Fix some tests.

[lightning.git] / pipeline_test.go

diff --git a/pipeline_test.go b/pipeline_test.go
index 2cd0db872b5af88099847a086597e431298ab0b6..606cac243d32c2c0f505ff3fe7becf8cce136455 100644 (file)
--- 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 (
@@ -89,40 +93,46 @@ 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.[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
 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.[469_471del];[469=]     .
+chr2:g.[471=];[471G>A] .
+chr2:g.[472=];[472G>A] .
 `))
 
        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)
        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      .       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   468     .       CGTG    C       .       .       .       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)
@@ -149,15 +159,17 @@ 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,f81388b184f4a,chr2:g.470_472del
+6,6,e36dce85efbef,chr2:g.471G>A
+6,6,e36dce85efbef,chr2:g.472G>A
+6,6,f81388b184f4a,chr2:g.469_471del
 `))
 }