1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
20 type pipelineSuite struct{}
22 var _ = check.Suite(&pipelineSuite{})
24 func (s *pipelineSuite) TestImport(c *check.C) {
25 for _, infile := range []string{
26 "testdata/pipeline1/",
29 c.Logf("TestImport: %s", infile)
32 statsin, importout := io.Pipe()
36 code := (&importer{}).RunCommand("lightning import", []string{"-local=true", "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags", infile}, bytes.NewReader(nil), importout, os.Stderr)
37 c.Check(code, check.Equals, 0)
40 statsout := &bytes.Buffer{}
44 code := (&statscmd{}).RunCommand("lightning stats", []string{"-local"}, statsin, statsout, os.Stderr)
45 c.Check(code, check.Equals, 0)
48 c.Logf("%s", statsout.String())
52 func (s *pipelineSuite) TestImportMerge(c *check.C) {
53 libfile := make([]string, 2)
57 for i, infile := range []string{
59 "testdata/pipeline1/",
61 i, infile := i, infile
62 c.Logf("TestImportMerge: %s", infile)
63 libfile[i] = fmt.Sprintf("%s/%d.gob", tmpdir, i)
67 args := []string{"-local=true", "-o=" + libfile[i], "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags"}
70 args = append(args, "-save-incomplete-tiles")
72 args = append(args, infile)
73 code := (&importer{}).RunCommand("lightning import", args, bytes.NewReader(nil), &bytes.Buffer{}, os.Stderr)
74 c.Check(code, check.Equals, 0)
79 merged := &bytes.Buffer{}
80 code := (&merger{}).RunCommand("lightning merge", []string{"-local", libfile[0], libfile[1]}, bytes.NewReader(nil), merged, os.Stderr)
81 c.Check(code, check.Equals, 0)
82 c.Logf("len(merged) %d", merged.Len())
84 statsout := &bytes.Buffer{}
85 code = (&statscmd{}).RunCommand("lightning stats", []string{"-local"}, bytes.NewReader(merged.Bytes()), statsout, os.Stderr)
86 c.Check(code, check.Equals, 0)
87 c.Check(statsout.Len() > 0, check.Equals, true)
88 c.Logf("%s", statsout.String())
90 err := os.Mkdir(tmpdir+"/merged", 0777)
91 c.Assert(err, check.IsNil)
92 c.Check(ioutil.WriteFile(tmpdir+"/merged/library.gob", merged.Bytes(), 0666), check.IsNil)
94 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)
95 c.Check(code, check.Equals, 0)
96 hgvsout, err := ioutil.ReadFile(tmpdir + "/out.tsv")
97 c.Check(err, check.IsNil)
98 c.Check(sortLines(string(hgvsout)), check.Equals, sortLines(`chr1:g.1_3delinsGGC N
99 chr1:g.[41_42delinsAA];[41=] N
100 chr1:g.[161=];[161A>T] N
101 chr1:g.[178=];[178A>T] N
103 chr1:g.[302=];[302_305delinsAAAA] .
104 . chr2:g.[1=];[1_3delinsAAA]
105 . chr2:g.125_127delinsAAA
106 chr2:g.[241_254del];[241=] .
107 chr2:g.[258_269delinsAA];[258=] .
108 chr2:g.[315C>A];[315=] .
109 chr2:g.[470_472del];[470=] .
110 chr2:g.[471=];[471_472delinsAA] .
113 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)
114 c.Check(code, check.Equals, 0)
115 vcfout, err := ioutil.ReadFile(tmpdir + "/out.vcf")
116 c.Check(err, check.IsNil)
117 c.Check(sortLines(string(vcfout)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
118 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testdata/pipeline1/input1.1.fasta testdata/pipeline1/input2.1.fasta
119 chr1 1 . NNN GGC . . . GT 1/1 0/0
120 chr1 41 . TT AA . . . GT 1/0 0/0
121 chr1 161 . A T . . . GT 0/1 0/0
122 chr1 178 . A T . . . GT 0/1 0/0
123 chr1 221 . TCCA T . . . GT 1/1 0/0
124 chr1 302 . TTTT AAAA . . . GT 0/1 0/0
125 chr2 1 . TTT AAA . . . GT 0/0 0/1
126 chr2 125 . CTT AAA . . . GT 0/0 1/1
127 chr2 240 . ATTTTTCTTGCTCTC A . . . GT 1/0 0/0
128 chr2 258 . CCTTGTATTTTT AA . . . GT 1/0 0/0
129 chr2 315 . C A . . . GT 1/0 0/0
130 chr2 469 . GTGG G . . . GT 1/0 0/0
131 chr2 471 . GG AA . . . GT 0/1 0/0
133 bedout, err := ioutil.ReadFile(tmpdir + "/export.bed")
134 c.Check(err, check.IsNil)
135 c.Logf("%s", string(bedout))
136 c.Check(sortLines(string(bedout)), check.Equals, sortLines(`chr1 0 248 0 1000 . 0 224
137 chr1 224 372 1 1000 . 248 348
138 chr1 348 496 2 1000 . 372 472
139 chr1 472 572 3 1000 . 496 572
140 chr2 0 248 4 1000 . 0 224
141 chr2 224 372 5 750 . 248 348
142 chr2 348 496 6 1000 . 372 472
143 chr2 472 572 7 1000 . 496 572
146 annotateout := &bytes.Buffer{}
147 code = (&annotatecmd{}).RunCommand("lightning annotate", []string{"-local", "-variant-hash=true", "-i", tmpdir + "/merged/library.gob"}, bytes.NewReader(nil), annotateout, os.Stderr)
148 c.Check(code, check.Equals, 0)
149 c.Check(annotateout.Len() > 0, check.Equals, true)
150 sorted := sortLines(annotateout.String())
152 c.Check(sorted, check.Equals, sortLines(`0,0,8d4fe9a63921b,chr1:g.161A>T
153 0,0,8d4fe9a63921b,chr1:g.178A>T
154 0,0,8d4fe9a63921b,chr1:g.1_3delinsGGC
155 0,0,8d4fe9a63921b,chr1:g.222_224del
156 0,0,ba4263ca4199c,chr1:g.1_3delinsGGC
157 0,0,ba4263ca4199c,chr1:g.222_224del
158 0,0,ba4263ca4199c,chr1:g.41_42delinsAA
159 1,1,139890345dbb8,chr1:g.302_305delinsAAAA
160 4,4,cbfca15d241d3,chr2:g.125_127delinsAAA
161 4,4,cbfca15d241d3,chr2:g.1_3delinsAAA
162 4,4,f5fafe9450b02,chr2:g.241_245delinsAAAAA
163 4,4,f5fafe9450b02,chr2:g.291C>A
164 4,4,fe9a71a42adb4,chr2:g.125_127delinsAAA
165 6,6,e36dce85efbef,chr2:g.471_472delinsAA
166 6,6,f81388b184f4a,chr2:g.470_472del
170 func sortLines(txt string) string {
171 lines := strings.Split(strings.TrimRightFunc(txt, func(c rune) bool { return c == '\n' }), "\n")
173 return strings.Join(lines, "\n") + "\n"