X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/52c08db40bdfc267f83dadc9df78d1f77a427ccd..d976ccad0ff7353367a4dc761a7d1b8d97c82ead:/pipeline_test.go

diff --git a/pipeline_test.go b/pipeline_test.go
index 2b0f393312..c208c645cc 100644
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -1,4 +1,8 @@
-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
 
 import (
 	"bytes"
@@ -6,6 +10,8 @@ import (
 	"io"
 	"io/ioutil"
 	"os"
+	"sort"
+	"strings"
 	"sync"
 
 	"gopkg.in/check.v1"
@@ -35,7 +41,7 @@ func (s *pipelineSuite) TestImport(c *check.C) {
 		wg.Add(1)
 		go func() {
 			defer wg.Done()
-			code := (&stats{}).RunCommand("lightning stats", []string{"-local"}, statsin, statsout, os.Stderr)
+			code := (&statscmd{}).RunCommand("lightning stats", []string{"-local"}, statsin, statsout, os.Stderr)
 			c.Check(code, check.Equals, 0)
 		}()
 		wg.Wait()
@@ -61,7 +67,7 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
 			args := []string{"-local=true", "-o=" + libfile[i], "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags"}
 			if i == 0 {
 				// ref only
-				args = append(args, "-include-no-calls")
+				args = append(args, "-save-incomplete-tiles")
 			}
 			args = append(args, infile)
 			code := (&importer{}).RunCommand("lightning import", args, bytes.NewReader(nil), &bytes.Buffer{}, os.Stderr)
@@ -76,58 +82,93 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
 	c.Logf("len(merged) %d", merged.Len())
 
 	statsout := &bytes.Buffer{}
-	code = (&stats{}).RunCommand("lightning stats", []string{"-local"}, bytes.NewReader(merged.Bytes()), statsout, os.Stderr)
+	code = (&statscmd{}).RunCommand("lightning stats", []string{"-local"}, bytes.NewReader(merged.Bytes()), statsout, os.Stderr)
 	c.Check(code, check.Equals, 0)
 	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(hgvsout.String(), check.Equals, `chr1:g.1_3delinsGGC
-chr1:g.[41_42delinsAA];[41=]
-chr1:g.[161=];[161A>T]
-chr1:g.[178=];[178A>T]
-chr1:g.222_224del
-chr1:g.[302=];[302_305delinsAAAA]
-chr2:g.[813_826del];[813=]
-chr2:g.[830_841delinsAA];[830=]
-chr2:g.[887C>A];[887=]
-chr2:g.[1042_1044del];[1042=]
-chr2:g.[1043=];[1043_1044delinsAA]
-`)
-
-	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)
+	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.[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
+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]	.
+`))
+
+	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(vcfout.String(), check.Equals, `chr1	1	NNN	GGC	1/1
-chr1	41	TT	AA	1/0
-chr1	161	A	T	0/1
-chr1	178	A	T	0/1
-chr1	221	TCCA	T	1/1
-chr1	302	TTTT	AAAA	0/1
-chr2	812	ATTTTTCTTGCTCTC	A	1/0
-chr2	830	CCTTGTATTTTT	AA	1/0
-chr2	887	C	A	1/0
-chr2	1041	GTGG	G	1/0
-chr2	1043	GG	AA	0/1
-`)
+	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	.	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)
 	c.Logf("%s", string(bedout))
-	c.Check(string(bedout), check.Equals, `chr1 0 248 0 1000 . 0 224
-chr1 224 372 1 500 . 248 348
-chr1 348 496 2 0 . 372 472
-chr1 472 572 3 0 . 496 572
-chr2 572 820 4 500 . 0 796
-chr2 796 944 5 0 . 820 920
-chr2 920 1068 6 1000 . 944 1044
-chr2 1044 1144 7 0 . 1068 1144
-`)
+	c.Check(sortLines(string(bedout)), check.Equals, sortLines(`chr1 0 248 0 1000 . 0 224
+chr1 224 372 1 1000 . 248 348
+chr1 348 496 2 1000 . 372 472
+chr1 472 572 3 1000 . 496 572
+chr2 0 248 4 1000 . 0 224
+chr2 224 372 5 750 . 248 348
+chr2 348 496 6 1000 . 372 472
+chr2 472 572 7 1000 . 496 572
+`))
+
+	annotateout := &bytes.Buffer{}
+	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())
+	c.Logf("%s", sorted)
+	c.Check(sorted, check.Equals, sortLines(`0,0,8d4fe9a63921b,chr1:g.161A>T
+0,0,8d4fe9a63921b,chr1:g.178A>T
+0,0,8d4fe9a63921b,chr1:g.1_3delinsGGC
+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
+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,f81388b184f4a,chr2:g.470_472del
+`))
+}
+
+func sortLines(txt string) string {
+	lines := strings.Split(strings.TrimRightFunc(txt, func(c rune) bool { return c == '\n' }), "\n")
+	sort.Strings(lines)
+	return strings.Join(lines, "\n") + "\n"
 }