Separate pvcf/vcf output.

[lightning.git] / pipeline_test.go

diff --git a/pipeline_test.go b/pipeline_test.go
index 38718306f5e92efdc36bb267d05d6769e0f52791..2cd0db872b5af88099847a086597e431298ab0b6 100644 (file)
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -106,23 +106,23 @@ 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", "vcf", "-input-dir", tmpdir + "/merged", "-output-bed", tmpdir + "/export.bed", "-output-per-chromosome=false"}, bytes.NewReader(nil), os.Stderr, 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)
        vcfout, err := ioutil.ReadFile(tmpdir + "/out.vcf")
        c.Check(err, check.IsNil)
-       c.Check(sortLines(string(vcfout)), 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
+       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
 `))
        bedout, err := ioutil.ReadFile(tmpdir + "/export.bed")
        c.Check(err, check.IsNil)