373ff6a7ddfe58f6cfd28..HEAD:/slice_test.go

diff --git a/slice_test.go b/slice_test.go
deleted file mode 100644
index 532b7bb2e5..0000000000
--- a/slice_test.go
+++ /dev/null
@@ -1,115 +0,0 @@
-// Copyright (C) The Lightning Authors. All rights reserved.
-//
-// SPDX-License-Identifier: AGPL-3.0
-
-package lightning
-
-import (
-	"io/ioutil"
-	"os"
-	"os/exec"
-
-	"github.com/kshedden/gonpy"
-	"gopkg.in/check.v1"
-)
-
-type sliceSuite struct{}
-
-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)
-	c.Check(err, check.IsNil)
-
-	c.Log("=== import testdata/ref ===")
-	exited := (&importer{}).RunCommand("import", []string{
-		"-local=true",
-		"-tag-library", "testdata/tags",
-		"-output-tiles",
-		"-save-incomplete-tiles",
-		"-o", tmpdir + "/lib1/library1.gob",
-		"testdata/ref.fasta",
-	}, nil, os.Stderr, os.Stderr)
-	c.Assert(exited, check.Equals, 0)
-
-	c.Log("=== import testdata/pipeline1 ===")
-	exited = (&importer{}).RunCommand("import", []string{
-		"-local=true",
-		"-tag-library", "testdata/tags",
-		"-output-tiles",
-		"-o", tmpdir + "/lib2/library2.gob",
-		tmpdir + "/pipeline1",
-	}, nil, os.Stderr, os.Stderr)
-	c.Assert(exited, check.Equals, 0)
-
-	c.Log("=== import pipeline1dup ===")
-	exited = (&importer{}).RunCommand("import", []string{
-		"-local=true",
-		"-tag-library", "testdata/tags",
-		"-output-tiles",
-		"-o", tmpdir + "/lib3/library3.gob",
-		tmpdir + "/pipeline1dup",
-	}, nil, os.Stderr, os.Stderr)
-	c.Assert(exited, check.Equals, 0)
-
-	slicedir := c.MkDir()
-
-	c.Log("=== slice ===")
-	exited = (&slicecmd{}).RunCommand("slice", []string{
-		"-local=true",
-		"-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()
-	c.Logf("%s", out)
-
-	c.Log("=== slice-numpy ===")
-	npydir := c.MkDir()
-	exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-		"-local=true",
-		"-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)
-
-	f, err := os.Open(npydir + "/matrix.0000.npy")
-	c.Assert(err, check.IsNil)
-	defer f.Close()
-	npy, err := gonpy.NewReader(f)
-	c.Assert(err, check.IsNil)
-	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, 3, 2, 1, 2, -1, -1, 1, 1})
-
-	annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
-	c.Assert(err, check.IsNil)
-	c.Logf("%s", annotations)
-	for _, s := range []string{
-		"chr1:g.161A>T",
-		"chr1:g.178A>T",
-		"chr1:g.1_3delinsGGC",
-		"chr1:g.222_224del",
-	} {
-		c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
-	}
-}