Merge branch '21543-lightning-subdir'

[lightning.git] / export_test.go

diff --git a/export_test.go b/export_test.go
deleted file mode 100644 (file)
index 1dc2ad8..0000000
--- a/export_test.go
+++ /dev/null
@@ -1,58 +0,0 @@
-package lightning
-
-import (
-       "bytes"
-       "io/ioutil"
-       "os"
-
-       "gopkg.in/check.v1"
-)
-
-type exportSuite struct{}
-
-var _ = check.Suite(&exportSuite{})
-
-func (s *exportSuite) TestFastaToHGVS(c *check.C) {
-       tmpdir := c.MkDir()
-
-       err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
-       c.Check(err, check.IsNil)
-
-       var buffer bytes.Buffer
-       exited := (&importer{}).RunCommand("import", []string{"-local=true", "-tag-library", "testdata/tags", "-output-tiles", "-save-incomplete-tiles", "testdata/pipeline1", "testdata/ref.fasta"}, &bytes.Buffer{}, &buffer, os.Stderr)
-       c.Assert(exited, check.Equals, 0)
-       ioutil.WriteFile(tmpdir+"/library.gob", buffer.Bytes(), 0644)
-       exited = (&exporter{}).RunCommand("export", []string{
-               "-local=true",
-               "-input-dir=" + tmpdir,
-               "-output-dir=" + tmpdir,
-               "-output-format=hgvs-onehot",
-               "-output-labels=" + tmpdir + "/labels.csv",
-               "-ref=testdata/ref.fasta",
-       }, &buffer, os.Stderr, os.Stderr)
-       c.Check(exited, check.Equals, 0)
-       output, err := ioutil.ReadFile(tmpdir + "/out.chr1.csv")
-       c.Check(err, check.IsNil)
-       c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1.1_3delinsGGC   1       0
-chr1.41_42delinsAA     1       0
-chr1.161A>T    1       0
-chr1.178A>T    1       0
-chr1.222_224del        1       0
-chr1.302_305delinsAAAA 1       0
-`))
-       output, err = ioutil.ReadFile(tmpdir + "/out.chr2.csv")
-       c.Check(err, check.IsNil)
-       c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2.1_3delinsAAA   0       1
-chr2.125_127delinsAAA  0       1
-chr2.241_254del        1       0
-chr2.258_269delinsAA   1       0
-chr2.315C>A    1       0
-chr2.470_472del        1       0
-chr2.471_472delinsAA   1       0
-`))
-       labels, err := ioutil.ReadFile(tmpdir + "/labels.csv")
-       c.Check(err, check.IsNil)
-       c.Check(string(labels), check.Equals, `0,"input1","out.csv"
-1,"input2","out.csv"
-`)
-}