slice_test.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package lightning
   6
   7 import (
   8         "io/ioutil"
   9         "os"
  10         "os/exec"
  11
  12         "gopkg.in/check.v1"
  13 )
  14
  15 type sliceSuite struct{}
  16
  17 var _ = check.Suite(&sliceSuite{})
  18
  19 func (s *sliceSuite) TestImportAndSlice(c *check.C) {
  20         tmpdir := c.MkDir()
  21
  22         err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
  23         c.Check(err, check.IsNil)
  24
  25         exited := (&importer{}).RunCommand("import", []string{
  26                 "-local=true",
  27                 "-tag-library", "testdata/tags",
  28                 "-output-tiles",
  29                 "-save-incomplete-tiles",
  30                 "-o", tmpdir + "/library1.gob",
  31                 "testdata/ref.fasta",
  32         }, nil, os.Stderr, os.Stderr)
  33         c.Assert(exited, check.Equals, 0)
  34
  35         exited = (&importer{}).RunCommand("import", []string{
  36                 "-local=true",
  37                 "-tag-library", "testdata/tags",
  38                 "-output-tiles",
  39                 // "-save-incomplete-tiles",
  40                 "-o", tmpdir + "/library2.gob",
  41                 "testdata/pipeline1",
  42         }, nil, os.Stderr, os.Stderr)
  43         c.Assert(exited, check.Equals, 0)
  44
  45         exited = (&merger{}).RunCommand("merge", []string{
  46                 "-local=true",
  47                 "-o", tmpdir + "/library.gob",
  48                 tmpdir + "/library1.gob",
  49                 tmpdir + "/library2.gob",
  50         }, nil, os.Stderr, os.Stderr)
  51         c.Assert(exited, check.Equals, 0)
  52
  53         input := tmpdir + "/library.gob"
  54
  55         exited = (&slicecmd{}).RunCommand("slice", []string{
  56                 "-local=true",
  57                 "-input-dir=" + input,
  58                 "-output-dir=" + tmpdir,
  59                 "-tags-per-file=2",
  60         }, nil, os.Stderr, os.Stderr)
  61         c.Check(exited, check.Equals, 0)
  62         out, _ := exec.Command("find", tmpdir, "-ls").CombinedOutput()
  63         c.Logf("%s", out)
  64 }