X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/0df66c8fae2cdaf70c811379a4c1522211838a9b..8fc5d19688d99d1ebacb9671b85ba30bbf3c3d35:/pipeline_test.go

diff --git a/pipeline_test.go b/pipeline_test.go
index 2cd0db872b..c208c645cc 100644
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -1,3 +1,7 @@
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
 package lightning
 
 import (
@@ -89,13 +93,13 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
 
 	code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "hgvs", "-input-dir", tmpdir + "/merged", "-output-dir", tmpdir, "-output-per-chromosome=false"}, bytes.NewReader(nil), os.Stderr, os.Stderr)
 	c.Check(code, check.Equals, 0)
-	hgvsout, err := ioutil.ReadFile(tmpdir + "/out.csv")
+	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
@@ -110,19 +114,21 @@ chr2:g.[471=];[471_472delinsAA]	.
 	c.Check(code, check.Equals, 0)
 	vcfout, err := ioutil.ReadFile(tmpdir + "/out.vcf")
 	c.Check(err, check.IsNil)
-	c.Check(sortLines(string(vcfout)), check.Equals, sortLines(`chr1	1	NNN	GGC	.	.	GT	1/1	0/0
-chr1	41	TT	AA	.	.	GT	1/0	0/0
-chr1	161	A	T	.	.	GT	0/1	0/0
-chr1	178	A	T	.	.	GT	0/1	0/0
-chr1	221	TCCA	T	.	.	GT	1/1	0/0
-chr1	302	TTTT	AAAA	.	.	GT	0/1	0/0
-chr2	1	TTT	AAA	.	.	GT	0/0	0/1
-chr2	125	CTT	AAA	.	.	GT	0/0	1/1
-chr2	240	ATTTTTCTTGCTCTC	A	.	.	GT	1/0	0/0
-chr2	258	CCTTGTATTTTT	AA	.	.	GT	1/0	0/0
-chr2	315	C	A	.	.	GT	1/0	0/0
-chr2	469	GTGG	G	.	.	GT	1/0	0/0
-chr2	471	GG	AA	.	.	GT	0/1	0/0
+	c.Check(sortLines(string(vcfout)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	testdata/pipeline1/input1.1.fasta	testdata/pipeline1/input2.1.fasta
+chr1	1	.	NNN	GGC	.	.	.	GT	1/1	0/0
+chr1	41	.	TT	AA	.	.	.	GT	1/0	0/0
+chr1	161	.	A	T	.	.	.	GT	0/1	0/0
+chr1	178	.	A	T	.	.	.	GT	0/1	0/0
+chr1	221	.	TCCA	T	.	.	.	GT	1/1	0/0
+chr1	302	.	TTTT	AAAA	.	.	.	GT	0/1	0/0
+chr2	1	.	TTT	AAA	.	.	.	GT	0/0	0/1
+chr2	125	.	CTT	AAA	.	.	.	GT	0/0	1/1
+chr2	240	.	ATTTTTCTTGCTCTC	A	.	.	.	GT	1/0	0/0
+chr2	258	.	CCTTGTATTTTT	AA	.	.	.	GT	1/0	0/0
+chr2	315	.	C	A	.	.	.	GT	1/0	0/0
+chr2	469	.	GTGG	G	.	.	.	GT	1/0	0/0
+chr2	471	.	GG	AA	.	.	.	GT	0/1	0/0
 `))
 	bedout, err := ioutil.ReadFile(tmpdir + "/export.bed")
 	c.Check(err, check.IsNil)