X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/3364ff0d5ecd6a0f820281625d16ef13f8521160..HEAD:/export_test.go

diff --git a/export_test.go b/export_test.go
deleted file mode 100644
index 1dc2ad87b6..0000000000
--- 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"
-`)
-}