Option to export one vcf/csv file per chromosome.

[lightning.git] / export_test.go

diff --git a/export_test.go b/export_test.go
index 7261f99ea3fb843e187826a82848fb3186d2b8fd..1dc2ad87b636a25fff7fe2cf3f2e6651c889a2fd 100644 (file)
--- a/export_test.go
+++ b/export_test.go
@@ -22,22 +22,27 @@ func (s *exportSuite) TestFastaToHGVS(c *check.C) {
        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)
-       var output bytes.Buffer
        exited = (&exporter{}).RunCommand("export", []string{
                "-local=true",
-               "-i=" + tmpdir + "/library.gob",
+               "-input-dir=" + tmpdir,
+               "-output-dir=" + tmpdir,
                "-output-format=hgvs-onehot",
                "-output-labels=" + tmpdir + "/labels.csv",
                "-ref=testdata/ref.fasta",
-       }, &buffer, &output, os.Stderr)
+       }, &buffer, os.Stderr, os.Stderr)
        c.Check(exited, check.Equals, 0)
-       c.Check(sortLines(output.String()), check.Equals, sortLines(`chr1.1_3delinsGGC  1       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
-chr2.1_3delinsAAA      0       1
+`))
+       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
@@ -47,7 +52,7 @@ 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","-"
-1,"input2","-"
+       c.Check(string(labels), check.Equals, `0,"input1","out.csv"
+1,"input2","out.csv"
 `)
 }