X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/896220cbd21811433f6db068f559677927e56757..353fe94dce384fdfbc78c3b4d9516ae21144b706:/pipeline_test.go

diff --git a/pipeline_test.go b/pipeline_test.go
index 67fff89fb6..391312e507 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 (
@@ -83,18 +87,20 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
 	c.Check(statsout.Len() > 0, check.Equals, true)
 	c.Logf("%s", statsout.String())
 
-	c.Check(ioutil.WriteFile(tmpdir+"/merged.gob", merged.Bytes(), 0666), check.IsNil)
+	err := os.Mkdir(tmpdir+"/merged", 0777)
+	c.Assert(err, check.IsNil)
+	c.Check(ioutil.WriteFile(tmpdir+"/merged/library.gob", merged.Bytes(), 0666), check.IsNil)
 
-	hgvsout := &bytes.Buffer{}
-	code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "hgvs", "-i", tmpdir + "/merged.gob"}, bytes.NewReader(nil), hgvsout, os.Stderr)
+	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)
-	c.Check(hgvsout.Len() > 0, check.Equals, true)
-	c.Logf("%s", hgvsout.String())
-	c.Check(sortLines(hgvsout.String()), 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	.
+	hgvsout, err := ioutil.ReadFile(tmpdir + "/out.tsv")
+	c.Check(err, check.IsNil)
+	c.Check(sortLines(string(hgvsout)), check.Equals, sortLines(`chr1:g.1_3delinsGGC	N
+chr1:g.[41T>A];[41=]	N
+chr1:g.[42T>A];[42=]	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
@@ -102,27 +108,31 @@ chr2:g.[241_254del];[241=]	.
 chr2:g.[258_269delinsAA];[258=]	.
 chr2:g.[315C>A];[315=]	.
 chr2:g.[470_472del];[470=]	.
-chr2:g.[471=];[471_472delinsAA]	.
+chr2:g.[471=];[471G>A]	.
+chr2:g.[472=];[472G>A]	.
 `))
 
-	vcfout := &bytes.Buffer{}
-	code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "vcf", "-i", tmpdir + "/merged.gob", "-output-bed", tmpdir + "/export.bed"}, bytes.NewReader(nil), vcfout, os.Stderr)
+	code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-dir", tmpdir, "-output-format", "pvcf", "-input-dir", tmpdir + "/merged", "-output-bed", tmpdir + "/export.bed", "-output-per-chromosome=false"}, bytes.NewReader(nil), os.Stderr, os.Stderr)
 	c.Check(code, check.Equals, 0)
-	c.Check(vcfout.Len() > 0, check.Equals, true)
-	c.Logf("%s", vcfout.String())
-	c.Check(sortLines(vcfout.String()), check.Equals, sortLines(`chr1	1	NNN	GGC	1/1	0/0
-chr1	41	TT	AA	1/0	0/0
-chr1	161	A	T	0/1	0/0
-chr1	178	A	T	0/1	0/0
-chr1	221	TCCA	T	1/1	0/0
-chr1	302	TTTT	AAAA	0/1	0/0
-chr2	1	TTT	AAA	0/0	0/1
-chr2	125	CTT	AAA	0/0	1/1
-chr2	240	ATTTTTCTTGCTCTC	A	1/0	0/0
-chr2	258	CCTTGTATTTTT	AA	1/0	0/0
-chr2	315	C	A	1/0	0/0
-chr2	469	GTGG	G	1/0	0/0
-chr2	471	GG	AA	0/1	0/0
+	vcfout, err := ioutil.ReadFile(tmpdir + "/out.vcf")
+	c.Check(err, check.IsNil)
+	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	.	T	A	.	.	.	GT	1/0	0/0
+chr1	42	.	T	A	.	.	.	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	.	G	A	.	.	.	GT	0/1	0/0
+chr2	472	.	G	A	.	.	.	GT	0/1	0/0
 `))
 	bedout, err := ioutil.ReadFile(tmpdir + "/export.bed")
 	c.Check(err, check.IsNil)
@@ -138,7 +148,7 @@ chr2 472 572 7 1000 . 496 572
 `))
 
 	annotateout := &bytes.Buffer{}
-	code = (&annotatecmd{}).RunCommand("lightning annotate", []string{"-local", "-variant-hash=true", "-i", tmpdir + "/merged.gob"}, bytes.NewReader(nil), annotateout, os.Stderr)
+	code = (&annotatecmd{}).RunCommand("lightning annotate", []string{"-local", "-variant-hash=true", "-i", tmpdir + "/merged/library.gob"}, bytes.NewReader(nil), annotateout, os.Stderr)
 	c.Check(code, check.Equals, 0)
 	c.Check(annotateout.Len() > 0, check.Equals, true)
 	sorted := sortLines(annotateout.String())
@@ -149,14 +159,16 @@ chr2 472 572 7 1000 . 496 572
 0,0,8d4fe9a63921b,chr1:g.222_224del
 0,0,ba4263ca4199c,chr1:g.1_3delinsGGC
 0,0,ba4263ca4199c,chr1:g.222_224del
-0,0,ba4263ca4199c,chr1:g.41_42delinsAA
+0,0,ba4263ca4199c,chr1:g.41T>A
+0,0,ba4263ca4199c,chr1:g.42T>A
 1,1,139890345dbb8,chr1:g.302_305delinsAAAA
 4,4,cbfca15d241d3,chr2:g.125_127delinsAAA
 4,4,cbfca15d241d3,chr2:g.1_3delinsAAA
 4,4,f5fafe9450b02,chr2:g.241_245delinsAAAAA
 4,4,f5fafe9450b02,chr2:g.291C>A
 4,4,fe9a71a42adb4,chr2:g.125_127delinsAAA
-6,6,e36dce85efbef,chr2:g.471_472delinsAA
+6,6,e36dce85efbef,chr2:g.471G>A
+6,6,e36dce85efbef,chr2:g.472G>A
 6,6,f81388b184f4a,chr2:g.470_472del
 `))
 }