Export hgvs one-hot numpy: -1 for missing / low quality tiles.

[lightning.git] / pipeline_test.go

diff --git a/pipeline_test.go b/pipeline_test.go
index e8c137212300788ab9a43cf4bbc33ca1c3f855c4..c208c645cc1b00b010fa0d3a5542ea5b6874b3cb 100644 (file)
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -95,11 +95,11 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
        c.Check(code, check.Equals, 0)
        hgvsout, err := ioutil.ReadFile(tmpdir + "/out.tsv")
        c.Check(err, check.IsNil)
-       c.Check(sortLines(string(hgvsout)), check.Equals, sortLines(`chr1:g.1_3delinsGGC        .
-chr1:g.[41_42delinsAA];[41=]   .
-chr1:g.[161=];[161A>T] .
-chr1:g.[178=];[178A>T] .
-chr1:g.222_224del      .
+       c.Check(sortLines(string(hgvsout)), check.Equals, sortLines(`chr1:g.1_3delinsGGC        N
+chr1:g.[41_42delinsAA];[41=]   N
+chr1:g.[161=];[161A>T] N
+chr1:g.[178=];[178A>T] N
+chr1:g.222_224del      N
 chr1:g.[302=];[302_305delinsAAAA]      .
 .      chr2:g.[1=];[1_3delinsAAA]
 .      chr2:g.125_127delinsAAA